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

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HPC-UGent: the central High Performance Computing infrastructure of Ghent University
Project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
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.
Keywords
POPULATION ANALYSIS, MM-PBSA, PROTEINS, POLARIZABLE FORCE-FIELD, ELECTRONEGATIVITY EQUALIZATION METHOD, BINDING, MOLECULAR-DYNAMICS SIMULATIONS, INITIO QUANTUM-CHEMISTRY, ELECTROSTATIC POTENTIALS, MECHANICAL CALCULATIONS

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Citation

Please use this url to cite or link to this publication:

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.
@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      = {POPULATION ANALYSIS,MM-PBSA,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},
}

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