An MM/3D-RISM approach for ligand binding affinities.
Genheden, Samuel LU ; Luchko, Tyler ; Gusarov, Sergey LU ; Kovalenko, Andriy and Ryde, Ulf LU
(2010)
In The Journal of Physical Chemistry Part B
114(25).
p.8505-8516
- Abstract
- We have modified the popular MM/PBSA or MM/GBSA approaches (molecular mechanics for a biomolecule, combined with a Poisson-Boltzmann or generalized Born electrostatic and surface area nonelectrostatic solvation energy) by employing instead the statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D reference interaction site model, or 3D-RISM-KH) coupled with molecular mechanics or molecular dynamics ( Blinov , N. ; et al. Biophys. J. 2010 ; Luchko , T. ; et al. J. Chem. Theory Comput. 2010 ). Unlike the PBSA or GBSA semiempirical approaches, the 3D-RISM-KH theory yields a full molecular picture of the solvation structure and thermodynamics from the first principles, with proper account of chemical... (More)
- We have modified the popular MM/PBSA or MM/GBSA approaches (molecular mechanics for a biomolecule, combined with a Poisson-Boltzmann or generalized Born electrostatic and surface area nonelectrostatic solvation energy) by employing instead the statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D reference interaction site model, or 3D-RISM-KH) coupled with molecular mechanics or molecular dynamics ( Blinov , N. ; et al. Biophys. J. 2010 ; Luchko , T. ; et al. J. Chem. Theory Comput. 2010 ). Unlike the PBSA or GBSA semiempirical approaches, the 3D-RISM-KH theory yields a full molecular picture of the solvation structure and thermodynamics from the first principles, with proper account of chemical specificities of both solvent and biomolecules, such as hydrogen bonding, hydrophobic interactions, salt bridges, etc. We test the method on the binding of seven biotin analogues to avidin in aqueous solution and show it to work well in predicting the ligand-binding affinities. We have compared the results of 3D-RISM-KH with four different generalized Born and two Poisson-Boltzmann methods. They give absolute binding energies that differ by up to 208 kJ/mol and mean absolute deviations in the relative affinities of 10-43 kJ/mol. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/1626344
- author
- Genheden, Samuel
LU
; Luchko, Tyler
; Gusarov, Sergey
LU
; Kovalenko, Andriy
and Ryde, Ulf
LU
- organization
- publishing date
- 2010
- type
- Contribution to journal
- publication status
- published
- subject
- in
- The Journal of Physical Chemistry Part B
- volume
- 114
- issue
- 25
- pages
- 8505 - 8516
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- wos:000278982200026
- pmid:20524650
- scopus:77953976984
- pmid:20524650
- ISSN
- 1520-5207
- DOI
- 10.1021/jp101461s
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
- id
- 9576491d-576d-49f3-9d21-fc7a87ece6c0 (old id 1626344)
- date added to LUP
- 2016-04-01 14:08:40
- date last changed
- 2023-02-07 02:35:23
@article{9576491d-576d-49f3-9d21-fc7a87ece6c0,
abstract = {{We have modified the popular MM/PBSA or MM/GBSA approaches (molecular mechanics for a biomolecule, combined with a Poisson-Boltzmann or generalized Born electrostatic and surface area nonelectrostatic solvation energy) by employing instead the statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D reference interaction site model, or 3D-RISM-KH) coupled with molecular mechanics or molecular dynamics ( Blinov , N. ; et al. Biophys. J. 2010 ; Luchko , T. ; et al. J. Chem. Theory Comput. 2010 ). Unlike the PBSA or GBSA semiempirical approaches, the 3D-RISM-KH theory yields a full molecular picture of the solvation structure and thermodynamics from the first principles, with proper account of chemical specificities of both solvent and biomolecules, such as hydrogen bonding, hydrophobic interactions, salt bridges, etc. We test the method on the binding of seven biotin analogues to avidin in aqueous solution and show it to work well in predicting the ligand-binding affinities. We have compared the results of 3D-RISM-KH with four different generalized Born and two Poisson-Boltzmann methods. They give absolute binding energies that differ by up to 208 kJ/mol and mean absolute deviations in the relative affinities of 10-43 kJ/mol.}},
author = {{Genheden, Samuel and Luchko, Tyler and Gusarov, Sergey and Kovalenko, Andriy and Ryde, Ulf}},
issn = {{1520-5207}},
language = {{eng}},
number = {{25}},
pages = {{8505--8516}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The Journal of Physical Chemistry Part B}},
title = {{An MM/3D-RISM approach for ligand binding affinities.}},
url = {{https://lup.lub.lu.se/search/files/136743105/141_rism.pdf}},
doi = {{10.1021/jp101461s}},
volume = {{114}},
year = {{2010}},
}