Identification of key sites controlling protein functional motions by using elastic network model combined with internal coordinates

The Journal of Chemical Physics
Peng Fei Zhang, Ji Guo Su

Abstract

The elastic network model (ENM) is an effective method to extract the intrinsic dynamical properties encoded in protein tertiary structures. We have proposed a new ENM-based analysis method to reveal the motion modes directly responsible for a specific protein function, in which an internal coordinate related to the specific function was introduced to construct the internal/Cartesian hybrid coordinate space. In the present work, the function-related internal coordinates combined with a linear perturbation method were applied to identify the key sites controlling specific protein functional motions. The change in the fluctuations of the internal coordinate in response to residue perturbation was calculated in the hybrid coordinate space by using the linear response theory. The residues with the large fluctuation changes were identified to be the key sites that allosterically control the specific protein function. Two proteins, i.e., human DNA polymerase β and the chaperonin from Methanococcus maripaludis, were investigated as case studies, in which several collective and local internal coordinates were applied to identify the functionally key residues of these two studied proteins. The calculation results are consistent with the...Continue Reading

References

Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Jul 19, 2002·Biophysical Journal·Sibsankar KunduGeorge N Phillips
Jul 31, 2002·Molecular Pathology : MP·J C Ranford, B Henderson
Apr 12, 2005·Proteins·Dengming Ming, Michael E Wall
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·M Karplus, J Kuriyan
Jun 1, 2005·Journal of Molecular Biology·Herman W T van Vlijmen, Martin Karplus
Dec 31, 2005·Nucleic Acids Research·Samuel FloresMark Gerstein
Dec 31, 2005·Physical Review Letters·Dengming Ming, Michael E Wall
Nov 14, 2006·Biophysical Journal·Ji Guo SuCun Xin Wang
Feb 16, 2008·Science·William E BalchJeffery W Kelly
Jun 10, 2008·Nature Structural & Molecular Biology·Christopher R BoothJudith Frydman
Jul 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lei YangRobert L Jernigan
Aug 29, 2009·PLoS Computational Biology·Jochen S Hub, Bert L de Groot
Jan 22, 2010·Nature·Junjie ZhangWah Chiu
Nov 11, 2011·The Journal of Chemical Physics·Ji Guo SuCun Xin Wang
Mar 27, 2012·Journal of Molecular Biology·Rebecca B BerlowJ Patrick Loria
May 12, 2012·The Journal of Biological Chemistry·Katherine A DoniganJoann B Sweasy
Jul 5, 2013·The Journal of Physical Chemistry. B·Ji Guo SuCun Xin Wang
Apr 11, 2014·Biochemistry·William A Beard, Samuel H Wilson
Sep 13, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ji Guo SuJi Hua Wang
Dec 2, 2014·The Journal of Physical Chemistry. a·Robert KalesckyPeng Tao
Apr 22, 2015·Journal of Structural Biology·Min Hyeok KimMoon Ki Kim
May 6, 2015·Journal of Molecular Biology·Tom LopezJudith Frydman
Jul 19, 2015·Nucleic Acids Research·Giovanni PinamontiGiovanni Bussi
Nov 13, 2015·Current Opinion in Structural Biology·Enrico Guarnera, Igor N Berezovsky
Nov 20, 2015·Nucleic Acids Research·Hongchun LiIvet Bahar
Dec 10, 2013·Journal of Chemical Theory and Computation·Edvin FuglebakkKonrad Hinsen
Dec 23, 2015·International Journal of Molecular Sciences·Xing-Yuan LiJi-Guo Su
Dec 31, 2015·Current Opinion in Structural Biology·José Ramón López-Blanco, Pablo Chacón

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Citations

Jan 27, 2021·Journal of Chemical Information and Modeling·Weikang GongChunhua Li
Mar 10, 2021·The Journal of Physical Chemistry. B·Elodie Laine, Sergei Grudinin

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