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Cited by 300

The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

Zhou, Ruhong·2003·Proteins: Structure, Function, and Bioinformatics
DOI 10.1002/prot.10483
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Abstract

The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large‐scale simulations. The current study uses the β‐hairpin from C‐terminus of protein G as an example to explore the folding free energy landscape with various GB models, and the results are compared to the explicit solvent simulations and experiments. All free energy landscapes are obtained from extensive conformation space sampling with a highly parallel replica exchange method. Because solvation model parameters are strongly coupled with force fields, five different force field/solvation model combinations are examined and compared in this study, namely the explicit solvent model: OPLSAA/SPC model, and the implicit solvent models: OPLSAA/SGB (Surface GB), AMBER94/GBSA (GB with Solvent Accessible Surface Area), AMBER96/GBSA, and AMBER99/GBSA. Surprisingly, we find that the free energy landscapes from implicit solvent models are quite different from that of the explicit solvent model. Except for AMBER96/GBSA, all other implicit solvent models find the lowest free energy state not the native state. All implicit solvent models show erroneous salt‐bridge effects between charged residues, particularly in OPLSAA/SGB model, where the overly strong salt‐bridge effect results in an overweighting of a non‐native structure with one hydrophobic residue F52 expelled from the hydrophobic core in order to make better salt bridges. On the other hand, both AMBER94/GBSA and AMBER99/GBSA models turn the β‐hairpin in to an α‐helix, and the α‐helical content is much higher than the previously reported α‐helices in an explicit solvent simulation with AMBER94 (AMBER94/TIP3P). Only AMBER96/GBSA shows a reasonable free energy landscape with the lowest free energy structure the native one despite an erroneous salt‐bridge between D47 and K50. Detailed results on free energy contour maps, lowest free energy structures, distribution of native contacts, α‐helical content during the folding process, NOE comparison with NMR, and temperature dependences are reported and discussed for all five models. Proteins 2003. © 2003 Wiley‐Liss, Inc.

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Metadata

Authors
Zhou, R.
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
2003-09-03
Volume
53
Issue
2
Pages
148-161
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
DOI
10.1002/prot.10483
OpenAlex
W2135469866
Cited by
300
References
49
FWCI
7.40
Type
journal article
Language
en
Open access
closed

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