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Assessment of atomic charge models for gas-phase computations on polypeptides

Toon Verstraelen UGent, Ewald Pauwels UGent, Frank De Proft, Veronique Van Speybroeck UGent, Paul Geerlings and Michel Waroquier UGent (2012) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 8(2). p.661-676
abstract
The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q0, that is suitable to describe biological systems bearing many locally charged functional groups.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MM-PBSA, POPULATION ANALYSIS, PROTEINS, POLARIZABLE FORCE-FIELD, ELECTRONEGATIVITY EQUALIZATION METHOD, BINDING, MOLECULAR-DYNAMICS SIMULATIONS, INITIO QUANTUM-CHEMISTRY, ELECTROSTATIC POTENTIALS, MECHANICAL CALCULATIONS
journal title
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
J. Chem. Theory Comput.
volume
8
issue
2
pages
661 - 676
Web of Science type
Article
Web of Science id
000300141600028
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
5.389 (2012)
JCR rank
3/34 (2012)
JCR quartile
1 (2012)
ISSN
1549-9618
DOI
10.1021/ct200512e
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1997717
handle
http://hdl.handle.net/1854/LU-1997717
date created
2012-01-20 09:25:16
date last changed
2013-09-17 10:49:55
@article{1997717,
  abstract     = {The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q0, that is suitable to describe biological systems bearing many locally charged functional groups.},
  author       = {Verstraelen, Toon and Pauwels, Ewald and De Proft, Frank and Van Speybroeck, Veronique and Geerlings, Paul and Waroquier, Michel},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  keyword      = {MM-PBSA,POPULATION ANALYSIS,PROTEINS,POLARIZABLE FORCE-FIELD,ELECTRONEGATIVITY EQUALIZATION METHOD,BINDING,MOLECULAR-DYNAMICS SIMULATIONS,INITIO QUANTUM-CHEMISTRY,ELECTROSTATIC POTENTIALS,MECHANICAL CALCULATIONS},
  language     = {eng},
  number       = {2},
  pages        = {661--676},
  title        = {Assessment of atomic charge models for gas-phase computations on polypeptides},
  url          = {http://dx.doi.org/10.1021/ct200512e},
  volume       = {8},
  year         = {2012},
}

Chicago
Verstraelen, Toon, Ewald Pauwels, Frank De Proft, Veronique Van Speybroeck, Paul Geerlings, and Michel Waroquier. 2012. “Assessment of Atomic Charge Models for Gas-phase Computations on Polypeptides.” Journal of Chemical Theory and Computation 8 (2): 661–676.
APA
Verstraelen, T., Pauwels, E., De Proft, F., Van Speybroeck, V., Geerlings, P., & Waroquier, M. (2012). Assessment of atomic charge models for gas-phase computations on polypeptides. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8(2), 661–676.
Vancouver
1.
Verstraelen T, Pauwels E, De Proft F, Van Speybroeck V, Geerlings P, Waroquier M. Assessment of atomic charge models for gas-phase computations on polypeptides. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2012;8(2):661–76.
MLA
Verstraelen, Toon, Ewald Pauwels, Frank De Proft, et al. “Assessment of Atomic Charge Models for Gas-phase Computations on Polypeptides.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8.2 (2012): 661–676. Print.