{"_id":"NcGkYhPycHLKvWfEZ","bibbaseid":"lopezredondo-fan-koide-koide-beckstein-stokes-zincbindingalterstheconformationaldynamicsanddrivesthetransportcycleofthecationdiffusionfacilitatoryiip-2021","author_short":["Lopez-Redondo, M.","Fan, S.","Koide, A.","Koide, S.","Beckstein, O.","Stokes, D. L."],"bibdata":{"bibtype":"article","type":"article","title":"Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP","volume":"153","issn":"0022-1295","url":"https://doi.org/10.1085/jgp.202112873","doi":"10.1085/jgp.202112873","abstract":"YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle.","number":"8","urldate":"2021-07-13","journal":"Journal of General Physiology","author":[{"propositions":[],"lastnames":["Lopez-Redondo"],"firstnames":["Maria"],"suffixes":[]},{"propositions":[],"lastnames":["Fan"],"firstnames":["Shujie"],"suffixes":[]},{"propositions":[],"lastnames":["Koide"],"firstnames":["Akiko"],"suffixes":[]},{"propositions":[],"lastnames":["Koide"],"firstnames":["Shohei"],"suffixes":[]},{"propositions":[],"lastnames":["Beckstein"],"firstnames":["Oliver"],"suffixes":[]},{"propositions":[],"lastnames":["Stokes"],"firstnames":["David","L."],"suffixes":[]}],"month":"July","year":"2021","bibtex":"@article{lopez-redondo_zinc_2021,\n\ttitle = {Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator {YiiP}},\n\tvolume = {153},\n\tissn = {0022-1295},\n\turl = {https://doi.org/10.1085/jgp.202112873},\n\tdoi = {10.1085/jgp.202112873},\n\tabstract = {YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle.},\n\tnumber = {8},\n\turldate = {2021-07-13},\n\tjournal = {Journal of General Physiology},\n\tauthor = {Lopez-Redondo, Maria and Fan, Shujie and Koide, Akiko and Koide, Shohei and Beckstein, Oliver and Stokes, David L.},\n\tmonth = jul,\n\tyear = {2021},\n}\n\n","author_short":["Lopez-Redondo, M.","Fan, S.","Koide, A.","Koide, S.","Beckstein, O.","Stokes, D. L."],"key":"lopez-redondo_zinc_2021","id":"lopez-redondo_zinc_2021","bibbaseid":"lopezredondo-fan-koide-koide-beckstein-stokes-zincbindingalterstheconformationaldynamicsanddrivesthetransportcycleofthecationdiffusionfacilitatoryiip-2021","role":"author","urls":{"Paper":"https://doi.org/10.1085/jgp.202112873"},"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://api.zotero.org/users/1446965/collections/GJIR5FQV/items?key=DK7eBbaofVxXe4ShaO2nLItp&format=bibtex&limit=100","dataSources":["aWZX3bdqYnwJ4TFqr","PGB7KMr8nSSyHsKme","4vn2CWL2AgyPs2kny","Y8jAQ6b2eCo2cdomS"],"keywords":[],"search_terms":["zinc","binding","alters","conformational","dynamics","drives","transport","cycle","cation","diffusion","facilitator","yiip","lopez-redondo","fan","koide","koide","beckstein","stokes"],"title":"Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP","year":2021}