Proteins: Structure, Function and Genetics, volume 83, issue 6, pages 1046-1053
Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras
Publication type: Journal Article
Publication date: 2015-04-08
Quartile SCImago
Q1
Quartile WOS
Q3
Impact factor: 2.9
ISSN: 08873585, 10970134
Biochemistry
Molecular Biology
Structural Biology
Abstract
The free energy profiles for the chemical reaction of the guanosine triphosphate hydrolysis GTP + H2O → GDP + Pi by Ras‐GAP for the wild‐type and G13V mutated Ras were computed by using molecular dynamics protocols with the QM(ab initio)/MM potentials. The results are consistent with the recent measurements of reaction kinetics in Ras‐GAP showing about two‐order reduction of the rate constant upon G13V mutation in Ras: the computed activation barrier on the free energy profile is increased by 3 kcal/mol upon the G13V replacement. The major reason for a higher energy barrier is a shift of the “arginine finger” (R789 from GAP) from the favorable position in the active site. The results of simulations provide support for the mechanism of the reference reaction according to which the Q61 side chain directly participates in chemical transformations at the proton transfer stage. Proteins 2015; 83:1046–1053. © 2015 Wiley Periodicals, Inc.
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- We do not take into account publications that without a DOI.
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- Statistics recalculated weekly.
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Mironov V. et al. Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras // Proteins: Structure, Function and Genetics. 2015. Vol. 83. No. 6. pp. 1046-1053.
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Mironov V., Khrenova M. G., Lychko L. A., Nemukhin A. Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras // Proteins: Structure, Function and Genetics. 2015. Vol. 83. No. 6. pp. 1046-1053.
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TY - JOUR
DO - 10.1002/prot.24802
UR - https://doi.org/10.1002%2Fprot.24802
TI - Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras
T2 - Proteins: Structure, Function and Genetics
AU - Lychko, Leonora A
AU - Mironov, Vladimir
AU - Khrenova, Maria G.
AU - Nemukhin, Alexander
PY - 2015
DA - 2015/04/08 00:00:00
PB - Wiley
SP - 1046-1053
IS - 6
VL - 83
SN - 0887-3585
SN - 1097-0134
ER -
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@article{2015_Mironov,
author = {Leonora A Lychko and Vladimir Mironov and Maria G. Khrenova and Alexander Nemukhin},
title = {Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras},
journal = {Proteins: Structure, Function and Genetics},
year = {2015},
volume = {83},
publisher = {Wiley},
month = {apr},
url = {https://doi.org/10.1002%2Fprot.24802},
number = {6},
pages = {1046--1053},
doi = {10.1002/prot.24802}
}
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Mironov, Vladimir, et al. “Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras.” Proteins: Structure, Function and Genetics, vol. 83, no. 6, Apr. 2015, pp. 1046-1053. https://doi.org/10.1002%2Fprot.24802.