Journal of Physical Chemistry B, volume 119, issue 40, pages 12838-12845
Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme
Publication type: Journal Article
Publication date: 2015-09-25
Journal:
Journal of Physical Chemistry B
Quartile SCImago
Q1
Quartile WOS
Q3
Impact factor: 3.3
ISSN: 15206106, 15205207
Materials Chemistry
Surfaces, Coatings and Films
Physical and Theoretical Chemistry
Abstract
Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras·GAP protein complex are fully investigated by using modern modeling tools. The previously hypothesized stages of the cleavage of the phosphorus-oxygen bond in GTP and the formation of the imide form of catalytic Gln61 from Ras upon creation of Pi are confirmed by using the higher-level quantum-based calculations. The steps of the enzyme regeneration are modeled for the first time, providing a comprehensive description of the catalytic cycle. It is found that for the reaction Ras·GAP·GTP·H2O → Ras·GAP·GDP·Pi, the highest barriers correspond to the process of regeneration of the active site but not to the process of substrate cleavage. The specific shape of the energy profile is responsible for an interesting kinetic mechanism of the GTP hydrolysis. The analysis of the process using the first-passage approach and consideration of kinetic equations suggest that the overall reaction rate is a result of the balance between relatively fast transitions and low probability of states from which these transitions are taking place. Our theoretical predictions are in excellent agreement with available experimental observations on GTP hydrolysis rates.
Citations by journals
|
1
2
3
4
5
|
|
|
Journal of Physical Chemistry B
|
Journal of Physical Chemistry B
5 publications, 10.2%
|
|
Angewandte Chemie - International Edition
|
Angewandte Chemie - International Edition
3 publications, 6.12%
|
|
Angewandte Chemie
|
Angewandte Chemie
3 publications, 6.12%
|
|
Organic and Biomolecular Chemistry
|
Organic and Biomolecular Chemistry
2 publications, 4.08%
|
|
Physical Chemistry Chemical Physics
|
Physical Chemistry Chemical Physics
2 publications, 4.08%
|
|
Molecules
|
Molecules
2 publications, 4.08%
|
|
ACS Catalysis
|
ACS Catalysis
2 publications, 4.08%
|
|
Biophysical Chemistry
|
Biophysical Chemistry
2 publications, 4.08%
|
|
Herald of the Russian Academy of Sciences
|
Herald of the Russian Academy of Sciences
1 publication, 2.04%
|
|
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy
|
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy
1 publication, 2.04%
|
|
Moscow University Chemistry Bulletin
|
Moscow University Chemistry Bulletin
1 publication, 2.04%
|
|
Russian Journal of Physical Chemistry B
|
Russian Journal of Physical Chemistry B
1 publication, 2.04%
|
|
Topics in Current Chemistry
|
Topics in Current Chemistry
1 publication, 2.04%
|
|
Computational and Structural Biotechnology Journal
|
Computational and Structural Biotechnology Journal
1 publication, 2.04%
|
|
PLoS ONE
|
PLoS ONE
1 publication, 2.04%
|
|
Journal of Molecular Biology
|
Journal of Molecular Biology
1 publication, 2.04%
|
|
Computational Biology and Chemistry
|
Computational Biology and Chemistry
1 publication, 2.04%
|
|
Biopolymers
|
Biopolymers
1 publication, 2.04%
|
|
Molecular Informatics
|
Molecular Informatics
1 publication, 2.04%
|
|
Chemistry - A European Journal
|
Chemistry - A European Journal
1 publication, 2.04%
|
|
Biochemistry
|
Biochemistry
1 publication, 2.04%
|
|
Journal of the American Chemical Society
|
Journal of the American Chemical Society
1 publication, 2.04%
|
|
Chemical Science
|
Chemical Science
1 publication, 2.04%
|
|
Chemical Communications
|
Chemical Communications
1 publication, 2.04%
|
|
Pure and Applied Chemistry
|
Pure and Applied Chemistry
1 publication, 2.04%
|
|
MedComm
|
MedComm
1 publication, 2.04%
|
|
Biophysica
|
Biophysica
1 publication, 2.04%
|
|
Russian Journal of Physical Chemistry A
|
Russian Journal of Physical Chemistry A
1 publication, 2.04%
|
|
International Journal of Biological Macromolecules
|
International Journal of Biological Macromolecules
1 publication, 2.04%
|
|
1
2
3
4
5
|
Citations by publishers
|
2
4
6
8
10
12
|
|
|
Wiley
|
Wiley
11 publications, 22.45%
|
|
American Chemical Society (ACS)
|
American Chemical Society (ACS)
9 publications, 18.37%
|
|
Elsevier
|
Elsevier
7 publications, 14.29%
|
|
Royal Society of Chemistry (RSC)
|
Royal Society of Chemistry (RSC)
6 publications, 12.24%
|
|
Pleiades Publishing
|
Pleiades Publishing
4 publications, 8.16%
|
|
Multidisciplinary Digital Publishing Institute (MDPI)
|
Multidisciplinary Digital Publishing Institute (MDPI)
3 publications, 6.12%
|
|
Springer Nature
|
Springer Nature
1 publication, 2.04%
|
|
Public Library of Science (PLoS)
|
Public Library of Science (PLoS)
1 publication, 2.04%
|
|
Walter de Gruyter
|
Walter de Gruyter
1 publication, 2.04%
|
|
Moscow University Press
|
Moscow University Press
1 publication, 2.04%
|
|
2
4
6
8
10
12
|
- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2016,2017,2018,2019,2020,2021,2022,2023,2024],"ids":[0,0,0,0,0,0,0,0,0],"codes":[0,0,0,0,0,0,0,0,0],"imageUrls":["","","","","","","","",""],"datasets":[{"label":"Citations number","data":[9,11,6,5,4,5,1,4,4],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["18.37","22.45","12.24","10.2","8.16","10.2","2.04","8.16","8.16"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Journal of Physical Chemistry B","Angewandte Chemie - International Edition","Angewandte Chemie","Organic and Biomolecular Chemistry","Physical Chemistry Chemical Physics","Molecules","ACS Catalysis","Biophysical Chemistry","Herald of the Russian Academy of Sciences","Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy","Moscow University Chemistry Bulletin","Russian Journal of Physical Chemistry B","Topics in Current Chemistry","Computational and Structural Biotechnology Journal","PLoS ONE","Journal of Molecular Biology","Computational Biology and Chemistry","Biopolymers","Molecular Informatics","Chemistry - A European Journal","Biochemistry","Journal of the American Chemical Society","Chemical Science","Chemical Communications","Pure and Applied Chemistry","MedComm","Biophysica","Russian Journal of Physical Chemistry A","International Journal of Biological Macromolecules"],"ids":[14990,19215,25450,541,1773,1770,4873,9050,1669,6337,10010,16359,23927,4268,24963,19701,16827,11945,10150,24708,9964,4813,9646,9073,11456,28715,27294,6134,23035],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/PRGhlgB4OKRltSNtT39eA6wlnOTGRap1QQ6FQHih_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/3SpVxcYL33bOvPq4sHxJLH2NeKNeDloahSUpNiO4_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp"],"datasets":[{"label":"","data":[5,3,3,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[10.2,6.12,6.12,4.08,4.08,4.08,4.08,4.08,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04,2.04],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Wiley","American Chemical Society (ACS)","Elsevier","Royal Society of Chemistry (RSC)","Pleiades Publishing","Multidisciplinary Digital Publishing Institute (MDPI)","Springer Nature","Public Library of Science (PLoS)","Walter de Gruyter","Moscow University Press"],"ids":[11,40,17,123,101,202,8,344,4,9299],"codes":[0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/oZgeErrVFhuDksyqFURLvYS1wtVSBWczh001igGo_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/PRGhlgB4OKRltSNtT39eA6wlnOTGRap1QQ6FQHih_medium.webp","\/storage\/images\/resized\/3SpVxcYL33bOvPq4sHxJLH2NeKNeDloahSUpNiO4_medium.webp","\/storage\/images\/resized\/pvlU1ac3KtgQWhw18PWQixiYpj68vOMFPdjtu7Nv_medium.webp"],"datasets":[{"label":"","data":[11,9,7,6,4,3,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[22.45,18.37,14.29,12.24,8.16,6.12,2.04,2.04,2.04,2.04],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}
Metrics
Cite this
GOST |
RIS |
BibTex |
MLA
Cite this
GOST
Copy
Khrenova M. G. et al. Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme // Journal of Physical Chemistry B. 2015. Vol. 119. No. 40. pp. 12838-12845.
GOST all authors (up to 50)
Copy
Khrenova M. G., Grigorenko B., Kolomeisky A., Nemukhin A. Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme // Journal of Physical Chemistry B. 2015. Vol. 119. No. 40. pp. 12838-12845.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1021/acs.jpcb.5b07238
UR - https://doi.org/10.1021%2Facs.jpcb.5b07238
TI - Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme
T2 - Journal of Physical Chemistry B
AU - Khrenova, Maria G.
AU - Grigorenko, Bella
AU - Kolomeisky, Anatoly
AU - Nemukhin, Alexander
PY - 2015
DA - 2015/09/25 00:00:00
PB - American Chemical Society (ACS)
SP - 12838-12845
IS - 40
VL - 119
SN - 1520-6106
SN - 1520-5207
ER -
Cite this
BibTex
Copy
@article{2015_Khrenova,
author = {Maria G. Khrenova and Bella Grigorenko and Anatoly Kolomeisky and Alexander Nemukhin},
title = {Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme},
journal = {Journal of Physical Chemistry B},
year = {2015},
volume = {119},
publisher = {American Chemical Society (ACS)},
month = {sep},
url = {https://doi.org/10.1021%2Facs.jpcb.5b07238},
number = {40},
pages = {12838--12845},
doi = {10.1021/acs.jpcb.5b07238}
}
Cite this
MLA
Copy
Khrenova, Maria G., et al. “Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.” Journal of Physical Chemistry B, vol. 119, no. 40, Sep. 2015, pp. 12838-12845. https://doi.org/10.1021%2Facs.jpcb.5b07238.