Structural Chemistry, volume 30, issue 2, pages 481-488
Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases
Kapusta Dmitry P
1
,
Firsov Denis A
1
,
Khrenova Maria G
1, 2
,
Grigorenko Bella L
1, 3
,
Nemukhin Alexander
1, 3
2
Publication type: Journal Article
Publication date: 2018-10-20
Journal:
Structural Chemistry
Quartile SCImago
Q3
Quartile WOS
Q3
Impact factor: 1.7
ISSN: 10400400, 15729001
Physical and Theoretical Chemistry
Condensed Matter Physics
Abstract
In this work, we focus on some structural aspects of enzyme catalysis by modeling effects of the electrostatic potential created by the solvation water shells on properties of enzyme-substrate (ES) complexes. We simulate structure and dynamics of shells of explicit water molecules around two zinc-dependent hydrolases, matrix metalloproteinase-2 and metallo-β-lactamase, using classical force field parameters. Geometry configurations of the ES complexes for both systems are taken from the results of quantum mechanics/molecular mechanics (QM/MM) calculations. Evaluation of the electrostatic potentials from water molecules acting on selected points in the enzyme active sites shows that the shape and the size of solvent shells are important when simulating properties of reacting species inside a protein. We show that a practical way to construct the water shells around the protein is to include all external waters molecules located within the sphere centered at the center of mass of the ES complex or select a water layer around the protein of a constant thickness. In these cases, the computed electrostatic potentials on the selected points in the active site show a reasonable convergence with respect to the size of the solvation shell. We show that the analysis of the fluctuating electrostatic potentials is helpful in selecting the average structures of ES complexes, from which the reaction energy profiles should be computed.
Citations by journals
|
1
2
|
|
|
Structural Chemistry
|
Structural Chemistry
2 publications, 50%
|
|
Proteins: Structure, Function and Genetics
|
Proteins: Structure, Function and Genetics
1 publication, 25%
|
|
Physical Review E
|
Physical Review E
1 publication, 25%
|
|
1
2
|
Citations by publishers
|
1
2
|
|
|
Springer Nature
|
Springer Nature
2 publications, 50%
|
|
Wiley
|
Wiley
1 publication, 25%
|
|
American Physical Society (APS)
|
American Physical Society (APS)
1 publication, 25%
|
|
1
2
|
- 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":[2019,2020,2021,2022],"ids":[0,0,0,0],"codes":[0,0,0,0],"imageUrls":["","","",""],"datasets":[{"label":"Citations number","data":[1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["25","25","25","25"],"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":["Structural Chemistry","Proteins: Structure, Function and Genetics","Physical Review E"],"ids":[14347,19687,12743],"codes":[0,0,0],"imageUrls":["\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/nrK64iXHTzj43wMrfN1ZoUQ0vanswGzWPN45K3jA_medium.webp"],"datasets":[{"label":"","data":[2,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6"],"percentage":[50,25,25],"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":["Springer Nature","Wiley","American Physical Society (APS)"],"ids":[8,11,1539],"codes":[0,0,0],"imageUrls":["\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/nrK64iXHTzj43wMrfN1ZoUQ0vanswGzWPN45K3jA_medium.webp"],"datasets":[{"label":"","data":[2,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6"],"percentage":[50,25,25],"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
Kapusta D. P. et al. Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases // Structural Chemistry. 2018. Vol. 30. No. 2. pp. 481-488.
GOST all authors (up to 50)
Copy
Kapusta D. P., Firsov D. A., Khrenova M. G., Grigorenko B. L., Nemukhin A. Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases // Structural Chemistry. 2018. Vol. 30. No. 2. pp. 481-488.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1007/s11224-018-1206-1
UR - https://doi.org/10.1007%2Fs11224-018-1206-1
TI - Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases
T2 - Structural Chemistry
AU - Kapusta, Dmitry P
AU - Firsov, Denis A
AU - Khrenova, Maria G
AU - Grigorenko, Bella L
AU - Nemukhin, Alexander
PY - 2018
DA - 2018/10/20 00:00:00
PB - Springer Nature
SP - 481-488
IS - 2
VL - 30
SN - 1040-0400
SN - 1572-9001
ER -
Cite this
BibTex
Copy
@article{2018_Kapusta,
author = {Dmitry P Kapusta and Denis A Firsov and Maria G Khrenova and Bella L Grigorenko and Alexander Nemukhin},
title = {Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases},
journal = {Structural Chemistry},
year = {2018},
volume = {30},
publisher = {Springer Nature},
month = {oct},
url = {https://doi.org/10.1007%2Fs11224-018-1206-1},
number = {2},
pages = {481--488},
doi = {10.1007/s11224-018-1206-1}
}
Cite this
MLA
Copy
Kapusta, Dmitry P., et al. “Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases.” Structural Chemistry, vol. 30, no. 2, Oct. 2018, pp. 481-488. https://doi.org/10.1007%2Fs11224-018-1206-1.