Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins

Shuxiang Li; Adrian H Elcock

doi:10.1021/acs.jpclett.5b00654

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Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins

Journal article

Peer reviewed

Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins

Shuxiang Li and Adrian H Elcock

The journal of physical chemistry letters, Vol.6(11), pp.2127-2133

06/04/2015

DOI: 10.1021/acs.jpclett.5b00654

PMCID: PMC4657862

PMID: 26266514

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Abstract

A recent report of (3)J(HNHα) scalar coupling constants for hundreds of two-residue peptides has provided an important opportunity to test simulation force fields for proteins. Here, we compare the abilities of three derivatives of the Amber ff99SB force field to reproduce these data. We report molecular dynamics (MD) simulations of 256 two-residue peptides and show that the recently developed residue-specific force field (RSFF2) produces a dramatic improvement in the agreement with experimental (3)J(HNHα) coupling constants. We further show that RSFF2 also appears to produce a modest improvement in reproducing the (3)J(HNHα) coupling constants of five model proteins. Perhaps surprisingly, an analysis of neighboring residue effects (NREs) on the (3)J(HNHα) coupling constants of the two-residue peptides indicates little difference between the force fields' abilities to reproduce experimental NREs. We speculate that this might indicate limitations in the force fields' descriptions of nonbonded interactions between adjacent side chains or with terminal capping groups.

Animals

Oryza

Peptides - chemistry

Chickens

Humans

Bacteria - classification

Protein Conformation

Proteins - chemistry

Molecular Dynamics Simulation

Details

Title: Subtitle: Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins
Creators: Shuxiang Li - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
Adrian H Elcock - Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
Resource Type: Journal article
Publication Details: The journal of physical chemistry letters, Vol.6(11), pp.2127-2133
DOI: 10.1021/acs.jpclett.5b00654
PMID: 26266514
PMCID: PMC4657862
NLM abbreviation: J Phys Chem Lett
ISSN: 1948-7185
eISSN: 1948-7185
Publisher: United States
Grant note: R01 GM087290 / NIGMS NIH HHS R01 GM099865 / NIGMS NIH HHS
Language: English
Date published: 06/04/2015
Academic Unit: Physics and Astronomy; Biochemistry and Molecular Biology
Record Identifier: 9984024421302771

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