Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins : accelerated QM/MM studies of pKa, redox reactions and solvation free energies
Kamerlin, Shina C L LU
; Haranczyk, Maciej
and Warshel, Arieh
(2009)
In The Journal of Physical Chemistry Part B
113(5).
p.72-1253
- Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the... (More)
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
(Less)
- author
- Kamerlin, Shina C L
LU
; Haranczyk, Maciej
and Warshel, Arieh
- publishing date
- 2009-02-05
- type
- Contribution to journal
- publication status
- published
- keywords
- Animals, Computer Simulation, Oxidation-Reduction, Proteins/chemistry, Quantum Theory, Solubility, Static Electricity
- in
- The Journal of Physical Chemistry Part B
- volume
- 113
- issue
- 5
- pages
- 20 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:62149122220
- pmid:19055405
- ISSN
- 1520-6106
- DOI
- 10.1021/jp8071712
- language
- English
- LU publication?
- no
- id
- a31c28d4-4d40-4444-b519-763e60ea74b3
- date added to LUP
- 2025-01-11 22:18:29
- date last changed
- 2025-04-20 11:59:09
@article{a31c28d4-4d40-4444-b519-763e60ea74b3,
abstract = {{<p>Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.</p>}},
author = {{Kamerlin, Shina C L and Haranczyk, Maciej and Warshel, Arieh}},
issn = {{1520-6106}},
keywords = {{Animals; Computer Simulation; Oxidation-Reduction; Proteins/chemistry; Quantum Theory; Solubility; Static Electricity}},
language = {{eng}},
month = {{02}},
number = {{5}},
pages = {{72--1253}},
publisher = {{The American Chemical Society (ACS)}},
series = {{The Journal of Physical Chemistry Part B}},
title = {{Progress in <i>ab initio</i> QM/MM free-energy simulations of electrostatic energies in proteins : accelerated QM/MM studies of p<i>K</i><sub>a</sub>, redox reactions and solvation free energies}},
url = {{http://dx.doi.org/10.1021/jp8071712}},
doi = {{10.1021/jp8071712}},
volume = {{113}},
year = {{2009}},
}