Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament. Garmay, Y., Shvetsov, A., Karelov, D., Lebedev, D., Radulescu, A., Petukhov, M., & Isaev-Ivanov, V. 2012. cited By 5; Conference of 5th European Conference on Neutron Scattering, ECNS 2011 ; Conference Date: 17 July 2011 Through 21 July 2011; Conference Code:88897

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Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

@CONFERENCE{Garmay2012,
author={Garmay, Yu. and Shvetsov, A. and Karelov, D. and Lebedev, D. and Radulescu, A. and Petukhov, M. and Isaev-Ivanov, V.},
title={Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament},
journal={Journal of Physics: Conference Series},
year={2012},
volume={340},
doi={10.1088/1742-6596/340/1/012094},
art_number={012094},
note={cited By 5; Conference of 5th European Conference on Neutron Scattering, ECNS 2011 ; Conference Date: 17 July 2011 Through 21 July 2011;  Conference Code:88897},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858591060&doi=10.1088%2f1742-6596%2f340%2f1%2f012094&partnerID=40&md5=2cb59944a3da46d332057e808a6cdb78},
affiliation={Petersburg Nuclear Physics Institute, Russian Federation; Jülich Center for Neutron Science, Germany; Research and Education Centre Biophysics, St. Petersburg State Polytecnic University, St. Petersburg, Russian Federation},
abstract={Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.},
correspondence_address1={Garmay, Yu.; Petersburg Nuclear Physics InstituteRussian Federation},
sponsors={},
publisher={Institute of Physics Publishing},
address={Prague},
issn={17426588},
language={English},
abbrev_source_title={J. Phys. Conf. Ser.},
document_type={Conference Paper},
source={Scopus},
}

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