A study of ab initio folding of chignolins using replica-exchange molecular dynamics simulations
More and more studies have confirmed the importance of polarization effects in hydrogen bonding interactions in protein folding simulations. In this paper, a recently developed charge update scheme termed polarized structure-specific backbone charge (PSBC) model was applied to the folding of 10-resi...
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Veröffentlicht in: | Physical chemistry chemical physics : PCCP 2023-09, Vol.25 (35), p.23658-23666 |
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Format: | Artikel |
Sprache: | eng |
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Zusammenfassung: | More and more studies have confirmed the importance of polarization effects in hydrogen bonding interactions in protein folding simulations. In this paper, a recently developed charge update scheme termed polarized structure-specific backbone charge (PSBC) model was applied to the folding of 10-residue chignolin. A comparison between simulations performed using PSBC and a nonpolarizable (AMBER99SB) force field demonstrably showed the importance of the electrostatic polarization effect in the folding of the short β-hairpin peptide by a series of analyses such as DSSP, free-energy landscape, hydrogen bond occupancy, and melting curve. The PSBC model was further validated by folding two other chignolin variants. |
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ISSN: | 1463-9076 1463-9084 |
DOI: | 10.1039/d3cp03070a |