Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics

Fan Jiang; Yun-Dong Wu

doi:10.1021/ja502735c

Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics

J Am Chem Soc. 2014 Jul 9;136(27):9536-9. doi: 10.1021/ja502735c. Epub 2014 Jun 26.

Authors

Fan Jiang¹, Yun-Dong Wu

Affiliation

¹ Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China.

PMID: 24953084
DOI: 10.1021/ja502735c

Abstract

Ab initio protein folding via physical-based all-atom simulation is still quite challenging. Using a recently developed residue-specific force field (RSFF1) in explicit solvent, we are able to fold a diverse set of 14 model proteins. The obtained structural features of unfolded state are in good agreement with previous observations. The replica-exchange molecular dynamics simulation is found to be efficient, resulting in multiple folding events for each protein. Transition path time is found to be significantly reduced under elevated temperature.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Models, Molecular
Molecular Dynamics Simulation*
Protein Folding*
Proteins / chemistry*

Substances

Proteins