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Cited by 338

The DOI matches its Crossref record; 80 of the 80 references it cites were found in a registry or an index.

Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field

Open access
Chen, Jianhan, Im, Wonpil, Brooks, Charles L.·2006·Journal of the American Chemical Society
DOI 10.1021/ja057216r
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Abstract

The efficient and accurate characterization of solvent effects is a key element in the theoretical and computational study of biological problems. Implicit solvent models, particularly generalized Born (GB) continuum electrostatics, have emerged as an attractive tool to study the structure and dynamics of biomolecules in various environments. Despite recent advances in this methodology, there remain limitations in the parametrization of many of these models. In the present work, we demonstrate that it is possible to achieve a balanced implicit solvent force field by further optimizing the input atomic radii in combination with adjusting the protein backbone torsional energetics. This parameter optimization is guided by the potentials of mean force (PMFs) between amino acid polar groups, calculated from explicit solvent free energy simulations, and by conformational equilibria of short peptides, obtained from extensive folding and unfolding replica exchange molecular dynamics (REX-MD) simulations. Through the application of this protocol, the delicate balance between the competing solvation forces and intramolecular forces appears to be better captured, and correct conformational equilibria for a range of both helical and beta-hairpin peptides are obtained. The same optimized force field also successfully folds both beta-hairpin trpzip2 and mini-protein Trp-Cage, indicating that it is quite robust. Such a balanced, physics-based force field will be highly applicable to a range of biological problems including protein folding and protein structural dynamics.

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Metadata

Authors
Chen, J., Im, W., & Brooks, C. L.
Venue
Journal of the American Chemical Society
Publisher
American Chemical Society (ACS)
Published
2006-03-01
Volume
128
Issue
11
Pages
3728-3736
ISSN
  • 0002-7863 (ISSN-L)
  • 1520-5126
DOI
10.1021/ja057216r
OpenAlex
W2007965478
Cited by
338
References
80
FWCI
9.45
Type
journal article
Language
en
Open access
green

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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

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