@article{agnewStructureIdentificationNative2025,
  title = {Structure and Identification of the Native {{PLP}} Synthase Complex from {{{\emph{Methanosarcina}}}}{\emph{ Acetivorans}} Lysate},
  author = {Agnew, Angela and Humm, Ethan and Zhou, Kang and Gunsalus, Robert P. and Zhou, Z. Hong},
  editor = {Harwood, Caroline S.},
  year = {2025},
  month = jan,
  journal = {mBio},
  volume = {16},
  number = {1},
  pages = {e03090-24},
  issn = {2150-7511},
  doi = {10.1128/mbio.03090-24},
  urldate = {2025-04-04},
  abstract = {ABSTRACT                                                            Many protein-protein interactions behave differently in biochemically purified forms as compared to their                 in vivo                 states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method,                 cryoID                 , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the                 cryoID                 approach, we successfully reconstructed and identified the native                 Methanosarcina acetivorans                 pyridoxal 5{$\prime$}-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8{$\alpha$}/8{$\beta$} TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the                 cryoID                 workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.                                               IMPORTANCE                 Archaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5{$\prime$}-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.                                       ,              Archaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5{$\prime$}-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\YFRTM77V\Agnew et al. - 2025 - Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans.pdf}
}

ABSTRACT Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5$\prime$-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8$α$/8$β$ TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial. IMPORTANCE Archaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5$\prime$-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression. , Archaea are one of the three domains of life, classified as a phylogenetically distinct lineage. There is a paucity of known enzyme structures from organisms of this domain, and this is often exacerbated by characteristically difficult growth conditions and a lack of readily available molecular biology toolkits to study proteins in archaeal cells. As a result, there is a gap in knowledge concerning the mechanisms governing archaeal protein behavior and their impacts on both the environment and human health; case in point, the synthesis of the widely utilized cofactor pyridoxal 5$\prime$-phosphate (PLP; a vitamer of vitamin B6, which humans cannot produce). By leveraging the power of single-particle cryo-EM and map-to-primary sequence identification, we determine the native structure of PLP synthase from cellular lysate. Our workflow allows the (i) rapid examination of new or less characterized systems with minimal sample requirements and (ii) discovery of structural states inaccessible by recombinant expression.

@article{itoStructureKaposisSarcomaassociated2025,
  title = {Structure of the {{Kaposi}}'s Sarcoma-Associated Herpesvirus {{gB}} in Post-Fusion Conformation},
  author = {Ito, Fumiaki and Zhen, James and Xie, Guodong and Huang, Haigen and Silva, Juan C. and Wu, Ting-Ting and Zhou, Z. Hong},
  year = {2025},
  month = jan,
  journal = {Journal of Virology},
  volume = {99},
  number = {2},
  pages = {e01533-24},
  publisher = {American Society for Microbiology},
  doi = {10.1128/jvi.01533-24},
  urldate = {2025-04-04},
  file = {C:\Users\shervinnia\Zotero\storage\C52XSXN4\Ito et al. - 2025 - Structure of the Kaposi’s sarcoma-associated herpesvirus gB in post-fusion conformation.pdf}
}

@article{liuNativeDGCStructure2025,
  title = {Native {{DGC}} Structure Rationalizes Muscular Dystrophy-Causing Mutations},
  author = {Liu, Shiheng and Su, Tiantian and Xia, Xian and Zhou, Z. Hong},
  year = {2025},
  month = jan,
  journal = {Nature},
  volume = {637},
  number = {8048},
  pages = {1261--1271},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/s41586-024-08324-w},
  urldate = {2025-04-04},
  abstract = {Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disorder marked by progressive muscle wasting leading to premature mortality1,2. Discovery of the DMD gene encoding dystrophin both revealed the cause of DMD and helped identify a family of at least ten dystrophin-associated proteins at the muscle cell membrane, collectively forming the dystrophin--glycoprotein complex (DGC)3--9. The DGC links the extracellular matrix to the cytoskeleton, but, despite its importance, its molecular architecture has remained elusive. Here we determined the native cryo-electron microscopy structure of rabbit DGC and conducted biochemical analyses to reveal its intricate molecular configuration. An unexpected {$\beta$}-helix comprising {$\beta$}-, {$\gamma$}- and {$\delta$}-sarcoglycan forms an extracellular platform that interacts with {$\alpha$}-dystroglycan, {$\beta$}-dystroglycan and {$\alpha$}-sarcoglycan, allowing {$\alpha$}-dystroglycan to contact the extracellular matrix. In the membrane, sarcospan anchors {$\beta$}-dystroglycan to the {$\beta$}-, {$\gamma$}- and {$\delta$}-sarcoglycan trimer, while in the cytoplasm, {$\beta$}-dystroglycan's juxtamembrane fragment binds dystrophin's ZZ domain. Through these interactions, the DGC links laminin 2 to intracellular actin. Additionally, dystrophin's WW domain, along with its EF-hand 1 domain, interacts with {$\alpha$}-dystrobrevin. A disease-causing mutation mapping to the WW domain weakens this interaction, as confirmed by deletion of the WW domain in biochemical assays. Our findings rationalize more than 110 mutations affecting single residues associated with various muscular dystrophy subtypes and contribute to ongoing therapeutic developments, including protein restoration, upregulation of compensatory genes and gene replacement.},
  copyright = {2024 The Author(s), under exclusive licence to Springer Nature Limited},
  langid = {english},
  keywords = {Cryoelectron microscopy,Molecular biology,Neuromuscular disease},
  file = {C:\Users\shervinnia\Zotero\storage\HHH3JKY5\Liu et al. - 2025 - Native DGC structure rationalizes muscular dystrophy-causing mutations.pdf}
}

Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disorder marked by progressive muscle wasting leading to premature mortality1,2. Discovery of the DMD gene encoding dystrophin both revealed the cause of DMD and helped identify a family of at least ten dystrophin-associated proteins at the muscle cell membrane, collectively forming the dystrophin–glycoprotein complex (DGC)3–9. The DGC links the extracellular matrix to the cytoskeleton, but, despite its importance, its molecular architecture has remained elusive. Here we determined the native cryo-electron microscopy structure of rabbit DGC and conducted biochemical analyses to reveal its intricate molecular configuration. An unexpected $β$-helix comprising $β$-, $γ$- and $δ$-sarcoglycan forms an extracellular platform that interacts with $α$-dystroglycan, $β$-dystroglycan and $α$-sarcoglycan, allowing $α$-dystroglycan to contact the extracellular matrix. In the membrane, sarcospan anchors $β$-dystroglycan to the $β$-, $γ$- and $δ$-sarcoglycan trimer, while in the cytoplasm, $β$-dystroglycan's juxtamembrane fragment binds dystrophin's ZZ domain. Through these interactions, the DGC links laminin 2 to intracellular actin. Additionally, dystrophin's WW domain, along with its EF-hand 1 domain, interacts with $α$-dystrobrevin. A disease-causing mutation mapping to the WW domain weakens this interaction, as confirmed by deletion of the WW domain in biochemical assays. Our findings rationalize more than 110 mutations affecting single residues associated with various muscular dystrophy subtypes and contribute to ongoing therapeutic developments, including protein restoration, upregulation of compensatory genes and gene replacement.

@article{liuOvercomingPreferredorientationProblem2025,
  title = {Overcoming the Preferred-Orientation Problem in Cryo-{{EM}} with Self-Supervised Deep Learning},
  author = {Liu, Yun-Tao and Fan, Hongcheng and Hu, Jason J. and Zhou, Z. Hong},
  year = {2025},
  month = jan,
  journal = {Nature Methods},
  volume = {22},
  number = {1},
  pages = {113--123},
  publisher = {Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/s41592-024-02505-1},
  urldate = {2025-04-04},
  abstract = {While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the `preferred' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep learning-based software to address map anisotropy and particle misalignment caused by the preferred-orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's ability to generate near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, {$\beta$}-galactosidases and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred-orientation problem.},
  copyright = {2024 The Author(s), under exclusive licence to Springer Nature America, Inc.},
  langid = {english},
  keywords = {Cryoelectron microscopy,Cryoelectron tomography,Machine learning,Software},
  file = {C:\Users\shervinnia\Zotero\storage\2WR59ZWV\Liu et al. - 2025 - Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning.pdf}
}

While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the `preferred' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep learning-based software to address map anisotropy and particle misalignment caused by the preferred-orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's ability to generate near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, $β$-galactosidases and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred-orientation problem.

@misc{louCurvatureGenerationEngineering2025,
  title = {Curvature Generation and Engineering Principles from {{Shewanella}} Oneidensis Multi-Flagellin Flagellum},
  author = {Lou, Qing and Fan, Hongcheng and Liu, Yang and Miller, Jeff F. and Huang, Yu and Zhou, Z. Hong},
  year = {2025},
  month = feb,
  primaryclass = {New Results},
  pages = {2025.02.07.637127},
  publisher = {bioRxiv},
  doi = {10.1101/2025.02.07.637127},
  urldate = {2025-04-04},
  abstract = {Motility driven by nanoscale flagella is vital to microbial survival and spread in fluid and structured environments. Absence of native flagellum structures, however, has limited our understanding of the mechanisms of microbial motility, hindering efforts to engineer microbe-based microbots for applications. Here, by cryogenic electron tomography (cryoET) and microscopy (cryoEM), we determined the structural basis of motility driven by the single flagellum anchored to one pole of Shewanella oneidensis MR-1 (S. oneidensis), an electrogenic bacterium commonly used in biotechnology. The structures of the curved flagellum, representing the conformation during motion, are captured, allowing delineation of molecular interactions among the subunits of its three components---filament, hook, and hook-filament junction. The structures of the filament, i.e., the propeller, reveal a varying composition of the flagellin isoforms FlaA and FlaB throughout the filament. Distinct inter-subunit interactions are identified at residues 129 and 134, which are the major determinants of functional differences in motility for the two isoforms. The hook---the universal joint---has a significantly larger curvature than that of the filament, despite both containing 11 curvature-defining conformers of their subunits. Transition between the propeller and universal joint is mediated by hook-filament junction, composed of 11 subunits of FlgK and FlgL, reconciling incompatibility between the filament and hook. Correlating these compositional and structural transitions with varying levels of curvature in flagellar segments reveals molecular mechanism enabling propulsive motility. Mechanistic understandings from S. oneidensis suggest engineering principles for nanoscale biomimetic systems. {$<$}img class="highwire-fragment fragment-image" alt="Figure" src="https://www.biorxiv.org/content/biorxiv/early/2025/02/08/2025.02.07.637127/F1.medium.gif" width="440" height="293"/{$>$}Download figureOpen in new tab},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\EXJFR9KW\Lou et al. - 2025 - Curvature generation and engineering principles from Shewanella oneidensis multi-flagellin flagellum.pdf}
}

Motility driven by nanoscale flagella is vital to microbial survival and spread in fluid and structured environments. Absence of native flagellum structures, however, has limited our understanding of the mechanisms of microbial motility, hindering efforts to engineer microbe-based microbots for applications. Here, by cryogenic electron tomography (cryoET) and microscopy (cryoEM), we determined the structural basis of motility driven by the single flagellum anchored to one pole of Shewanella oneidensis MR-1 (S. oneidensis), an electrogenic bacterium commonly used in biotechnology. The structures of the curved flagellum, representing the conformation during motion, are captured, allowing delineation of molecular interactions among the subunits of its three components—filament, hook, and hook-filament junction. The structures of the filament, i.e., the propeller, reveal a varying composition of the flagellin isoforms FlaA and FlaB throughout the filament. Distinct inter-subunit interactions are identified at residues 129 and 134, which are the major determinants of functional differences in motility for the two isoforms. The hook—the universal joint—has a significantly larger curvature than that of the filament, despite both containing 11 curvature-defining conformers of their subunits. Transition between the propeller and universal joint is mediated by hook-filament junction, composed of 11 subunits of FlgK and FlgL, reconciling incompatibility between the filament and hook. Correlating these compositional and structural transitions with varying levels of curvature in flagellar segments reveals molecular mechanism enabling propulsive motility. Mechanistic understandings from S. oneidensis suggest engineering principles for nanoscale biomimetic systems. $<$img class="highwire-fragment fragment-image" alt="Figure" src="https://www.biorxiv.org/content/biorxiv/early/2025/02/08/2025.02.07.637127/F1.medium.gif" width="440" height="293"/$>$Download figureOpen in new tab

@article{sunStructuralBasisDistinct2025,
  title = {Structural Basis of a Distinct {$\alpha$}-Synuclein Strain That Promotes Tau Inclusion in Neurons},
  author = {Sun, Chuanqi and Zhou, Kang and DePaola, Peter and Li, Cally and Lee, Virginia M. Y. and Zhou, Z. Hong and Peng, Chao and Jiang, Lin},
  year = {2025},
  month = apr,
  journal = {Journal of Biological Chemistry},
  volume = {301},
  number = {4},
  pages = {108351},
  issn = {0021-9258},
  doi = {10.1016/j.jbc.2025.108351},
  urldate = {2025-04-04},
  abstract = {Amyloidoses are predominantly associated with the accumulation of persistent aggregates of a particular protein. For example, the protein {$\alpha$}-synuclein characteristically aggregates in Parkinson's disease (PD), while amyloid beta and tau deposits are associated with Alzheimer's disease (AD). However, {$\alpha$}-synuclein-positive inclusions have been reportedly found in some tauopathies, and vice versa; tau-positive inclusions can be found in synucleinopathies. This suggests that there may be coexistence or crosstalk between these proteinopathies. This coexistence suggests that the simultaneous presence of these misfolded proteins may amplify pathogenic mechanisms. However, the crosstalk between these two types of proteopathies remains poorly understood. We now determine the structure of {$\alpha$}-synuclein fibrils that directly promote tau aggregation by cryogenic electron microscopy. Helical reconstruction at 2.6~{\AA} resolution reveals a new {$\alpha$}-synuclein fibril polymorph we term ``strain B''; its core is unique, incorporating both the N- and C-termini of {$\alpha$}-synuclein. The design of peptides meant to inhibit the formation of this structure demonstrates that the C-terminal domain fragment (D105-E115) of {$\alpha$}-synuclein is critical for the formation of ``strain B'' fibrils and may play a key role in its interaction with tau. We hypothesize that the unique structure of pathological {$\alpha$}-synuclein significantly contributes to tau co-aggregation and plays a role in the intricate interactions among Alzheimer's, Parkinson's, and other neurodegenerative diseases. These findings open new avenues for drug targeting, discovery, and improve our understanding of neurodegenerative pathology.},
  keywords = {-synuclein,Alzheimer's disease,co-aggregation,Parkinson's disease,tau},
  file = {C:\Users\shervinnia\Zotero\storage\NI4PSENK\S0021925825002005.html}
}

Amyloidoses are predominantly associated with the accumulation of persistent aggregates of a particular protein. For example, the protein $α$-synuclein characteristically aggregates in Parkinson's disease (PD), while amyloid beta and tau deposits are associated with Alzheimer's disease (AD). However, $α$-synuclein-positive inclusions have been reportedly found in some tauopathies, and vice versa; tau-positive inclusions can be found in synucleinopathies. This suggests that there may be coexistence or crosstalk between these proteinopathies. This coexistence suggests that the simultaneous presence of these misfolded proteins may amplify pathogenic mechanisms. However, the crosstalk between these two types of proteopathies remains poorly understood. We now determine the structure of $α$-synuclein fibrils that directly promote tau aggregation by cryogenic electron microscopy. Helical reconstruction at 2.6 Å resolution reveals a new $α$-synuclein fibril polymorph we term ``strain B''; its core is unique, incorporating both the N- and C-termini of $α$-synuclein. The design of peptides meant to inhibit the formation of this structure demonstrates that the C-terminal domain fragment (D105-E115) of $α$-synuclein is critical for the formation of ``strain B'' fibrils and may play a key role in its interaction with tau. We hypothesize that the unique structure of pathological $α$-synuclein significantly contributes to tau co-aggregation and plays a role in the intricate interactions among Alzheimer's, Parkinson's, and other neurodegenerative diseases. These findings open new avenues for drug targeting, discovery, and improve our understanding of neurodegenerative pathology.

@article{xiaTrypanosomeDoubletMicrotubule2025,
  title = {Trypanosome Doublet Microtubule Structures Reveal Flagellum Assembly and Motility Mechanisms},
  author = {Xia, Xian and Shimogawa, Michelle M. and Wang, Hui and Liu, Samuel and Wijono, Angeline and Langousis, Gerasimos and Kassem, Ahmad M. and Wohlschlegel, James A. and Hill, Kent L. and Zhou, Z. Hong},
  year = {2025},
  month = mar,
  journal = {Science},
  volume = {387},
  number = {6739},
  pages = {eadr3314},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/science.adr3314},
  urldate = {2025-04-04},
  abstract = {The flagellum of Trypanosoma brucei drives the parasite's characteristic screw-like motion and is essential for its replication, transmission, and pathogenesis. However, the molecular details of this process remain unclear. Here, we present high-resolution (up to 2.8 angstrom) cryo--electron microscopy structures of T. brucei flagellar doublet microtubules (DMTs). Integrated modeling identified 154 different axonemal proteins inside and outside the DMT and, together with genetic and proteomic interrogation, revealed conserved and trypanosome-specific foundations of flagellum assembly and motility. We captured axonemal dynein motors in their pre--power stroke state. Comparing atomic models between pre-- and post--power strokes defined how dynein structural changes drive sliding of adjacent DMTs during flagellar beating. This study illuminates structural dynamics underlying flagellar motility and identifies pathogen-specific proteins to consider for therapeutic interventions targeting neglected diseases.},
  file = {C:\Users\shervinnia\Zotero\storage\3FS92FFX\Xia et al. - 2025 - Trypanosome doublet microtubule structures reveal flagellum assembly and motility mechanisms.pdf}
}

The flagellum of Trypanosoma brucei drives the parasite's characteristic screw-like motion and is essential for its replication, transmission, and pathogenesis. However, the molecular details of this process remain unclear. Here, we present high-resolution (up to 2.8 angstrom) cryo–electron microscopy structures of T. brucei flagellar doublet microtubules (DMTs). Integrated modeling identified 154 different axonemal proteins inside and outside the DMT and, together with genetic and proteomic interrogation, revealed conserved and trypanosome-specific foundations of flagellum assembly and motility. We captured axonemal dynein motors in their pre–power stroke state. Comparing atomic models between pre– and post–power strokes defined how dynein structural changes drive sliding of adjacent DMTs during flagellar beating. This study illuminates structural dynamics underlying flagellar motility and identifies pathogen-specific proteins to consider for therapeutic interventions targeting neglected diseases.

@article{backAlveolinProteinsToxoplasma2024,
  title = {Alveolin Proteins in the {{Toxoplasma}} Inner Membrane Complex Form a Highly Interconnected Structure That Maintains Parasite Shape and Replication},
  author = {Back, Peter S. and Senthilkumar, Vignesh and Choi, Charles P. and Quan, Justin J. and Lou, Qing and Snyder, Anne K. and Ly, Andrew M. and Lau, Justin G. and Zhou, Z. Hong and Ward, Gary E. and Bradley, Peter J.},
  year = {2024},
  month = sep,
  journal = {PLOS Biology},
  volume = {22},
  number = {9},
  pages = {e3002809},
  publisher = {Public Library of Science},
  issn = {1545-7885},
  doi = {10.1371/journal.pbio.3002809},
  urldate = {2025-04-04},
  abstract = {Apicomplexan parasites possess several specialized structures to invade their host cells and replicate successfully. One of these is the inner membrane complex (IMC), a peripheral membrane-cytoskeletal system underneath the plasma membrane. It is composed of a series of flattened, membrane-bound vesicles and a cytoskeletal subpellicular network (SPN) comprised of intermediate filament-like proteins called alveolins. While the alveolin proteins are conserved throughout the Apicomplexa and the broader Alveolata, their precise functions and interactions remain poorly understood. Here, we describe the function of one of these alveolin proteins in Toxoplasma, IMC6. Disruption of IMC6 resulted in striking morphological defects that led to aberrant invasion and replication but surprisingly minor effects on motility. Deletion analyses revealed that the alveolin domain alone is largely sufficient to restore localization and partially sufficient for function. As this highlights the importance of the IMC6 alveolin domain, we implemented unnatural amino acid photoreactive crosslinking to the alveolin domain and identified multiple binding interfaces between IMC6 and 2 other cytoskeletal IMC proteins---IMC3 and ILP1. This provides direct evidence of protein--protein interactions in the alveolin domain and supports the long-held hypothesis that the alveolin domain is responsible for filament formation. Collectively, our study features the conserved alveolin proteins as critical components that maintain the parasite's structural integrity and highlights the alveolin domain as a key mediator of SPN architecture.},
  langid = {english},
  keywords = {Cross-linking,Cytoskeletal proteins,Parasite replication,Parasitic diseases,Protein domains,Protein interactions,Toxoplasma gondii,Vacuoles},
  file = {C:\Users\shervinnia\Zotero\storage\IL4S7QVL\Back et al. - 2024 - Alveolin proteins in the Toxoplasma inner membrane complex form a highly interconnected structure th.pdf}
}

Apicomplexan parasites possess several specialized structures to invade their host cells and replicate successfully. One of these is the inner membrane complex (IMC), a peripheral membrane-cytoskeletal system underneath the plasma membrane. It is composed of a series of flattened, membrane-bound vesicles and a cytoskeletal subpellicular network (SPN) comprised of intermediate filament-like proteins called alveolins. While the alveolin proteins are conserved throughout the Apicomplexa and the broader Alveolata, their precise functions and interactions remain poorly understood. Here, we describe the function of one of these alveolin proteins in Toxoplasma, IMC6. Disruption of IMC6 resulted in striking morphological defects that led to aberrant invasion and replication but surprisingly minor effects on motility. Deletion analyses revealed that the alveolin domain alone is largely sufficient to restore localization and partially sufficient for function. As this highlights the importance of the IMC6 alveolin domain, we implemented unnatural amino acid photoreactive crosslinking to the alveolin domain and identified multiple binding interfaces between IMC6 and 2 other cytoskeletal IMC proteins—IMC3 and ILP1. This provides direct evidence of protein–protein interactions in the alveolin domain and supports the long-held hypothesis that the alveolin domain is responsible for filament formation. Collectively, our study features the conserved alveolin proteins as critical components that maintain the parasite's structural integrity and highlights the alveolin domain as a key mediator of SPN architecture.

@article{caiStructuralHeterogeneityRabies2024,
  title = {Structural {{Heterogeneity}} of the {{Rabies Virus Virion}}},
  author = {Cai, Xiaoying and Zhou, Kang and {Alvarez-Cabrera}, Ana Lucia and Si, Zhu and Wang, Hui and He, Yao and Li, Cally and Zhou, Z. Hong},
  year = {2024},
  month = sep,
  journal = {Viruses},
  volume = {16},
  number = {9},
  pages = {1447},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {1999-4915},
  doi = {10.3390/v16091447},
  urldate = {2025-04-04},
  abstract = {Rabies virus (RABV) is among the first recognized viruses of public health concern and has historically contributed to the development of viral vaccines. Despite these significances, the three-dimensional structure of the RABV virion remains unknown due to the challenges in isolating structurally homogenous virion samples in sufficient quantities needed for structural investigation. Here, by combining the capabilities of cryogenic electron tomography (cryoET) and microscopy (cryoEM), we determined the three-dimensional structure of the wild-type RABV virion. Tomograms of RABV virions reveal a high level of structural heterogeneity among the bullet-shaped virion particles encompassing the glycoprotein (G) trimer-decorated envelope and the nucleocapsid composed of RNA, nucleoprotein (N), and matrix protein (M). The structure of the trunk region of the virion was determined by cryoEM helical reconstruction, revealing a one-start N-RNA helix bound by a single layer of M proteins at an N:M ratio of 1. The N-M interaction differs from that in fellow rhabdovirus vesicular stomatitis virus (VSV), which features two layers of M stabilizing the N-RNA helix at an M:N ratio of 2. These differences in both M-N stoichiometry and binding allow RABV to flex its N-RNA helix more freely and point to different mechanisms of viral assembly between these two bullet-shaped rhabdoviruses.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {cryogenic electron microscopy,cryogenic electron tomography,dynamics,flexibility,rabies virus,rhabdoviruses,wild type},
  file = {C:\Users\shervinnia\Zotero\storage\DV59DN8Z\Cai et al. - 2024 - Structural Heterogeneity of the Rabies Virus Virion.pdf}
}

Rabies virus (RABV) is among the first recognized viruses of public health concern and has historically contributed to the development of viral vaccines. Despite these significances, the three-dimensional structure of the RABV virion remains unknown due to the challenges in isolating structurally homogenous virion samples in sufficient quantities needed for structural investigation. Here, by combining the capabilities of cryogenic electron tomography (cryoET) and microscopy (cryoEM), we determined the three-dimensional structure of the wild-type RABV virion. Tomograms of RABV virions reveal a high level of structural heterogeneity among the bullet-shaped virion particles encompassing the glycoprotein (G) trimer-decorated envelope and the nucleocapsid composed of RNA, nucleoprotein (N), and matrix protein (M). The structure of the trunk region of the virion was determined by cryoEM helical reconstruction, revealing a one-start N-RNA helix bound by a single layer of M proteins at an N:M ratio of 1. The N-M interaction differs from that in fellow rhabdovirus vesicular stomatitis virus (VSV), which features two layers of M stabilizing the N-RNA helix at an M:N ratio of 2. These differences in both M-N stoichiometry and binding allow RABV to flex its N-RNA helix more freely and point to different mechanisms of viral assembly between these two bullet-shaped rhabdoviruses.

@article{chalivendraSelectedHumanizationYeast2024,
  title = {Selected Humanization of Yeast {{U1 snRNP}} Leads to Global Suppression of Pre-{{mRNA}} Splicing and Mitochondrial Dysfunction in the Budding Yeast},
  author = {Chalivendra, Subbaiah and Shi, Shasha and Li, Xueni and Kuang, Zhiling and Giovinazzo, Joseph and Zhang, Lingdi and Rossi, John and Wang, Jingxin and Saviola, Anthony J. and Welty, Robb and Liu, Shiheng and Vaeth, Katherine F. and Zhou, Z. Hong and Hansen, Kirk C. and Taliaferro, J. Matthew and Zhao, Rui},
  year = {2024},
  month = aug,
  journal = {RNA},
  volume = {30},
  number = {8},
  pages = {1070--1088},
  publisher = {Cold Spring Harbor Lab},
  issn = {1355-8382, 1469-9001},
  doi = {10.1261/rna.079917.123},
  urldate = {2025-04-04},
  abstract = {The recognition of the 5{$\prime$} splice site (5{$\prime$} ss) is one of the earliest steps of pre-mRNA splicing. To better understand, the mechanism and regulation of 5{$\prime$} ss recognition, we selectively humanized components of the yeast U1 (yU1) snRNP to reveal the function of these components in 5{$\prime$} ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yU1 snRNA and the 5{$\prime$} ss RNA duplex. We replaced the zinc-finger (ZnF) domain of yeast U1C (yU1C) with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yeast Luc7 (yLuc7) protein (to mimic the lack of Luc7Ls in human U1 snRNP). We found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of Prp40 and Snu71 (two other essential yU1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7--Prp40--Snu71 trimer into yU1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.},
  langid = {english},
  pmid = {38688558},
  keywords = {5' splice site recognition,Luc7,U1 snRNP,U1C},
  file = {C:\Users\shervinnia\Zotero\storage\RM53B4A8\Chalivendra et al. - 2024 - Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitocho.pdf}
}

The recognition of the 5$\prime$ splice site (5$\prime$ ss) is one of the earliest steps of pre-mRNA splicing. To better understand, the mechanism and regulation of 5$\prime$ ss recognition, we selectively humanized components of the yeast U1 (yU1) snRNP to reveal the function of these components in 5$\prime$ ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yU1 snRNA and the 5$\prime$ ss RNA duplex. We replaced the zinc-finger (ZnF) domain of yeast U1C (yU1C) with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yeast Luc7 (yLuc7) protein (to mimic the lack of Luc7Ls in human U1 snRNP). We found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of Prp40 and Snu71 (two other essential yU1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7–Prp40–Snu71 trimer into yU1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.

@article{dasVPS4ASelectiveReceptor2024,
  title = {{{VPS4A}} Is the Selective Receptor for Lipophagy in Mice and Humans},
  author = {Das, Debajyoti and Sharma, Mridul and Gahlot, Deepanshi and Nia, Shervin S. and Gain, Chandrima and Mecklenburg, Matthew and Zhou, Z. Hong and Bourdenx, Mathieu and Thukral, Lipi and {Martinez-Lopez}, Nuria and Singh, Rajat},
  year = {2024},
  month = nov,
  journal = {Molecular Cell},
  volume = {84},
  number = {22},
  pages = {4436-4453.e8},
  publisher = {Elsevier},
  issn = {1097-2765},
  doi = {10.1016/j.molcel.2024.10.022},
  urldate = {2025-04-04},
  langid = {english},
  pmid = {39520981},
  keywords = {autophagy,human,lipid droplet,lipophagy,liver,lysosome,MASLD,phosphorylation,receptor,VPS4A},
  file = {C:\Users\shervinnia\Zotero\storage\SJ6T734F\Das et al. - 2024 - VPS4A is the selective receptor for lipophagy in mice and humans.pdf}
}

@article{draganovaUniversalSuppressorMutation2024,
  title = {The Universal Suppressor Mutation Restores Membrane Budding Defects in the {{HSV-1}} Nuclear Egress Complex by Stabilizing the Oligomeric Lattice},
  author = {Draganova, Elizabeth B. and Wang, Hui and Wu, Melanie and Liao, Shiqing and Vu, Amber and Pino, Gonzalo L. Gonzalez-Del and Zhou, Z. Hong and Roller, Richard J. and Heldwein, Ekaterina E.},
  year = {2024},
  month = jan,
  journal = {PLOS Pathogens},
  volume = {20},
  number = {1},
  pages = {e1011936},
  publisher = {Public Library of Science},
  issn = {1553-7374},
  doi = {10.1371/journal.ppat.1011936},
  urldate = {2024-06-13},
  abstract = {Nuclear egress is an essential process in herpesvirus replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress--budding at the inner nuclear membrane--is coordinated by the nuclear egress complex (NEC). Composed of the viral proteins UL31 and UL34, NEC deforms the membrane around the capsid as the latter buds into the perinuclear space. NEC oligomerization into a hexagonal membrane-bound lattice is essential for budding because NEC mutants designed to perturb lattice interfaces reduce its budding ability. Previously, we identified an NEC suppressor mutation capable of restoring budding to a mutant with a weakened hexagonal lattice. Using an established in-vitro budding assay and HSV-1 infected cell experiments, we show that the suppressor mutation can restore budding to a broad range of budding-deficient NEC mutants thereby acting as a universal suppressor. Cryogenic electron tomography of the suppressor NEC mutant lattice revealed a hexagonal lattice reminiscent of wild-type NEC lattice instead of an alternative lattice. Further investigation using x-ray crystallography showed that the suppressor mutation promoted the formation of new contacts between the NEC hexamers that, ostensibly, stabilized the hexagonal lattice. This stabilization strategy is powerful enough to override the otherwise deleterious effects of mutations that destabilize the NEC lattice by different mechanisms, resulting in a functional NEC hexagonal lattice and restoration of membrane budding.},
  langid = {english},
  keywords = {Capsids,Crystal lattices,Crystal structure,Microbial mutation,Plasmid construction,Salt bridges,Vesicles,Viral replication},
  file = {C:\Users\shervinnia\Zotero\storage\HYR3GXAY\Draganova et al. - 2024 - The universal suppressor mutation restores membran.pdf}
}

Nuclear egress is an essential process in herpesvirus replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress–budding at the inner nuclear membrane–is coordinated by the nuclear egress complex (NEC). Composed of the viral proteins UL31 and UL34, NEC deforms the membrane around the capsid as the latter buds into the perinuclear space. NEC oligomerization into a hexagonal membrane-bound lattice is essential for budding because NEC mutants designed to perturb lattice interfaces reduce its budding ability. Previously, we identified an NEC suppressor mutation capable of restoring budding to a mutant with a weakened hexagonal lattice. Using an established in-vitro budding assay and HSV-1 infected cell experiments, we show that the suppressor mutation can restore budding to a broad range of budding-deficient NEC mutants thereby acting as a universal suppressor. Cryogenic electron tomography of the suppressor NEC mutant lattice revealed a hexagonal lattice reminiscent of wild-type NEC lattice instead of an alternative lattice. Further investigation using x-ray crystallography showed that the suppressor mutation promoted the formation of new contacts between the NEC hexamers that, ostensibly, stabilized the hexagonal lattice. This stabilization strategy is powerful enough to override the otherwise deleterious effects of mutations that destabilize the NEC lattice by different mechanisms, resulting in a functional NEC hexagonal lattice and restoration of membrane budding.

@article{itoStructuralBasisPolyuridine2024,
  title = {Structural Basis for Polyuridine Tract Recognition by {{SARS-CoV-2 Nsp15}}},
  author = {Ito, Fumiaki and Yang, Hanjing and Zhou, Z Hong and Chen, Xiaojiang S},
  year = {2024},
  month = apr,
  journal = {Protein \& Cell},
  pages = {pwae009},
  issn = {1674-800X},
  doi = {10.1093/procel/pwae009},
  urldate = {2024-06-13},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\FJM88GSR\\Ito et al. - 2024 - Structural basis for polyuridine tract recognition.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\EFI3VNY6\\7645160.html}
}

@article{jihIncredibleBulkHuman2024,
  title = {The Incredible Bulk: {{Human}} Cytomegalovirus Tegument Architectures Uncovered by {{AI-empowered}} Cryo-{{EM}}},
  shorttitle = {The Incredible Bulk},
  author = {Jih, Jonathan and Liu, Yun-Tao and Liu, Wei and Zhou, Z. Hong},
  year = {2024},
  month = feb,
  journal = {Science Advances},
  volume = {10},
  number = {8},
  pages = {eadj1640},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/sciadv.adj1640},
  urldate = {2024-06-13},
  abstract = {The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning--enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head--linker--capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.},
  file = {C:\Users\shervinnia\Zotero\storage\4AXHGP8R\Jih et al. - 2024 - The incredible bulk Human cytomegalovirus tegumen.pdf}
}

The compartmentalization of eukaryotic cells presents considerable challenges to the herpesvirus life cycle. The herpesvirus tegument, a bulky proteinaceous aggregate sandwiched between herpesviruses' capsid and envelope, is uniquely evolved to address these challenges, yet tegument structure and organization remain poorly characterized. We use deep-learning–enhanced cryogenic electron microscopy to investigate the tegument of human cytomegalovirus virions and noninfectious enveloped particles (NIEPs; a genome packaging-aborted state), revealing a portal-biased tegumentation scheme. We resolve atomic structures of portal vertex-associated tegument (PVAT) and identify multiple configurations of PVAT arising from layered reorganization of pUL77, pUL48 (large tegument protein), and pUL47 (inner tegument protein) assemblies. Analyses show that pUL77 seals the last-packaged viral genome end through electrostatic interactions, pUL77 and pUL48 harbor a head–linker–capsid-binding motif conducive to PVAT reconfiguration, and pUL47/48 dimers form 45-nm-long filaments extending from the portal vertex. These results provide a structural framework for understanding how herpesvirus tegument facilitates and evolves during processes spanning viral genome packaging to delivery.

@article{kangArchitecturalOrganizationSitu2024,
  title = {Architectural Organization and in Situ Fusion Protein Structure of Lymphocytic Choriomeningitis Virus},
  author = {Kang, Joon S. and Zhou, Kang and Wang, Hui and Tang, Sijia and Lyles, Kristin Van Mouwerik and Luo, Ming and Zhou, Z. Hong},
  year = {2024},
  month = sep,
  journal = {Journal of Virology},
  volume = {98},
  number = {10},
  pages = {e00640-24},
  publisher = {American Society for Microbiology},
  doi = {10.1128/jvi.00640-24},
  urldate = {2025-04-04},
  file = {C:\Users\shervinnia\Zotero\storage\Z4YW4CKU\Kang et al. - 2024 - Architectural organization and in situ fusion protein structure of lymphocytic choriomeningitis viru.pdf}
}

@article{liuMolecularSociologyVirusinduced2024,
  title = {Molecular Sociology of Virus-Induced Cellular Condensates Supporting Reovirus Assembly and Replication},
  author = {Liu, Xiaoyu and Xia, Xian and Martynowycz, Michael W. and Gonen, Tamir and Zhou, Z. Hong},
  year = {2024},
  month = dec,
  journal = {Nature Communications},
  volume = {15},
  number = {1},
  pages = {10638},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-024-54968-7},
  urldate = {2025-04-04},
  abstract = {Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., ``molecular sociology'') of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.},
  copyright = {2024 The Author(s)},
  langid = {english},
  keywords = {Biopolymers in vivo,Cryoelectron tomography,Virus structures},
  file = {C:\Users\shervinnia\Zotero\storage\9Y9MRVQZ\Liu et al. - 2024 - Molecular sociology of virus-induced cellular condensates supporting reovirus assembly and replicati.pdf}
}

Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., ``molecular sociology'') of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.

@misc{liuOvercomingPreferredOrientation2024,
  title = {Overcoming the Preferred Orientation Problem in {{cryoEM}} with Self-Supervised Deep-Learning},
  author = {Liu, Yun-Tao and Fan, Hongcheng and Hu, Jason J. and Zhou, Z. Hong},
  year = {2024},
  month = apr,
  primaryclass = {New Results},
  pages = {2024.04.11.588921},
  publisher = {bioRxiv},
  doi = {10.1101/2024.04.11.588921},
  urldate = {2024-06-13},
  abstract = {While advances in single-particle cryoEM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the so-called ``preferred'' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep-learning-based software to address the preferred orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's capability of generating near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, {$\beta$}-galactosidases, and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred orientation problem.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\6M8U6YJ2\Liu et al. - 2024 - Overcoming the preferred orientation problem in cr.pdf}
}

While advances in single-particle cryoEM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the so-called ``preferred'' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep-learning-based software to address the preferred orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's capability of generating near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, $β$-galactosidases, and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred orientation problem.

@article{mecklenburgPathsAttenuateRadiolysisInduced2024,
  title = {Paths to {{Attenuate Radiolysis-Induced Secondary Damage}} in {{Biological CryoEM}}},
  author = {Mecklenburg, Matthew and Nia, Shervin S and Saha, Ambarneil and Hong Zhou, Z},
  year = {2024},
  month = jul,
  journal = {Microscopy and Microanalysis},
  volume = {30},
  number = {Supplement\_1},
  pages = {ozae044.877},
  issn = {1431-9276},
  doi = {10.1093/mam/ozae044.877},
  urldate = {2025-04-04},
  abstract = {The imaging electrons in a transmission electron microscope are a beam of bond-breaking beta-radiation. Imaging soft materials is a challenge because of beam damage and poor contrast between the substrate and specimen. Typically, only 10-100 electrons can strike an atomically sized area before disintegration [1]. Peptide, hydrogen, disulfide bonds etc. are all irreparably broken by radiolysis while being simultaneously imaged. The total dose for loss of useful information is roughly the Henderson limit (often accumulated in a few seconds, see Figure 1), about 20 MGy [2], which is roughly 9 orders of magnitude larger than an average person receives per year [3]. This primary damage cannot be abated in small molecules, protein, or virus samples. In addition, unlike the case for x-rays, the inelastic scattering is more likely than elastic scattering for elements in atomic number less than about iron [4]. This leads to poor contrast using parallel beam imaging modalities.},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\ZXD7QZSK\\Mecklenburg et al. - 2024 - Paths to Attenuate Radiolysis-Induced Secondary Damage in Biological CryoEM.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\C67US3J9\\7720210.html}
}

The imaging electrons in a transmission electron microscope are a beam of bond-breaking beta-radiation. Imaging soft materials is a challenge because of beam damage and poor contrast between the substrate and specimen. Typically, only 10-100 electrons can strike an atomically sized area before disintegration [1]. Peptide, hydrogen, disulfide bonds etc. are all irreparably broken by radiolysis while being simultaneously imaged. The total dose for loss of useful information is roughly the Henderson limit (often accumulated in a few seconds, see Figure 1), about 20 MGy [2], which is roughly 9 orders of magnitude larger than an average person receives per year [3]. This primary damage cannot be abated in small molecules, protein, or virus samples. In addition, unlike the case for x-rays, the inelastic scattering is more likely than elastic scattering for elements in atomic number less than about iron [4]. This leads to poor contrast using parallel beam imaging modalities.

@article{milojevicCapturingIntermediatesMembrane2024,
  title = {Capturing Intermediates and Membrane Remodeling in Class {{III}} Viral Fusion},
  author = {Milojevi{\'c}, Lenka and Si, Zhu and Xia, Xian and Chen, Lauren and He, Yao and Tang, Sijia and Luo, Ming and Zhou, Z. Hong},
  year = {2024},
  month = dec,
  journal = {Science Advances},
  volume = {10},
  number = {49},
  pages = {eadn8579},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/sciadv.adn8579},
  urldate = {2025-04-04},
  abstract = {Enveloped viruses enter cells by fusing their envelopes to host cell membranes. Vesicular stomatitis virus (VSV) glycoprotein (G) is a prototype for class III fusion proteins. Although structures of the stable pre- and postfusion ectodomain of G are known, its fusogenic intermediates are insufficiently characterized. Here, we incubated VSV virions with late endosome-mimicking liposomes at pH 5.5 and used cryo--electron tomography (cryo-ET) to visualize stages of VSV's membrane fusion pathway, capture refolding intermediates of G, and reconstruct a sequence of G conformational changes. We observe that the G trimer disassembles into monomers and parallel dimers that explore a broad conformational space. Extended intermediates engage target membranes and mediate fusion, resulting in viral uncoating and linearization of the ribonucleoprotein genome. These viral fusion intermediates provide mechanistic insights into class III viral fusion processes, opening avenues for future research and structure-based design of fusion inhibition-based antiviral therapeutics.},
  file = {C:\Users\shervinnia\Zotero\storage\XXVZZ2UF\Milojević et al. - 2024 - Capturing intermediates and membrane remodeling in class III viral fusion.pdf}
}

Enveloped viruses enter cells by fusing their envelopes to host cell membranes. Vesicular stomatitis virus (VSV) glycoprotein (G) is a prototype for class III fusion proteins. Although structures of the stable pre- and postfusion ectodomain of G are known, its fusogenic intermediates are insufficiently characterized. Here, we incubated VSV virions with late endosome-mimicking liposomes at pH 5.5 and used cryo–electron tomography (cryo-ET) to visualize stages of VSV's membrane fusion pathway, capture refolding intermediates of G, and reconstruct a sequence of G conformational changes. We observe that the G trimer disassembles into monomers and parallel dimers that explore a broad conformational space. Extended intermediates engage target membranes and mediate fusion, resulting in viral uncoating and linearization of the ribonucleoprotein genome. These viral fusion intermediates provide mechanistic insights into class III viral fusion processes, opening avenues for future research and structure-based design of fusion inhibition-based antiviral therapeutics.

@article{rajanDrebrinProtectsAssembled2024,
  title = {Drebrin {{Protects Assembled Actin}} from {{INF2-FFC-mediated Severing}} and {{Stabilizes Cell Protrusions}}},
  author = {Rajan, Sudeepa and Aguirre, Roman and Hong Zhou, Z. and Hauser, Peter and Reisler, Emil},
  year = {2024},
  month = feb,
  journal = {Journal of Molecular Biology},
  volume = {436},
  number = {4},
  pages = {168421},
  issn = {0022-2836},
  doi = {10.1016/j.jmb.2023.168421},
  urldate = {2024-06-13},
  abstract = {Highly specialized cells, such as neurons and podocytes, have arborized morphologies that serve their specific functions. Actin cytoskeleton and its associated proteins are responsible for the distinctive shapes of cells. The mechanism of their cytoskeleton regulation -- contributing to cell shape maintenance -- is yet to be fully clarified. Inverted formin 2 (INF2), one of the modulators of the cytoskeleton, is an atypical formin that can both polymerize and depolymerize actin filaments depending on its molar ratio to actin. Prior work has established that INF2 binds to the sides of actin filaments and severs them. Drebrin is another actin-binding protein that also binds filaments laterally and stabilizes them, but the interplay between drebrin and INF2 on actin filament stabilization is not well understood. Here, we have used biochemical assays, electron microscopy, and total internal reflection fluorescence microscopy imaging to show that drebrin protects actin filaments from severing by INF2 without inhibiting its polymerization activity. Notably, truncated drebrin -- DrbA1-300 -- is sufficient for this protection, though not as effective as the full-length protein. INF2 and drebrin are abundantly expressed in highly specialized cells and are crucial for the temporal regulation of their actin cytoskeleton, consistent with their involvement in peripheral neuropathy.},
  keywords = {actin severing,cell shape,cytoskeleton,neurons,TIRFM},
  file = {C:\Users\shervinnia\Zotero\storage\ZDCTM7MV\S0022283623005387.html}
}

Highly specialized cells, such as neurons and podocytes, have arborized morphologies that serve their specific functions. Actin cytoskeleton and its associated proteins are responsible for the distinctive shapes of cells. The mechanism of their cytoskeleton regulation – contributing to cell shape maintenance – is yet to be fully clarified. Inverted formin 2 (INF2), one of the modulators of the cytoskeleton, is an atypical formin that can both polymerize and depolymerize actin filaments depending on its molar ratio to actin. Prior work has established that INF2 binds to the sides of actin filaments and severs them. Drebrin is another actin-binding protein that also binds filaments laterally and stabilizes them, but the interplay between drebrin and INF2 on actin filament stabilization is not well understood. Here, we have used biochemical assays, electron microscopy, and total internal reflection fluorescence microscopy imaging to show that drebrin protects actin filaments from severing by INF2 without inhibiting its polymerization activity. Notably, truncated drebrin – DrbA1-300 – is sufficient for this protection, though not as effective as the full-length protein. INF2 and drebrin are abundantly expressed in highly specialized cells and are crucial for the temporal regulation of their actin cytoskeleton, consistent with their involvement in peripheral neuropathy.

@misc{stevensStructureGuidedMutagenesisTargeting2024,
  title = {Structure-{{Guided Mutagenesis Targeting Interactions}} between Pp150 {{Tegument Protein}} and {{Small Capsid Protein Identify Five Lethal}} and {{Two Live Attenuated HCMV Mutants}}},
  author = {Stevens, Alex and {Cruz-cosme}, Ruth and Armstrong, Najealicka and Tang, Qiyi and Zhou, Z. Hong},
  year = {2024},
  month = apr,
  primaryclass = {New Results},
  pages = {2024.01.22.576707},
  publisher = {bioRxiv},
  doi = {10.1101/2024.01.22.576707},
  urldate = {2024-06-13},
  abstract = {Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single point mutation at the pp150-MCP interface significantly attenuated viral replication, unlike the situation of pp150-deletion mutation where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150 K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2024, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\L3UDU3QN\Stevens et al. - 2024 - Structure-Guided Mutagenesis Targeting Interaction.pdf}
}

Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single point mutation at the pp150-MCP interface significantly attenuated viral replication, unlike the situation of pp150-deletion mutation where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150 K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.

@article{stevensStructureguidedMutagenesisTargeting2024a,
  title = {Structure-Guided Mutagenesis Targeting Interactions between Pp150 Tegument Protein and Small Capsid Protein Identify Five Lethal and Two Live-Attenuated {{HCMV}} Mutants},
  author = {Stevens, Alexander and {Cruz-Cosme}, Ruth and Armstrong, Najealicka and Tang, Qiyi and Zhou, Z. Hong},
  year = {2024},
  month = aug,
  journal = {Virology},
  volume = {596},
  pages = {110115},
  issn = {0042-6822},
  doi = {10.1016/j.virol.2024.110115},
  urldate = {2024-06-13},
  abstract = {Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150~kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single amino acid mutation (pp150~K255E) at the pp150-MCP interface significantly attenuated viral replication, unlike in pp150-deletion mutants where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150~K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.},
  keywords = {Capsid,HCMV,Replication,Structure,Tegument},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\K54TMR34\\Stevens et al. - 2024 - Structure-guided mutagenesis targeting interaction.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\4XAIWPG9\\S0042682224001363.html}
}

Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150 kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single amino acid mutation (pp150 K255E) at the pp150-MCP interface significantly attenuated viral replication, unlike in pp150-deletion mutants where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150 K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.

@article{stevensStructureguidedMutagenesisTargeting2024b,
  title = {Structure-Guided Mutagenesis Targeting Interactions between Pp150 Tegument Protein and Small Capsid Protein Identify Five Lethal and Two Live-Attenuated {{HCMV}} Mutants},
  author = {Stevens, Alexander and {Cruz-Cosme}, Ruth and Armstrong, Najealicka and Tang, Qiyi and Zhou, Z. Hong},
  year = {2024},
  month = aug,
  journal = {Virology},
  volume = {596},
  pages = {110115},
  issn = {0042-6822},
  doi = {10.1016/j.virol.2024.110115},
  urldate = {2025-04-04},
  abstract = {Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150~kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single amino acid mutation (pp150~K255E) at the pp150-MCP interface significantly attenuated viral replication, unlike in pp150-deletion mutants where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150~K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.},
  keywords = {Capsid,HCMV,Replication,Structure,Tegument},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\RYIRXH9P\\Stevens et al. - 2024 - Structure-guided mutagenesis targeting interactions between pp150 tegument protein and small capsid.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\FYF9ITDE\\S0042682224001363.html}
}

Human cytomegalovirus (HCMV) replication relies on a nucleocapsid coat of the 150 kDa, subfamily-specific tegument phosphoprotein (pp150) to regulate cytoplasmic virion maturation. While recent structural studies revealed pp150-capsid interactions, the role of specific amino-acids involved in these interactions have not been established experimentally. In this study, pp150 and the small capsid protein (SCP), one of pp150's binding partners found atop the major capsid protein (MCP), were subjected to mutational and structural analyses. Mutations to clusters of polar or hydrophobic residues along the pp150-SCP interface abolished viral replication, with no replication detected in mutant virus-infected cells. Notably, a single amino acid mutation (pp150 K255E) at the pp150-MCP interface significantly attenuated viral replication, unlike in pp150-deletion mutants where capsids degraded outside host nuclei. These functionally significant mutations targeting pp150-capsid interactions, particularly the pp150 K255E replication-attenuated mutant, can be explored to overcome the historical challenges of developing effective antivirals and vaccines against HCMV infection.

@misc{stevensStructuresNativeDoublet2024,
  title = {Structures of {{Native Doublet Microtubules}} from {{Trichomonas}} Vaginalis {{Reveal Parasite-Specific Proteins}} as {{Potential Drug Targets}}},
  author = {Stevens, Alexander and Kashyap, Saarang and Crofut, Ethan H. and Wang, Shuqi E. and Muratore, Katherine A. and Johnson, Patricia J. and Zhou, Z. Hong},
  year = {2024},
  month = jun,
  primaryclass = {New Results},
  pages = {2024.06.11.598142},
  publisher = {bioRxiv},
  doi = {10.1101/2024.06.11.598142},
  urldate = {2025-04-04},
  abstract = {Doublet microtubules (DMTs) are flagellar components required for the protist Trichomonas vaginalis (Tv) to swim through the human genitourinary tract to cause trichomoniasis, the most common non-viral sexually transmitted disease. Lack of DMT structures has prevented structure-guided drug design to manage Tv infection. Here, we determined the cryo-EM structure of native Tv-DMTs, identifying 29 unique proteins, including 18 microtubule inner proteins and 9 microtubule outer proteins. While the A-tubule is simplistic compared to DMTs of other organisms, the B-tubule features specialized, parasite-specific proteins, like TvFAP40 and TvFAP35 that form filaments near the inner and outer junctions, respectively, to stabilize DMTs and enable Tv locomotion. Notably, a small molecule, assigned as IP6, is coordinated within a pocket of TvFAP40 and has characteristics of a drug molecule. This first atomic model of the Tv-DMT highlights the diversity of eukaryotic motility machinery and provides a structural framework to inform the rational design of therapeutics.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2024, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\H9LYDR3F\Stevens et al. - 2024 - Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Protei.pdf}
}

Doublet microtubules (DMTs) are flagellar components required for the protist Trichomonas vaginalis (Tv) to swim through the human genitourinary tract to cause trichomoniasis, the most common non-viral sexually transmitted disease. Lack of DMT structures has prevented structure-guided drug design to manage Tv infection. Here, we determined the cryo-EM structure of native Tv-DMTs, identifying 29 unique proteins, including 18 microtubule inner proteins and 9 microtubule outer proteins. While the A-tubule is simplistic compared to DMTs of other organisms, the B-tubule features specialized, parasite-specific proteins, like TvFAP40 and TvFAP35 that form filaments near the inner and outer junctions, respectively, to stabilize DMTs and enable Tv locomotion. Notably, a small molecule, assigned as IP6, is coordinated within a pocket of TvFAP40 and has characteristics of a drug molecule. This first atomic model of the Tv-DMT highlights the diversity of eukaryotic motility machinery and provides a structural framework to inform the rational design of therapeutics.

@article{wangCompositionSituStructure2024,
  title = {Composition and in Situ Structure of the {{Methanospirillum}} Hungatei Cell Envelope and Surface Layer},
  author = {Wang, Hui and Zhang, Jiayan and Liao, Shiqing and Henstra, Anne M. and Leon, Deborah and Erde, Jonathan and Loo, Joseph A. and Ogorzalek Loo, Rachel R. and Zhou, Z. Hong and Gunsalus, Robert P.},
  year = {2024},
  month = dec,
  journal = {Science Advances},
  volume = {10},
  number = {50},
  pages = {eadr8596},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/sciadv.adr8596},
  urldate = {2025-04-04},
  abstract = {Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo--electron tomography, we visualized the S-layer lattice surrounding Methanospirillum hungatei, a methanogenic archaeon. Though more compact than known structures, M. hungatei's S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer's cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment. M. hungatei cell's end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.},
  file = {C:\Users\shervinnia\Zotero\storage\GZ2XF3W3\Wang et al. - 2024 - Composition and in situ structure of the Methanospirillum hungatei cell envelope and surface layer.pdf}
}

Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo–electron tomography, we visualized the S-layer lattice surrounding Methanospirillum hungatei, a methanogenic archaeon. Though more compact than known structures, M. hungatei's S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer's cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment. M. hungatei cell's end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.

@article{wangTomoNetStreamlinedCryogenic2024,
  title = {{{TomoNet}}: {{A}} Streamlined Cryogenic Electron Tomography Software Pipeline with Automatic Particle Picking on Flexible Lattices},
  shorttitle = {{{TomoNet}}},
  author = {Wang, Hui and Liao, Shiqing and Yu, Xinye and Zhang, Jiayan and Zhou, Z. Hong},
  year = {2024},
  month = jan,
  journal = {Biological Imaging},
  volume = {4},
  pages = {e7},
  issn = {2633-903X},
  doi = {10.1017/S2633903X24000060},
  urldate = {2024-06-13},
  abstract = {Cryogenic electron tomography (cryoET) is capable of determining in situ biological structures of molecular complexes at near-atomic resolution by averaging half a million subtomograms. While abundant complexes/particles are often clustered in arrays, precisely locating and seamlessly averaging such particles across many tomograms present major challenges. Here, we developed TomoNet, a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution. TomoNet features built-in automatic particle picking and three-dimensional (3D) classification functions and integrates commonly used packages to streamline high-resolution subtomogram averaging for structures in 1D, 2D, or 3D arrays. Automatic particle picking is accomplished in two complementary ways: one based on template matching and the other using deep learning. TomoNet's hierarchical file organization and visual display facilitate efficient data management as required for large cryoET datasets. Applications of TomoNet to three types of datasets demonstrate its capability of efficient and accurate particle picking on flexible and imperfect lattices to obtain high-resolution 3D biological structures: virus-like particles, bacterial surface layers within cellular lamellae, and membranes decorated with nuclear egress protein complexes. These results demonstrate TomoNet's potential for broad applications to various cryoET projects targeting high-resolution in situ structures.},
  langid = {english},
  keywords = {automatic particle picking,cryoET,deep learning,in situ structures,lattice structure,subtomogram averaging},
  file = {C:\Users\shervinnia\Zotero\storage\4CQMNG7Q\Wang et al. - 2024 - TomoNet A streamlined cryogenic electron tomograp.pdf}
}

Cryogenic electron tomography (cryoET) is capable of determining in situ biological structures of molecular complexes at near-atomic resolution by averaging half a million subtomograms. While abundant complexes/particles are often clustered in arrays, precisely locating and seamlessly averaging such particles across many tomograms present major challenges. Here, we developed TomoNet, a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution. TomoNet features built-in automatic particle picking and three-dimensional (3D) classification functions and integrates commonly used packages to streamline high-resolution subtomogram averaging for structures in 1D, 2D, or 3D arrays. Automatic particle picking is accomplished in two complementary ways: one based on template matching and the other using deep learning. TomoNet's hierarchical file organization and visual display facilitate efficient data management as required for large cryoET datasets. Applications of TomoNet to three types of datasets demonstrate its capability of efficient and accurate particle picking on flexible and imperfect lattices to obtain high-resolution 3D biological structures: virus-like particles, bacterial surface layers within cellular lamellae, and membranes decorated with nuclear egress protein complexes. These results demonstrate TomoNet's potential for broad applications to various cryoET projects targeting high-resolution in situ structures.

@article{xiaRNAGenomePackaging2024,
  title = {{{RNA}} Genome Packaging and Capsid Assembly of Bluetongue Virus Visualized in Host Cells},
  author = {Xia, Xian and Sung, Po-Yu and Martynowycz, Michael W. and Gonen, Tamir and Roy, Polly and Zhou, Z. Hong},
  year = {2024},
  month = apr,
  journal = {Cell},
  volume = {187},
  number = {9},
  pages = {2236-2249.e17},
  issn = {0092-8674},
  doi = {10.1016/j.cell.2024.03.007},
  urldate = {2024-06-13},
  abstract = {Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8~{\AA}, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed ``duality'' characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.},
  keywords = {assembly intermediates,bluetongue virus,capsid assembly,cryo-FIB,cryoEM,cryoET,dsRNA virus,duality model,RNA packaging,viral replication cycle},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\GEVRNN5I\\Xia et al. - 2024 - RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\P97BAEV5\\S009286742400299X.html}
}

Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed ``duality'' characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.

@article{zhenStructuresEpsteinBarrVirus2024,
  title = {Structures of {{Epstein-Barr}} Virus and {{Kaposi}}'s Sarcoma-Associated Herpesvirus Virions Reveal Species-Specific Tegument and Envelope Features},
  author = {Zhen, James and Chen, Jia and Huang, Haigen and Liao, Shiqing and Liu, Shiheng and Yuan, Yan and Sun, Ren and Longnecker, Richard and Wu, Ting-Ting and Zhou, Z. Hong},
  year = {2024},
  month = oct,
  journal = {Journal of Virology},
  volume = {98},
  number = {11},
  pages = {e01194-24},
  publisher = {American Society for Microbiology},
  doi = {10.1128/jvi.01194-24},
  urldate = {2025-04-04},
  file = {C:\Users\shervinnia\Zotero\storage\JNM43UMC\Zhen et al. - 2024 - Structures of Epstein-Barr virus and Kaposi’s sarcoma-associated herpesvirus virions reveal species-.pdf}
}

@misc{zhouAtomicStructuresBacteriocin2024,
  title = {Atomic Structures of a Bacteriocin Targeting {{Gram-positive}} Bacteria},
  author = {Zhou, Z. Hong and Cai, Xiaoying and He, Yao and Yu, Iris and Imani, Anthony and Scholl, Dean and Miller, Jeff},
  year = {2024},
  month = mar,
  issn = {2693-5015},
  doi = {10.21203/rs.3.rs-4007122/v1},
  urldate = {2024-06-13},
  abstract = {Due to envelope differences between Gram-positive and Gram-negative bacteria1, engineering precision bactericidal contractile nanomachines2 requires atomic-level understanding of their structures; however, only those killing a Gram-negative bacterium are currently known3,4. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar protein linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with differences between their targeted envelopes. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire length of the diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.},
  file = {C:\Users\shervinnia\Zotero\storage\J9GEUA2Z\Zhou et al. - 2024 - Atomic structures of a bacteriocin targeting Gram-.pdf}
}

Due to envelope differences between Gram-positive and Gram-negative bacteria1, engineering precision bactericidal contractile nanomachines2 requires atomic-level understanding of their structures; however, only those killing a Gram-negative bacterium are currently known3,4. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar protein linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with differences between their targeted envelopes. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire length of the diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.

@article{alexanderProteinTargetHighlights2023,
  title = {Protein Target Highlights in {{CASP15}}: {{Analysis}} of Models by Structure Providers},
  shorttitle = {Protein Target Highlights in {{CASP15}}},
  author = {Alexander, Leila T. and Durairaj, Janani and Kryshtafovych, Andriy and Abriata, Luciano A. and Bayo, Yusupha and Bhabha, Gira and Breyton, C{\'e}cile and Caulton, Simon G. and Chen, James and Degroux, S{\'e}raphine and Ekiert, Damian C. and Erlandsen, Benedikte S. and Freddolino, Peter L. and Gilzer, Dominic and Greening, Chris and Grimes, Jonathan M. and Grinter, Rhys and Gurusaran, Manickam and Hartmann, Marcus D. and Hitchman, Charlie J. and Keown, Jeremy R. and Kropp, Ashleigh and Kursula, Petri and Lovering, Andrew L. and Lemaitre, Bruno and Lia, Andrea and Liu, Shiheng and Logotheti, Maria and Lu, Shuze and Mark{\'u}sson, Sigurbj{\"o}rn and Miller, Mitchell D. and Minasov, George and Niemann, Hartmut H. and Opazo, Felipe and Phillips Jr, George N. and Davies, Owen R. and Rommelaere, Samuel and {Rosas-Lemus}, Monica and Roversi, Pietro and Satchell, Karla and Smith, Nathan and Wilson, Mark A. and Wu, Kuan-Lin and Xia, Xian and Xiao, Han and Zhang, Wenhua and Zhou, Z. Hong and Fidelis, Krzysztof and Topf, Maya and Moult, John and Schwede, Torsten},
  year = {2023},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {91},
  number = {12},
  pages = {1571--1599},
  issn = {1097-0134},
  doi = {10.1002/prot.26545},
  urldate = {2024-06-13},
  abstract = {We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.},
  langid = {english},
  keywords = {CASP,cryoEM,protein structure prediction,X-ray crystallography},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\LTTNLGVN\\Alexander et al. - 2023 - Protein target highlights in CASP15 Analysis of m.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\4SLVGWMG\\prot.html}
}

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

@article{benavidesPreparationStabilityPegylated2023,
  title = {Preparation and Stability of Pegylated Poly({{S-alkyl-L-homocysteine}}) Coacervate Core Micelles in Aqueous Media},
  author = {Benavides, Isaac and Scott, Wendell A. and Cai, Xiaoying and Zhou, Z. Hong and Deming, Timothy J.},
  year = {2023},
  month = sep,
  journal = {The European Physical Journal E},
  volume = {46},
  number = {9},
  pages = {81},
  issn = {1292-895X},
  doi = {10.1140/epje/s10189-023-00339-x},
  urldate = {2024-06-13},
  abstract = {We report development and preparation of synthetic polypeptide based, coacervate core polyelectrolyte complex micelles, PCMs, in aqueous media, which were characterized and evaluated for the encapsulation and in vitro release of a model single-stranded RNA, polyadenylic acid, poly(A). Cationic, {$\alpha$}-helical polypeptides pegylated at their N-termini, PEG113-b-5bn and PEG113-b-5cn, were designed to form coacervate core PCMs upon mixing with multivalent anions in aqueous media. Sodium tripolyphosphate (TPP) and poly(A) were used as model multivalent anions that allowed optimization of polypeptide composition and chain length for formation of stable, nanoscale PCMs. PEG113-b-5c27 was selected for preparation of PCMs that were characterized under different environmental conditions using dynamic light scattering, atomic force microscopy and cryoelectron microscopy. The PCMs were found to efficiently encapsulate poly(A), were stable at physiologically relevant pH and solution ionic strength, and were able to release poly(A) in the presence of excess polyvalent anions. These PCMs were found to be a promising model system for further development of polypeptide based therapeutic delivery vehicles.},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\LV4KXF9K\Benavides et al. - 2023 - Preparation and stability of pegylated poly(S-alky.pdf}
}

We report development and preparation of synthetic polypeptide based, coacervate core polyelectrolyte complex micelles, PCMs, in aqueous media, which were characterized and evaluated for the encapsulation and in vitro release of a model single-stranded RNA, polyadenylic acid, poly(A). Cationic, $α$-helical polypeptides pegylated at their N-termini, PEG113-b-5bn and PEG113-b-5cn, were designed to form coacervate core PCMs upon mixing with multivalent anions in aqueous media. Sodium tripolyphosphate (TPP) and poly(A) were used as model multivalent anions that allowed optimization of polypeptide composition and chain length for formation of stable, nanoscale PCMs. PEG113-b-5c27 was selected for preparation of PCMs that were characterized under different environmental conditions using dynamic light scattering, atomic force microscopy and cryoelectron microscopy. The PCMs were found to efficiently encapsulate poly(A), were stable at physiologically relevant pH and solution ionic strength, and were able to release poly(A) in the presence of excess polyvalent anions. These PCMs were found to be a promising model system for further development of polypeptide based therapeutic delivery vehicles.

@article{floraExosomesHippelLindauNullCancer2023,
  title = {Exosomes from {{Von Hippel-Lindau-Null Cancer Cells Promote Metastasis}} in {{Renal Cell Carcinoma}}},
  author = {Flora, Kailey and Ishihara, Moe and Zhang, Zhicheng and Bowen, Elizabeth S. and Wu, Aimee and Ayoub, Tala and Huang, Julian and {Cano-Ruiz}, Celine and Jackson, Maia and Reghu, Kaveeya and Ayoub, Yasmeen and Zhu, Yazhen and Tseng, Hsian-Rong and Zhou, Z. Hong and Hu, Junhui and Wu, Lily},
  year = {2023},
  month = jan,
  journal = {International Journal of Molecular Sciences},
  volume = {24},
  number = {24},
  pages = {17307},
  publisher = {Multidisciplinary Digital Publishing Institute},
  issn = {1422-0067},
  doi = {10.3390/ijms242417307},
  urldate = {2024-06-13},
  abstract = {Exosomes are extracellular vesicles that modulate essential physiological and pathological signals. Communication between cancer cells that express the von Hippel-Lindau (VHL) tumor suppressor gene and those that do not is instrumental to distant metastasis in renal cell carcinoma (RCC). In a novel metastasis model, VHL(-) cancer cells are the metastatic driver, while VHL(+) cells receive metastatic signals from VHL(-) cells and undergo aggressive transformation. This study investigates whether exosomes could be mediating metastatic crosstalk. Exosomes isolated from paired VHL(+) and VHL(-) cancer cell lines were assessed for physical, biochemical, and biological characteristics. Compared to the VHL(+) cells, VHL(-) cells produce significantly more exosomes that augment epithelial-to-mesenchymal transition (EMT) and migration of VHL(+) cells. Using a Cre-loxP exosome reporter system, the fluorescent color conversion and migration were correlated with dose-dependent delivery of VHL(-) exosomes. VHL(-) exosomes even induced a complete cascade of distant metastasis when added to VHL(+) tumor xenografts in a duck chorioallantoic membrane (dCAM) model, while VHL(+) exosomes did not. Therefore, this study supports that exosomes from VHL(-) cells could mediate critical cell-to-cell crosstalk to promote metastasis in RCC.},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  langid = {english},
  keywords = {CAM model,cell-cell communication,EMT,exosomes,metastasis,renal cell carcinoma},
  file = {C:\Users\shervinnia\Zotero\storage\MN6LV7YD\Flora et al. - 2023 - Exosomes from Von Hippel-Lindau-Null Cancer Cells .pdf}
}

Exosomes are extracellular vesicles that modulate essential physiological and pathological signals. Communication between cancer cells that express the von Hippel-Lindau (VHL) tumor suppressor gene and those that do not is instrumental to distant metastasis in renal cell carcinoma (RCC). In a novel metastasis model, VHL(-) cancer cells are the metastatic driver, while VHL(+) cells receive metastatic signals from VHL(-) cells and undergo aggressive transformation. This study investigates whether exosomes could be mediating metastatic crosstalk. Exosomes isolated from paired VHL(+) and VHL(-) cancer cell lines were assessed for physical, biochemical, and biological characteristics. Compared to the VHL(+) cells, VHL(-) cells produce significantly more exosomes that augment epithelial-to-mesenchymal transition (EMT) and migration of VHL(+) cells. Using a Cre-loxP exosome reporter system, the fluorescent color conversion and migration were correlated with dose-dependent delivery of VHL(-) exosomes. VHL(-) exosomes even induced a complete cascade of distant metastasis when added to VHL(+) tumor xenografts in a duck chorioallantoic membrane (dCAM) model, while VHL(+) exosomes did not. Therefore, this study supports that exosomes from VHL(-) cells could mediate critical cell-to-cell crosstalk to promote metastasis in RCC.

@article{hu2023discovery,
  title = {Discovery, Structure, and Function of Filamentous 3-Methylcrotonyl-{{CoA}} Carboxylase},
  author = {Hu, Jason J and Lee, Jane KJ and Liu, Yun-Tao and Yu, Clinton and Huang, Lan and Aphasizheva, Inna and Aphasizhev, Ruslan and Zhou, Z Hong},
  year = {2023},
  journal = {Structure (London, England : 1993)},
  volume = {31},
  number = {1},
  pages = {100--110},
  publisher = {Elsevier}
}

@article{ito2023structural,
  title = {Structural Basis for {{HIV-1}} Antagonism of Host {{APOBEC3G}} via {{Cullin E3}} Ligase},
  author = {Ito, Fumiaki and {Alvarez-Cabrera}, Ana L and Liu, Shiheng and Yang, Hanjing and Shiriaeva, Anna and Zhou, Z Hong and Chen, Xiaojiang S},
  year = {2023},
  journal = {Science Advances},
  volume = {9},
  number = {1},
  pages = {eade3168},
  publisher = {American Association for the Advancement of Science}
}

@article{itoStructuralBasisHIV12023,
  title = {Structural Basis of {{HIV-1 Vif-mediated E3}} Ligase Targeting of Host {{APOBEC3H}}},
  author = {Ito, Fumiaki and {Alvarez-Cabrera}, Ana L. and Kim, Kyumin and Zhou, Z. Hong and Chen, Xiaojiang S.},
  year = {2023},
  month = aug,
  journal = {Nature Communications},
  volume = {14},
  number = {1},
  pages = {5241},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-40955-x},
  urldate = {2024-06-13},
  abstract = {Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific human A3s for proteasomal degradation. Vif recruits cellular transcription cofactor CBF-{$\beta$} and Cullin-5 (CUL5) RING E3 ubiquitin ligase to bind different A3s distinctively, but how this is accomplished remains unclear in the absence of the atomic structure of the complex. Here, we present the cryo-EM structures of HIV-1 Vif in complex with human A3H, CBF-{$\beta$} and components of CUL5 ubiquitin ligase (CUL5, ELOB, and ELOC). Vif nucleates the entire complex by directly binding four human proteins, A3H, CBF-{$\beta$}, CUL5, and ELOC. The structures reveal a large interface area between A3H and Vif, primarily mediated by an {$\alpha$}-helical side of A3H and a five-stranded {$\beta$}-sheet of Vif. This A3H-Vif interface unveils the basis for sensitivity-modulating polymorphism of both proteins, including a previously reported gain-of-function mutation in Vif isolated from HIV/AIDS patients. Our structural and functional results provide insights into the remarkable interplay between HIV and humans and would inform development efforts for anti-HIV therapeutics.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {cryoEM,HIV infections,Microbiology,Virus-host interactions},
  file = {C:\Users\shervinnia\Zotero\storage\NE99FUDA\Ito et al. - 2023 - Structural basis of HIV-1 Vif-mediated E3 ligase t.pdf}
}

Human APOBEC3 (A3) cytidine deaminases are antiviral factors that are particularly potent against retroviruses. As a countermeasure, HIV-1 uses a viral infectivity factor (Vif) to target specific human A3s for proteasomal degradation. Vif recruits cellular transcription cofactor CBF-$β$ and Cullin-5 (CUL5) RING E3 ubiquitin ligase to bind different A3s distinctively, but how this is accomplished remains unclear in the absence of the atomic structure of the complex. Here, we present the cryo-EM structures of HIV-1 Vif in complex with human A3H, CBF-$β$ and components of CUL5 ubiquitin ligase (CUL5, ELOB, and ELOC). Vif nucleates the entire complex by directly binding four human proteins, A3H, CBF-$β$, CUL5, and ELOC. The structures reveal a large interface area between A3H and Vif, primarily mediated by an $α$-helical side of A3H and a five-stranded $β$-sheet of Vif. This A3H-Vif interface unveils the basis for sensitivity-modulating polymorphism of both proteins, including a previously reported gain-of-function mutation in Vif isolated from HIV/AIDS patients. Our structural and functional results provide insights into the remarkable interplay between HIV and humans and would inform development efforts for anti-HIV therapeutics.

@misc{kangTheoreticalFrameworkExperimental2023,
  title = {Theoretical Framework and Experimental Solution for the Air-Water Interface Adsorption Problem in {{cryoEM}}},
  author = {Kang, Joon S. and Zhou, Xueting and Liu, Yun-Tao and Wang, Kaituo and Zhou, Z. Hong},
  year = {2023},
  month = oct,
  primaryclass = {New Results},
  pages = {2023.05.23.541984},
  publisher = {bioRxiv},
  doi = {10.1101/2023.05.23.541984},
  urldate = {2024-06-13},
  abstract = {As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously ``disappear'' on cryoEM grids, but the reasons for such misbehavior are not well understood, limiting systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air-water interface (AWI) to lower the total potential surface energy --- rationalizing the use of surfactant, which is a direct solution to reducing the surface tension of the aqueous solution. By conducting cryogenic electron tomography (cryoET) with the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradual reduction of the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that applicable surfactants do not damage the biological complex, thus suggesting that they might offer a practical, simple, and general solution to the problem for high-resolution cryoEM. Application of this solution to a real-world AWI adsorption problem with a more challenging membrane protein, namely, the ClC-1 channel, has led to its first near-atomic structure using cryoEM.},
  archiveprefix = {bioRxiv},
  chapter = {New Results},
  copyright = {{\copyright} 2023, Posted by Cold Spring Harbor Laboratory. The copyright holder for this pre-print is the author. All rights reserved. The material may not be redistributed, re-used or adapted without the author's permission.},
  langid = {english},
  file = {C:\Users\shervinnia\Zotero\storage\3LX85MKX\Kang et al. - 2023 - Theoretical framework and experimental solution fo.pdf}
}

As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously ``disappear'' on cryoEM grids, but the reasons for such misbehavior are not well understood, limiting systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air-water interface (AWI) to lower the total potential surface energy — rationalizing the use of surfactant, which is a direct solution to reducing the surface tension of the aqueous solution. By conducting cryogenic electron tomography (cryoET) with the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradual reduction of the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that applicable surfactants do not damage the biological complex, thus suggesting that they might offer a practical, simple, and general solution to the problem for high-resolution cryoEM. Application of this solution to a real-world AWI adsorption problem with a more challenging membrane protein, namely, the ClC-1 channel, has led to its first near-atomic structure using cryoEM.

@article{lam2023immunization,
  title = {Immunization of Mice with Virus-like Vesicles of Kaposi Sarcoma-Associated Herpesvirus Reveals a Role for Antibodies Targeting {{ORF4}} in Activating Complement-Mediated Neutralization},
  author = {Lam, Alex K and Roshan, Romin and Miley, Wendell and Labo, Nazzarena and Zhen, James and Kurland, Andrew P and Cheng, Celine and Huang, Haigen and Teng, Pu-Lin and Harelson, Claire and others},
  year = {2023},
  journal = {Journal of Virology},
  volume = {97},
  number = {2},
  pages = {e01600--22},
  publisher = {Am Soc Microbiol}
}

@article{lee2023cryoem,
  title = {{{CryoEM}} Reveals Oligomeric Isomers of a Multienzyme Complex and Assembly Mechanics},
  author = {Lee, Jane KJ and Liu, Yun-Tao and Hu, Jason J and Aphasizheva, Inna and Aphasizhev, Ruslan and Zhou, Z Hong},
  year = {2023},
  journal = {Journal of Structural Biology: X},
  volume = {7},
  pages = {100088},
  publisher = {Elsevier}
}

@article{liu2023native,
  title = {Native Structure of Mosquito Salivary Protein Uncovers Domains Relevant to Pathogen Transmission},
  author = {Liu, Shiheng and Xia, Xian and Calvo, Eric and Zhou, Z Hong},
  year = {2023},
  journal = {Nature Communications},
  volume = {14},
  number = {1},
  pages = {899},
  publisher = {Nature Publishing Group UK London}
}

@article{liuResolvingPreferredOrientation2023,
  title = {Resolving the {{Preferred Orientation Problem}} in {{CryoEM Reconstruction}} with {{Self-Supervised Deep Learning}}},
  author = {Liu, Yun-Tao and Hu, Jason and Zhou, Z Hong},
  year = {2023},
  month = aug,
  journal = {Microscopy and Microanalysis},
  volume = {29},
  number = {Supplement\_1},
  pages = {1918--1919},
  issn = {1431-9276},
  doi = {10.1093/micmic/ozad067.991},
  urldate = {2024-06-13},
  abstract = {Cryogenic electron microscopy (cryoEM) is a crucial technique for imaging biological macromolecules in their native state, enabling the determination of structures at atomic resolution. However, one major challenge encountered in cryoEM is the so-called ``preferred orientation'' problem. This problem arises due to specific regions of macromolecules preferentially adhering to the air-water interface or substrate support, which results in missing, or non-uniformly distributed, views of the macromolecule [1]. As a consequence, 3D reconstructions of the macromolecule with preferred orientation exhibit artifacts such as skewed secondary structures (alpha helices and beta sheets), broken peptide or nucleotide chains, distorted protein sidechain or nucleotide base densities, making atomic modeling from the cryoEM reconstructions difficult.},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\FYFT54Y9\\Liu et al. - 2023 - Resolving the Preferred Orientation Problem in Cry.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\9MAN2AHM\\7228117.html}
}

Cryogenic electron microscopy (cryoEM) is a crucial technique for imaging biological macromolecules in their native state, enabling the determination of structures at atomic resolution. However, one major challenge encountered in cryoEM is the so-called ``preferred orientation'' problem. This problem arises due to specific regions of macromolecules preferentially adhering to the air-water interface or substrate support, which results in missing, or non-uniformly distributed, views of the macromolecule [1]. As a consequence, 3D reconstructions of the macromolecule with preferred orientation exhibit artifacts such as skewed secondary structures (alpha helices and beta sheets), broken peptide or nucleotide chains, distorted protein sidechain or nucleotide base densities, making atomic modeling from the cryoEM reconstructions difficult.

@article{liuStructuralBasisGRNA2023,
  title = {Structural Basis of {{gRNA}} Stabilization and {{mRNA}} Recognition in Trypanosomal {{RNA}} Editing},
  author = {Liu, Shiheng and Wang, Hong and Li, Xiaorun and Zhang, Fan and Lee, Jane K.J. and Li, Zihang and Yu, Clinton and Hu, Jason J. and Zhao, Xiaojing and Suematsu, Takuma and {Alvarez-Cabrera}, Ana L. and Liu, Qiushi and Zhang, Liye and Huang, Lan and Aphasizheva, Inna and Aphasizhev, Ruslan and Zhou, Z. Hong},
  year = {2023},
  month = jul,
  journal = {Science},
  volume = {381},
  number = {6653},
  pages = {eadg4725},
  publisher = {American Association for the Advancement of Science},
  doi = {10.1126/science.adg4725},
  urldate = {2024-06-13},
  abstract = {In Trypanosoma brucei, the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)--programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo--electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA--binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.},
  file = {C:\Users\shervinnia\Zotero\storage\EUGIVXNQ\Liu et al. - 2023 - Structural basis of gRNA stabilization and mRNA re.pdf}
}

In Trypanosoma brucei, the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)–programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo–electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA–binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.

@article{shimogawaFAP106InteractionHub2023,
  title = {{{FAP106}} Is an Interaction Hub for Assembling Microtubule Inner Proteins at the Cilium Inner Junction},
  author = {Shimogawa, Michelle M. and Wijono, Angeline S. and Wang, Hui and Zhang, Jiayan and Sha, Jihui and Szombathy, Natasha and Vadakkan, Sabeeca and Pelayo, Paula and Jonnalagadda, Keya and Wohlschlegel, James and Zhou, Z. Hong and Hill, Kent L.},
  year = {2023},
  month = aug,
  journal = {Nature Communications},
  volume = {14},
  number = {1},
  pages = {5225},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-40230-z},
  urldate = {2024-06-13},
  abstract = {Motility of pathogenic protozoa depends on flagella (synonymous with cilia) with axonemes containing nine doublet microtubules (DMTs) and two singlet microtubules. Microtubule inner proteins (MIPs) within DMTs influence axoneme stability and motility and provide lineage-specific adaptations, but individual MIP functions and assembly mechanisms are mostly unknown. Here, we show in the sleeping sickness parasite Trypanosoma brucei, that FAP106, a conserved MIP at the DMT inner junction, is required for trypanosome motility and functions as a critical interaction hub, directing assembly of several conserved and lineage-specific MIPs. We use comparative cryogenic electron tomography (cryoET) and quantitative proteomics to identify MIP candidates. Using RNAi knockdown together with fitting of AlphaFold models into cryoET maps, we demonstrate that one of these candidates, MC8, is a trypanosome-specific MIP required for parasite motility. Our work advances understanding of MIP assembly mechanisms and identifies lineage-specific motility proteins that are attractive targets to consider for therapeutic intervention.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {Cellular motility,Cilia,cryoET,Microtubules,Parasite biology},
  file = {C:\Users\shervinnia\Zotero\storage\28SPTW4N\Shimogawa et al. - 2023 - FAP106 is an interaction hub for assembling microt.pdf}
}

Motility of pathogenic protozoa depends on flagella (synonymous with cilia) with axonemes containing nine doublet microtubules (DMTs) and two singlet microtubules. Microtubule inner proteins (MIPs) within DMTs influence axoneme stability and motility and provide lineage-specific adaptations, but individual MIP functions and assembly mechanisms are mostly unknown. Here, we show in the sleeping sickness parasite Trypanosoma brucei, that FAP106, a conserved MIP at the DMT inner junction, is required for trypanosome motility and functions as a critical interaction hub, directing assembly of several conserved and lineage-specific MIPs. We use comparative cryogenic electron tomography (cryoET) and quantitative proteomics to identify MIP candidates. Using RNAi knockdown together with fitting of AlphaFold models into cryoET maps, we demonstrate that one of these candidates, MC8, is a trypanosome-specific MIP required for parasite motility. Our work advances understanding of MIP assembly mechanisms and identifies lineage-specific motility proteins that are attractive targets to consider for therapeutic intervention.

@article{stevensAsymmetricReconstructionAquareovirus2023,
  title = {Asymmetric Reconstruction of the Aquareovirus Core at Near-Atomic Resolution and Mechanism of Transcription Initiation},
  author = {Stevens, Alexander and Cui, Yanxiang and Shivakoti, Sakar and Zhou, Z Hong},
  year = {2023},
  month = jul,
  journal = {Protein \& Cell},
  volume = {14},
  number = {7},
  pages = {546--550},
  issn = {1674-800X},
  doi = {10.1093/procel/pwad002},
  urldate = {2024-06-13},
  abstract = {Dear Editor,Aquareovirus (ARV, Reoviridae) causes hemorrhagic disease in the economically important golden shiner and grass carp of America and China, respectively (Nason et al., 2000; Fang et al., 2005). Reoviridae members are characterized by endogenous transcription of their multipartite genomes within capsids of 1--3 layers and are further classified based on the presence (Spinareovirinae subfamily, 9 genera) or absence (Sedoreovirinae subfamily, 6 genera) of mRNA-capping turrets along the innermost layer (King et al., 2012). The innermost layer of reoviruses is always an icosahedral, T = 2*, inner capsid particle (ICP) or core, which is transcriptionally competent (Farsetta et al., 2000). Among turreted reoviruses, cytoplasmic polyhedrosis virus (CPV) has a single-layered capsid, which is equivalent to the ICP within double- or triple-layered reoviruses (Hill et al., 1999; Zhang et al., 1999; Yu et al., 2011). This simple structural organization makes CPV an attractive model to study turreted reoviruses, but renders it inadequate to describe possible impacts of shedding the external layers from the numerous, multi-layered Spinareovirinae members (Zhang et al., 2022). Here we used a sequential symmetry expansion and relaxation approach to resolve the first asymmetric reconstruction of the ARV ICP by cryoEM to 3.3 {\AA} (Fig. S2). Comparison with existing ARV virion and infectious subvirion particle (ISVP) structures (Ding et al., 2018) reveals expansion of the ICP and concomitant conformational changes to the transcription related proteins.},
  file = {C\:\\Users\\shervinnia\\Zotero\\storage\\FRPMUNA4\\Stevens et al. - 2023 - Asymmetric reconstruction of the aquareovirus core.pdf;C\:\\Users\\shervinnia\\Zotero\\storage\\HI93RGV2\\7026202.html}
}

Dear Editor,Aquareovirus (ARV, Reoviridae) causes hemorrhagic disease in the economically important golden shiner and grass carp of America and China, respectively (Nason et al., 2000; Fang et al., 2005). Reoviridae members are characterized by endogenous transcription of their multipartite genomes within capsids of 1–3 layers and are further classified based on the presence (Spinareovirinae subfamily, 9 genera) or absence (Sedoreovirinae subfamily, 6 genera) of mRNA-capping turrets along the innermost layer (King et al., 2012). The innermost layer of reoviruses is always an icosahedral, T = 2*, inner capsid particle (ICP) or core, which is transcriptionally competent (Farsetta et al., 2000). Among turreted reoviruses, cytoplasmic polyhedrosis virus (CPV) has a single-layered capsid, which is equivalent to the ICP within double- or triple-layered reoviruses (Hill et al., 1999; Zhang et al., 1999; Yu et al., 2011). This simple structural organization makes CPV an attractive model to study turreted reoviruses, but renders it inadequate to describe possible impacts of shedding the external layers from the numerous, multi-layered Spinareovirinae members (Zhang et al., 2022). Here we used a sequential symmetry expansion and relaxation approach to resolve the first asymmetric reconstruction of the ARV ICP by cryoEM to 3.3 Å (Fig. S2). Comparison with existing ARV virion and infectious subvirion particle (ISVP) structures (Ding et al., 2018) reveals expansion of the ICP and concomitant conformational changes to the transcription related proteins.

@article{sun2023cryo,
  title = {Cryo-{{EM}} Structure of Amyloid Fibril Formed by {{$\alpha$}}-Synuclein Hereditary {{A53E}} Mutation Reveals a Distinct Protofilament Interface},
  author = {Sun, Chuanqi and Zhou, Kang and DePaola IV, Peter and Shin, WooShik and Hillyer, Trae and Sawaya, MichaelR and Zhu, Ruowei and Peng, Chao and Zhou, Z Hong and Jiang, Lin},
  year = {2023},
  journal = {Journal of Biological Chemistry},
  pages = {104566},
  publisher = {Elsevier}
}

@article{wang2023structure,
  title = {Structure of {{LARP7}} Protein P65--Telomerase {{RNA}} Complex in Telomerase Revealed by Cryo-{{EM}} and {{NMR}}},
  author = {Wang, Yaqiang and He, Yao and Wang, Yanjiao and Yang, Yuan and Singh, Mahavir and Eichhorn, Catherine D and Cheng, Xinyi and Jiang, Yi Xiao and Zhou, Z Hong and Feigon, Juli},
  year = {2023},
  journal = {Journal of Molecular Biology},
  volume = {435},
  number = {11},
  pages = {168044},
  publisher = {Elsevier}
}

@article{wangHierarchicalOrganizationAssembly2023a,
  title = {Hierarchical Organization and Assembly of the Archaeal Cell Sheath from an Amyloid-like Protein},
  author = {Wang, Hui and Zhang, Jiayan and Toso, Daniel and Liao, Shiqing and Sedighian, Farzaneh and Gunsalus, Robert and Zhou, Z. Hong},
  year = {2023},
  month = oct,
  journal = {Nature Communications},
  volume = {14},
  number = {1},
  pages = {6720},
  publisher = {Nature Publishing Group},
  issn = {2041-1723},
  doi = {10.1038/s41467-023-42368-2},
  urldate = {2024-06-13},
  abstract = {Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 {\AA}-resolution structure reveals that the sheath cylinder consists of axially stacked {$\beta$}-hoops, each of which is comprised of two to six 400 nm-diameter rings of {$\beta$}-strand arches ({$\beta$}-rings). With both similarities to and differences from amyloid cross-{$\beta$} fibril architecture, each {$\beta$}-ring contains two giant {$\beta$}-sheets contributed by~{\textasciitilde}\,450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into {$\beta$}-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent {$\beta$}-hoops into the immature sheath cylinder at the junction of two daughter cells.},
  copyright = {2023 The Author(s)},
  langid = {english},
  keywords = {Cell growth,Cellular microbiology,cryoEM,cryoET},
  file = {C:\Users\shervinnia\Zotero\storage\5CR4DTJZ\Wang et al. - 2023 - Hierarchical organization and assembly of the arch.pdf}
}

Certain archaeal cells possess external proteinaceous sheath, whose structure and organization are both unknown. By cellular cryogenic electron tomography (cryoET), here we have determined sheath organization of the prototypical archaeon, Methanospirillum hungatei. Fitting of Alphafold-predicted model of the sheath protein (SH) monomer into the 7.9 Å-resolution structure reveals that the sheath cylinder consists of axially stacked $β$-hoops, each of which is comprised of two to six 400 nm-diameter rings of $β$-strand arches ($β$-rings). With both similarities to and differences from amyloid cross-$β$ fibril architecture, each $β$-ring contains two giant $β$-sheets contributed by ~\,450 SH monomers that entirely encircle the outer circumference of the cell. Tomograms of immature cells suggest models of sheath biogenesis: oligomerization of SH monomers into $β$-ring precursors after their membrane-proximal cytoplasmic synthesis, followed by translocation through the unplugged end of a dividing cell, and insertion of nascent $β$-hoops into the immature sheath cylinder at the junction of two daughter cells.

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  publisher = {Elsevier}
}

@article{cui2019conservative,
  title = {Conservative Transcription in Three Steps Visualized in a Double-Stranded {{RNA}} Virus},
  author = {Cui, Yanxiang and Zhang, Yinong and Zhou, Kang and Sun, Jingchen and Zhou, Z Hong},
  year = {2019},
  journal = {Nature Structural \& Molecular Biology},
  pages = {1--12},
  publisher = {Nature Publishing Group}
}

@article{cui2019ph,
  title = {{{pH-dependent}} Gating Mechanism of the {{Helicobacter}} Pylori Urea Channel Revealed by Cryo-{{EM}}},
  author = {Cui, Yanxiang and Zhou, Kang and Strugatsky, David and Wen, Yi and Sachs, George and Zhou, Z Hong and Munson, Keith},
  year = {2019},
  journal = {Science advances},
  volume = {5},
  number = {3},
  pages = {eaav8423},
  publisher = {American Association for the Advancement of Science}
}

@inproceedings{das2019distance,
  title = {Distance Sensitive {{D-loop}} Dynamics and near-Atomic Resolution of {{F-actin}} Phalloidin Structure by {{cryoEM}}},
  booktitle = {Journal of Biomolecular Structure \& Dynamics},
  author = {Das, Sanchaita and Ge, Peng and Durer, Zeynep A Oztug and Grintsevich, Elena E and Zhou, Z Hong and Reisler, Emil},
  year = {2019},
  volume = {37},
  pages = {2--3},
  publisher = {TAYLOR \& FRANCIS INC 530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA}
}

@article{ding2019situ,
  title = {In Situ Structures of Rotavirus Polymerase in Action and Mechanism of {{mRNA}} Transcription and Release},
  author = {Ding, Ke and Celma, Cristina C and Zhang, Xing and Chang, Thomas and Shen, Wesley and Atanasov, Ivo and Roy, Polly and Zhou, Z Hong},
  year = {2019},
  journal = {Nature communications},
  volume = {10},
  number = {1},
  pages = {2216},
  publisher = {Nature Publishing Group}
}

@article{gao2019structures,
  title = {Structures and Operating Principles of the Replisome},
  author = {Gao, Yang and Cui, Yanxiang and Fox, Tara and Lin, Shiqiang and Wang, Huaibin and {de Val}, Natalia and Zhou, Z Hong and Yang, Wei},
  year = {2019},
  journal = {Science},
  pages = {eaav7003},
  publisher = {American Association for the Advancement of Science}
}

@article{gong2019dna,
  title = {{{DNA-packing}} Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus {{KSHV}}},
  author = {Gong, Danyang and Dai, Xinghong and Jih, Jonathan and Liu, Yun-Tao and Bi, Guo-Qiang and Sun, Ren and Zhou, Z Hong},
  year = {2019},
  journal = {Cell},
  publisher = {Elsevier}
}

@article{hardenbrook2019determining,
  title = {Determining the High-Resolution Structures of the Anthrax Toxin Protective Antigen Pore Bound to Its Lethal and Edema Factors},
  author = {Hardenbrook, Nathan J and Liu, Shiheng and Zhou, Kang and Jang, Jiansen and Zhou, Z Hong and Krantz, Bryan},
  year = {2019},
  journal = {Biophysical Journal},
  volume = {116},
  number = {3},
  pages = {514a},
  publisher = {Elsevier}
}

@article{he2019situ,
  title = {In Situ Structures of {{RNA-dependent RNA}} Polymerase inside Bluetongue Virus before and after Uncoating},
  author = {He, Yao and Shivakoti, Sakar and Ding, Ke and Cui, Yanxiang and Roy, Polly and Zhou, Z Hong},
  year = {2019},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {116},
  number = {33},
  pages = {16535--16540},
  publisher = {National Acad Sciences}
}

@article{imhofCryoElectronTomography2019,
  title = {Cryo Electron Tomography with Volta Phase Plate Reveals Novel Structural Foundations of the 96-Nm Axonemal Repeat in the Pathogen {{Trypanosoma}} Brucei},
  author = {Imhof, Simon and Zhang, Jiayan and Wang, Hui and Bui, Khanh Huy and Nguyen, Hoangkim and Atanasov, Ivo and Hui, Wong H and Yang, Shun Kai and Zhou, Z Hong and Hill, Kent L},
  editor = {Carter, Andrew P and Kuriyan, John and Engel, Benjamin D and Morriswood, Brooke},
  year = {2019},
  month = nov,
  journal = {eLife},
  volume = {8},
  pages = {e52058},
  publisher = {eLife Sciences Publications, Ltd},
  issn = {2050-084X},
  doi = {10.7554/eLife.52058},
  urldate = {2024-06-13},
  abstract = {The 96-nm axonemal repeat includes dynein motors and accessory structures as the foundation for motility of eukaryotic flagella and cilia. However, high-resolution 3D axoneme structures are unavailable for organisms among the Excavates, which include pathogens of medical and economic importance. Here we report cryo electron tomography structures of the 96-nm repeat from Trypanosoma brucei, a protozoan parasite in the Excavate lineage that causes African trypanosomiasis. We examined bloodstream and procyclic life cycle stages, and a knockdown lacking DRC11/CMF22 of the nexin dynein regulatory complex (NDRC). Sub-tomogram averaging yields a resolution of 21.8 {\AA} for the 96-nm repeat. We discovered several lineage-specific structures, including novel inter-doublet linkages and microtubule inner proteins (MIPs). We establish that DRC11/CMF22 is required for the NDRC proximal lobe that binds the adjacent doublet microtubule. We propose that lineage-specific elaboration of axoneme structure in T. brucei reflects adaptations to support unique motility needs in diverse host environments.},
  keywords = {axoneme,cilium,dynein,motility,parasite,trypanosome},
  file = {C:\Users\shervinnia\Zotero\storage\8F774EJW\Imhof et al. - 2019 - Cryo electron tomography with volta phase plate re.pdf}
}

The 96-nm axonemal repeat includes dynein motors and accessory structures as the foundation for motility of eukaryotic flagella and cilia. However, high-resolution 3D axoneme structures are unavailable for organisms among the Excavates, which include pathogens of medical and economic importance. Here we report cryo electron tomography structures of the 96-nm repeat from Trypanosoma brucei, a protozoan parasite in the Excavate lineage that causes African trypanosomiasis. We examined bloodstream and procyclic life cycle stages, and a knockdown lacking DRC11/CMF22 of the nexin dynein regulatory complex (NDRC). Sub-tomogram averaging yields a resolution of 21.8 Å for the 96-nm repeat. We discovered several lineage-specific structures, including novel inter-doublet linkages and microtubule inner proteins (MIPs). We establish that DRC11/CMF22 is required for the NDRC proximal lobe that binds the adjacent doublet microtubule. We propose that lineage-specific elaboration of axoneme structure in T. brucei reflects adaptations to support unique motility needs in diverse host environments.

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  year = {2019},
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  pages = {1},
  publisher = {Nature Publishing Group}
}

@article{li2019cryo,
  title = {{{CRYO-EM}} of {{FULL-LENGTH}} {{$\alpha$}}-{{SYNUCLEIN REVEALS FIBRIL POLYMORPHS}} with a {{COMMON STRUCTURAL KERNEL}}},
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  year = {2019},
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  volume = {15},
  number = {7},
  pages = {P293},
  publisher = {No longer published by Elsevier}
}

@article{li2019p1,
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  year = {2019},
  journal = {Alzheimer's \& Dementia},
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  pages = {P293--P293},
  publisher = {Wiley Online Library}
}

@article{li2019unified,
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  pages = {1--6},
  publisher = {Nature Publishing Group}
}

@article{liu2019atomic,
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}

@article{liu2019cryo,
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  volume = {570},
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  pages = {257--261},
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}

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}

@article{olsen2019cryo,
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}

@article{sun2019efficient,
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  year = {2019},
  journal = {Biophysics Reports},
  volume = {5},
  number = {3},
  pages = {111--122},
  publisher = {Springer}
}

@article{wang2019structure,
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  number = {4},
  pages = {e3000218},
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}

@article{wongpalee2019cryoem,
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  number = {1},
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}

@article{yang2019atomic,
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  volume = {27},
  number = {12},
  pages = {1811--1819},
  publisher = {Cell Press}
}

@article{zhang2019atomic,
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  author = {Zhang, Yibo and Liu, Wei and Li, Zihang and Kumar, Vinay and {Alvarez-Cabrera}, Ana L and Leibovitch, Emily C and Cui, Yanxiang and Mei, Ye and Bi, Guo-Qiang and Jacobson, Steve and others},
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  number = {1},
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  publisher = {Nature Publishing Group}
}

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}

@article{zheng2019atomic,
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  number = {1},
  pages = {124},
  publisher = {Nature Publishing Group}
}

@article{dai2018structure,
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  year = {2018},
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  publisher = {Nature Publishing Group}
}

@article{dai2018structure,
  title = {Structure of the Herpes Simplex Virus 1 Capsid with Associated Tegument Protein Complexes},
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  year = {2018},
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  volume = {360},
  number = {6384},
  pages = {eaao7298},
  publisher = {American Association for the Advancement of Science}
}

@article{ding2018situ,
  title = {In Situ Structures of the Polymerase Complex and {{RNA}} Genome Show How Aquareovirus Transcription Machineries Respond to Uncoating},
  author = {Ding, Ke and Nguyen, Lisa and Zhou, Z Hong},
  year = {2018},
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}

@article{ding2018solution,
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  number = {4},
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  publisher = {Elsevier}
}

@article{guenther2018atomic,
  title = {Atomic-Level Evidence for Packing and Positional Amyloid Polymorphism by Segment from {{TDP-43 RRM2}}},
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  volume = {25},
  number = {4},
  pages = {311},
  publisher = {Nature Publishing Group}
}

@article{hardenbrook2018cryo,
  title = {Cryo-{{EM}} Structure of the Anthrax Toxin Protective Antigen Channel Bound to Lethal Factor},
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  year = {2018},
  journal = {Biophysical Journal},
  volume = {114},
  number = {3},
  pages = {262a},
  publisher = {Elsevier}
}

@article{ho2018malaria,
  title = {Malaria Parasite Translocon Structure and Mechanism of Effector Export},
  author = {Ho, Chi-Min and Beck, Josh R and Lai, Mason and Cui, Yanxiang and Goldberg, Daniel E and Egea, Pascal F and Zhou, Z Hong},
  year = {2018},
  journal = {Nature},
  volume = {561},
  number = {7721},
  pages = {70--75},
  publisher = {Nature Publishing Group}
}

@article{hughes2018mechanism,
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  author = {Hughes, Taylor ET and Lodowski, David and Huynh, Kevin and Yazici, Aysenur and {del Rosario}, John and Kapoor, Abhijeet and Basak, Sandip and Samanta, Amrita and Chakrapani, Sudha and Zhou, Z Hong and others},
  year = {2018},
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  volume = {114},
  number = {3},
  pages = {396a},
  publisher = {Elsevier}
}

@article{hughes2018structural,
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  author = {Hughes, Taylor ET and Lodowski, David T and Huynh, Kevin W and Yazici, Aysenur and Del Rosario, John and Kapoor, Abhijeet and Basak, Sandip and Samanta, Amrita and Han, Xu and Chakrapani, Sudha and others},
  year = {2018},
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  pages = {1},
  publisher = {Nature Publishing Group}
}

@article{hughes2018structural,
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  author = {Hughes, Taylor ET and Pumroy, Ruth A and Yazici, Aysenur Torun and Kasimova, Marina A and Fluck, Edwin C and Huynh, Kevin W and Samanta, Amrita and Molugu, Sudheer K and Zhou, Z Hong and Carnevale, Vincenzo and others},
  year = {2018},
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  volume = {9},
  number = {1},
  pages = {4198},
  publisher = {Nature Publishing Group UK London}
}

@article{huynh2018cryoem,
  title = {{{CryoEM}} Structure of the Human {{SLC4A4}} Sodium-Coupled Acid-Base Transporter {{NBCe1}}},
  author = {Huynh, Kevin W and Jiang, Jiansen and Abuladze, Natalia and Tsirulnikov, Kirill and Kao, Liyo and Shao, Xuesi and Newman, Debra and Azimov, Rustam and Pushkin, Alexander and Zhou, Z Hong and others},
  year = {2018},
  journal = {Nature communications},
  volume = {9},
  number = {1},
  pages = {900},
  publisher = {Nature Publishing Group}
}

@article{jiang2018atomic,
  title = {Atomic Structure of the {{E2}} Inner Core of Human Pyruvate Dehydrogenase Complex},
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  publisher = {American Chemical Society}
}

@article{jiang2018structure,
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@article{li2018cryo,
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@article{li2018cryoem,
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}

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}

@article{si2018different,
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}

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@article{tao2018accumulation,
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@article{tao2018differentiation,
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}

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}

@article{yu2018building,
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  number = {2},
  pages = {313--318},
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}

@article{zhao2018cryo,
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  year = {2018},
  journal = {Foundations of Crystallography},
  volume = {74},
  pages = {a416}
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@article{liu2010atomic,
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@article{liu2010structural,
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@article{cheng2008subnanometer,
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@article{dai2008unique,
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@article{deng2008cryo,
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@article{jiang2008activation,
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@article{liu2008symmetry,
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@article{song2008quantitative,
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@article{yu20083,
  title = {3.88 {{{\AA}}} Structure of Cytoplasmic Polyhedrosis Virus by Cryo-Electron Microscopy},
  author = {Yu, Xuekui and Jin, Lei and Zhou, Z Hong},
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@article{yu2008structures,
  title = {Structures of the Human Pyruvate Dehydrogenase Complex Cores: A Highly Conserved Catalytic Center with Flexible {{N-terminal}} Domains},
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@incollection{zhou2008structure,
  title = {Structure and Assembly of Human Herpesviruses: New Insights from Cryo-Electron Microscopy and Tomography},
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@article{zhou2008towards,
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@article{cheng2007structure,
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@article{deng2007direct,
  title = {Direct Visualization of the Putative Portal in the {{Kaposi}}'s Sarcoma-Associated Herpesvirus Capsid by Cryoelectron Tomography},
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@incollection{liu2007comparative,
  title = {Comparative Virion Structures of Human Herpesviruses},
  booktitle = {Human Herpesviruses: {{Biology}}, Therapy, and Immunoprophylaxis},
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@article{yu2007cryo,
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@article{zhou2007cryo,
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@article{dai2006structural,
  title = {Structural Organization of Tropism-Switching Bordetella Bacteriophage Revealed by Integrative Electron Cryotomography and Cryomicroscopy},
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@article{zhou2006ultrastructure,
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@article{cong2005fast,
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@inproceedings{tsen2005high,
  title = {High-Resolution Modeling of the Major Capsid Protein and Its Interaction with Tegument Proteins in Human Cytornegalovirus.},
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@article{yu2005dissecting,
  title = {Dissecting Human Cytomegalovirus Gene Function and Capsid Maturation by Ribozyme Targeting and Electron Cryomicroscopy},
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@article{yu2005three,
  title = {Three-Dimensional Localization of the Smallest Capsid Protein in the Human Cytomegalovirus Capsid},
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@article{booth20049aa,
  title = {A {{9{\AA}}} Single Particle Reconstruction from {{CCD}} Captured Images on a {{200kV}} Electron Cryomicroscope},
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@article{chen2004genetic,
  title = {Genetic, Biochemical, and Structural Characterization of a New Densovirus Isolated from a Chronically Infected {{Aedes}} Albopictus {{C6}}/36 Cell Line},
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@article{cheng2004three,
  title = {Three-Dimensional Structure Determination of Capsid {{ofAedes}} Albopictus {{C6}}/36 Cell Densovirus},
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  year = {2004},
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@article{qiao2004induction,
  title = {Induction of Sterilizing Immunity against {{West Nile Virus}} ({{WNV}}), by Immunization with {{WNV-like}} Particles Produced in Insect Cells},
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@inproceedings{wan2004full,
  title = {Full Contrast Transfer Function Correction in {{3D}} Cryo-{{EM}} Reconstruction},
  booktitle = {Communications, Circuits and Systems, 2004. {{ICCCAS}} 2004. 2004 International Conference On},
  author = {Wan, Yi and Chiu, Wah and Zhou, Z Hong},
  year = {2004},
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@article{baker2003architecture,
  title = {Architecture of the Herpes Simplex Virus Major Capsid Protein Derived from Structural Bioinformatics},
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  year = {2003},
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@article{bortz2003identification,
  title = {Identification of Proteins Associated with Murine Gammaherpesvirus 68 Virions},
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  year = {2003},
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@article{dai2003database,
  title = {Database Integration and the Web Portal Development for the {{IMIRS 3D}} Reconstruction Package},
  author = {Dai, Wei and Liang, Yuyao and Zhou, Z Hong},
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  volume = {9},
  number = {S02},
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@article{dai2003web,
  title = {Web Portal to an Image Database for High-Resolution Three-Dimensional Reconstruction},
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  volume = {144},
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@article{gu20033d,
  title = {{{3D}} Electron Microscopy Reveals the Variable Deposition and Protein Dynamics of the Peripheral Pyruvate Dehydrogenase Component about the Core},
  author = {Gu, Yingqi and Zhou, Z Hong and McCarthy, Diane B and Reed, Lester J and Stoops, James K},
  year = {2003},
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  number = {12},
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@article{kong2003conformational,
  title = {Conformational Flexibility of Pyruvate Dehydrogenase Complexes: A Computational Analysis by Quantized Elastic Deformational Model},
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  year = {2003},
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@article{liang2003high,
  title = {High-Resolution {{3D}} Reconstruction of Cytoplasmic Polyhedrosis Virus},
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@article{lo2003three,
  title = {Three-Dimensional Localization of {{pORF65}} in {{Kaposi}}'s Sarcoma-Associated Herpesvirus Capsid},
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  year = {2003},
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  volume = {77},
  number = {7},
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@article{lu2003reversible,
  title = {Reversible Aggregation of Mouse Prion Protein Derivatives with {{PrPSC-like}} Structural Properties},
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  year = {2003},
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  number = {2},
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@article{xia2003structural,
  title = {Structural Comparisons of Empty and Full Cytoplasmic Polyhedrosis Virus Protein-{{RNA}} Interactions and Implications for Endogenous {{RNA}} Transcription Mechanism},
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  year = {2003},
  journal = {Journal of Biological Chemistry},
  volume = {278},
  number = {2},
  pages = {1094--1100},
  publisher = {{American Society for Biochemistry and Molecular Biology}}
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@article{yu2003three,
  title = {Three-Dimensional Structures of the {{A}}, {{B}}, and {{C}} Capsids of Rhesus Monkey Rhadinovirus: Insights into Gammaherpesvirus Capsid Assembly, Maturation, and {{DNA}} Packaging},
  author = {Yu, Xue-Kui and O'Connor, Christine M and Atanasov, Ivo and Damania, Blossom and Kedes, Dean H and Zhou, Z Hong},
  year = {2003},
  journal = {Journal of virology},
  volume = {77},
  number = {24},
  pages = {13182--13193},
  publisher = {Am Soc Microbiol}
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@article{zhou2003cytoplasmic,
  title = {Cytoplasmic Polyhedrosis Virus Structure at 8 {{{\AA}}} by Electron Cryomicroscopy: Structural Basis of Capsid Stability and {{mRNA}} Processing Regulation},
  author = {Zhou, Z Hong and Zhang, Hong and Jakana, Joanita and Lu, Xing-Ying and Zhang, Jing-Qiang},
  year = {2003},
  journal = {Structure (London, England : 1993)},
  volume = {11},
  number = {6},
  pages = {651--663},
  publisher = {Elsevier}
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@article{zhou2003dehydrogenase,
  title = {Dehydrogenase Complexes},
  author = {Zhou, Z Hong and Stoops, James K},
  year = {2003},
  journal = {Thiamine: Catalytic Mechanisms in Normal and Disease States},
  pages = {309},
  publisher = {CRC Press}
}

@article{zhou2003determination,
  title = {Determination of Icosahedral Virus Structures by Electron Cryomicroscopy at Subnanometer Resolution},
  author = {Zhou, Z Hong and Chiu, Wah},
  year = {2003},
  journal = {Advances in protein chemistry},
  volume = {64},
  pages = {93--124},
  publisher = {ACADEMIC PRESS, INC}
}

@inproceedings{baker2002building,
  title = {Building a Model for the {{HSV-1}} Major Capsid Protein Using Electron Cryomicroscopy and Bioinformatics},
  booktitle = {Biophysical Journal},
  author = {Baker, {\relax ML} and Jiang, W and Zhou, {\relax ZH} and Dougherty, M and Chiu, W},
  year = {2002},
  volume = {82},
  pages = {491A--491A},
  publisher = {BIOPHYSICAL SOCIETY}
}

@article{chiu2002deriving,
  title = {Deriving Folds of Macromolecular Complexes through Electron Cryomicroscopy and Bioinformatics Approaches},
  author = {Chiu, Wah and Baker, Matthew L and Jiang, Wen and Zhou, Z Hong},
  year = {2002},
  journal = {Current opinion in structural biology},
  volume = {12},
  number = {2},
  pages = {263--269},
  publisher = {Elsevier}
}

@article{liang2002imirs,
  title = {{{IMIRS}}: A High-Resolution {{3D}} Reconstruction Package Integrated with a Relational Image Database},
  author = {Liang, Yuyao and Ke, Eugene Y and Zhou, Z Hong},
  year = {2002},
  journal = {Journal of structural biology},
  volume = {137},
  number = {3},
  pages = {292--304},
  publisher = {Elsevier}
}

@article{zhang2002molecular,
  title = {Molecular Interactions and Viral Stability Revealed by Structural Analyses of Chemically Treated Cypovirus Capsids},
  author = {Zhang, Hong and Yu, Xue-Kui and Lu, Xing-Ying and Zhang, Jing-Qiang and Zhou, Z Hong},
  year = {2002},
  journal = {Virology},
  volume = {298},
  number = {1},
  pages = {45--52},
  publisher = {Elsevier}
}

@article{chen2001pattern,
  title = {The Pattern of Tegument-Capsid Interaction in the Herpes Simplex Virus Type 1 Virion Is Not Influenced by the Small Hexon-Associated Protein {{VP26}}},
  author = {Chen, Dong-Hua and Jakana, Joanita and McNab, David and Mitchell, Joyce and Zhou, Z Hong and Dougherty, Matthew and Chiu, Wah and Rixon, Frazer J},
  year = {2001},
  journal = {Journal of virology},
  volume = {75},
  number = {23},
  pages = {11863--11867},
  publisher = {Am Soc Microbiol}
}

@article{he2001finding,
  title = {Finding and Using Local Symmetry in Identifying Lower Domain Movements in Hexon Subunits of the Herpes Simplex Virus Type 1 b Capsid},
  author = {He, Jing and Schmid, Michael F and Zhou, Z Hong and Rixon, Frazer and Chiu, Wah},
  year = {2001},
  journal = {Journal of molecular biology},
  volume = {309},
  number = {4},
  pages = {903--914},
  publisher = {Elsevier}
}

@article{zheng2001three,
  title = {Three-Dimensional Structure of the Wild-Type {{RHDV}}},
  author = {Zheng, Dong and Xue, Tao and Chen, Donghua and Zheng, Ming and Zhou, {\relax ZH} and Xu, Wei},
  year = {2001},
  journal = {Chinese Science Bulletin},
  volume = {46},
  number = {12},
  pages = {1005--1008},
  publisher = {Science in China Press}
}

@article{zhou2001direct,
  title = {Direct Evidence for the Size and Conformational Variability of the Pyruvate Dehydrogenase Complex Revealed by Three-Dimensional Electron Microscopy {{The}} ``Breathing'' Core and Its Functional Relationship to Protein Dynamics},
  author = {Zhou, Z Hong and Liao, Wangcai and Cheng, R Holland and Lawson, {\relax JE} and McCarthy, {\relax DB} and Reed, Lester J and Stoops, James K},
  year = {2001},
  journal = {Journal of Biological Chemistry},
  volume = {276},
  number = {24},
  pages = {21704--21713},
  publisher = {ASBMB}
}

@article{zhou2001electron,
  title = {Electron Cryomicroscopy and Bioinformatics Suggest Protein Fold Models for Rice Dwarf Virus},
  author = {Zhou, Z Hong and Baker, Matthew L and Jiang, Wen and Dougherty, Matthew and Jakana, Joanita and Dong, Gang and Lu, Guangying and Chiu, Wah},
  year = {2001},
  journal = {Nature structural biology},
  volume = {8},
  number = {10},
  pages = {868--873},
  publisher = {Nature Publishing Group}
}

@article{zhou2001remarkable,
  title = {The Remarkable Structural and Functional Organization of the Eukaryotic Pyruvate Dehydrogenase Complexes},
  author = {Zhou, Z Hong and McCarthy, Diane B and O'Connor, Catherine M and Reed, Lester J and Stoops, James K},
  year = {2001},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {98},
  number = {26},
  pages = {14802--14807},
  publisher = {National Acad Sciences}
}

@article{mertens2000family,
  title = {Family Reoviridae},
  author = {Mertens, {\relax PPC} and Arella, M and Attoui, H and Belloncik, S and Bergoin, M and Boccardo, G and Booth, {\relax TF} and Chiu, W and Diprose, {\relax JM} and Duncan, R and others},
  year = {2000},
  journal = {Virus Taxonomy},
  pages = {395--480},
  publisher = {Academic Press, San Diego, CA}
}

@article{wu2000three,
  title = {Three-Dimensional Structure of the Human Herpesvirus 8 Capsid},
  author = {Wu, Lijun and Lo, Pierrette and Yu, Xuekui and Stoops, James K and Forghani, B and Zhou, Z Hong},
  year = {2000},
  journal = {Journal of virology},
  volume = {74},
  number = {20},
  pages = {9646--9654},
  publisher = {Am Soc Microbiol}
}

@article{zhou2000seeing,
  title = {Seeing the Herpesvirus Capsid at 8.5 {{{\AA}}}},
  author = {Zhou, Z Hong and Dougherty, Matthew and Jakana, Joanita and He, Jing and Rixon, Frazer J and Chiu, Wah},
  year = {2000},
  journal = {Science},
  volume = {288},
  number = {5467},
  pages = {877--880},
  publisher = {American Association for the Advancement of Science}
}

@article{chen1999three,
  title = {Three-Dimensional Visualization of Tegument/Capsid Interactions in the Intact Human Cytomegalovirus},
  author = {Chen, Dong H and Jiang, Hong and Lee, Manfred and Liu, Fenyong and Zhou, Z Hong},
  year = {1999},
  journal = {Virology},
  volume = {260},
  number = {1},
  pages = {10--16},
  publisher = {Elsevier}
}

@article{saad1999roles,
  title = {Roles of Triplex and Scaffolding Proteins in Herpes Simplex Virus Type 1 Capsid Formation Suggested by Structures of Recombinant Particles},
  author = {Saad, Ali and Zhou, Z Hong and Jakana, Joanita and Chiu, Wah and Rixon, Frazer J},
  year = {1999},
  journal = {Journal of virology},
  volume = {73},
  number = {8},
  pages = {6821--6830},
  publisher = {Am Soc Microbiol}
}

@article{zhang1999visualization,
  title = {Visualization of Protein-{{RNA}} Interactions in Cytoplasmic Polyhedrosis Virus},
  author = {Zhang, H and Zhang, J and Yu, X and Lu, X and Zhang, Q and Jakana, J and Chen, {\relax DH} and Zhang, X and Zhou, {\relax ZH}},
  year = {1999},
  journal = {Journal of virology},
  volume = {73},
  number = {2},
  pages = {1624--1629},
  publisher = {Am Soc Microbiol}
}

@article{zhou1999visualization,
  title = {Visualization of Tegument-Capsid Interactions and {{DNA}} in Intact Herpes Simplex Virus Type 1 Virions},
  author = {Zhou, Z Hong and Chen, Dong Hua and Jakana, Joanita and Rixon, Frazer J and Chiu, Wah},
  year = {1999},
  journal = {Journal of virology},
  volume = {73},
  number = {4},
  pages = {3210--3218},
  publisher = {Am Soc Microbiol}
}

@article{lu1998structure,
  title = {Structure of Double-Shelled Rice Dwarf Virus},
  author = {Lu, Guangying and Zhou, Z Hong and Baker, Matthew L and Jakana, Joanita and Cai, Deyou and Wei, Xincheng and Chen, Shengxiang and Gu, Xiaocheng and Chiu, Wah},
  year = {1998},
  journal = {Journal of virology},
  volume = {72},
  number = {11},
  pages = {8541--8549},
  publisher = {Am Soc Microbiol}
}

@article{yu1998structure,
  title = {Structure of Cytoplasmic Polyhedrosis Virus from Bombyx Mori},
  author = {Yu, Xuekui and Lu, Xinyin and Zhang, Hong and Zhou, Zhenghong and Zhang, Qinfen and Zhang, Xing and Zhang, Jingqiang},
  year = {1998},
  journal = {Acta Biochimica et Biophysica Sinica},
  volume = {31},
  number = {5},
  pages = {563--566}
}

@article{zhou1998identification,
  title = {Identification of the Sites of Interaction between the Scaffold and Outer Shell in Herpes Simplex Virus-1 Capsids by Difference Electron Imaging},
  author = {Zhou, Z Hong and Macnab, Sharon J and Jakana, Joanita and Scott, L Ridgway and Chiu, Wah and Rixon, Frazer J},
  year = {1998},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {95},
  number = {6},
  pages = {2778--2783},
  publisher = {National Acad Sciences}
}

@article{zhou1998refinement,
  title = {Refinement of Herpesvirus {{B-capsid}} Structure on Parallel Supercomputers},
  author = {Zhou, {\relax ZH} and Chiu, W and Haskell, K and Spears Jr, H and Jakana, J and Rixon, {\relax FJ} and Scott, {\relax LR}},
  year = {1998},
  journal = {Biophysical Journal},
  volume = {74},
  number = {1},
  pages = {576--588},
  publisher = {Cell Press}
}

@inproceedings{haskell1997improved,
  title = {Improved {{3D}} Reconstruction of Virus Structures through Parallel Processing.},
  booktitle = {{{PPSC}}},
  author = {Haskell, {\relax KH} and Zhou, {\relax ZH} and Spears Jr, H and Chiu, W and Scott, {\relax LR}},
  year = {1997},
  publisher = {Citeseer}
}

@article{zhou1996ctf,
  title = {{{CTF}} Determination of Images of Ice-Embedded Single Particles Using a Graphics Interface},
  author = {Zhou, Z Hong and Hardt, Steve and Wang, Bin and Sherman, Michael B and Jakana, Joanita and Chiu, Wah},
  year = {1996},
  journal = {Journal of structural biology},
  volume = {116},
  number = {1},
  pages = {216--222},
  publisher = {Elsevier}
}

@article{lamture1995luminescence,
  title = {Luminescence Properties of Terbium ({{III}}) Complexes with 4-Substituted Dipicolinic Acid Analogs},
  author = {Lamture, Jagannath B and Zhou, Z Hong and Kumar, A Suresh and Wensel, Theodore G},
  year = {1995},
  journal = {Inorganic Chemistry},
  volume = {34},
  number = {4},
  pages = {864--869},
  publisher = {ACS Publications}
}

@article{zhou1995assembly,
  title = {Assembly of {{VP26}} in Herpes Simplex Virus-1 Inferred from Structures of Wild-Type and Recombinant Capsids},
  author = {Zhou, Z. H. and He, J. and Jakana, J. and Tatman, J. D. and Rixon, F. J. and Chiu, W.},
  year = {1995},
  journal = {Nature structural biology},
  volume = {2},
  number = {11}
}

@misc{zhou1995high,
  title = {High Resolution 3-{{Dimensional}} Electron Cryomicroscopy and Reconstructions of Herpes Simplex Virus Capsids},
  author = {Zhou, Z Hong},
  year = {1995}
}

@article{zhou1995three,
  title = {Three-Dimensional Structure of Rice Dwarf Virus by Electron Cryomicroscopy},
  author = {Zhou, {\relax ZH} and Jakana, J and Chiu, W and others},
  year = {1995},
  journal = {高技术通讯: 英文版},
  number = {1},
  pages = {1--4}
}

@article{zhou1994protein,
  title = {Protein Subunit Structures in the Herpes Simplex Virus {{A-capsid}} Determined from 400 {{kV}} Spot-Scan Electron Cryomicroscopy},
  author = {Zhou, Z Hong and Prasad, BV Venkataram and Jakana, Joanita and Rixon, Frazer J and Chiu, Wah},
  year = {1994},
  journal = {Journal of molecular biology},
  volume = {242},
  number = {4},
  pages = {456--469},
  publisher = {Elsevier}
}

@inproceedings{zhou1994subunit,
  title = {Subunit Structures in Capsomeres of Herpes-Simplex Virus Capsid Revealed by 400kv Spot-Scan Electron Cryomicroscopy},
  booktitle = {Biophysical Journal},
  author = {ZHOU, {\relax ZH} and Jakana, J and Prasad, {\relax BVV} and RIXON, {\relax FJ} and Chiu, W},
  year = {1994},
  volume = {66},
  pages = {A135--A135},
  publisher = {BIOPHYSICAL SOCIETY 9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3998}
}

@article{zhou1993prospects,
  title = {Prospects for Using an {{IVEM}} with a {{FEG}} for Imaging Macromolecules towards Atomic Resolution},
  author = {Zhou, Zheng Hong and Chiu, Wah},
  year = {1993},
  journal = {Ultramicroscopy},
  volume = {49},
  number = {1-4},
  pages = {407--416},
  publisher = {North-Holland}
}

@incollection{xie1992progress,
  title = {Progress of the Soft X-Ray Microscopy Project at Hefei},
  booktitle = {X-Ray Microscopy {{III}}},
  author = {Xie, X-S and Jia, C-Z and Zhou, Z-H and Zhang, Y-H and Zhau, Y-F and Wang, M},
  year = {1992},
  pages = {157--159},
  publisher = {Springer Berlin Heidelberg}
}