SPICA Force Field for Proteins and Peptides

Shuhei Kawamoto, Huihui Liu, Yusuke Miyazaki, Sangjae Seo, Mayank Dixit, Russell Devane, Christopher Macdermaid, Giacomo Fiorin, Michael L. Klein, Wataru Shinoda

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the Surface Property fItting Coarse grAined (SPICA) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulations with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. An elastic network model was adopted to maintain the secondary structure within a single chain. The side-chain analogues reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable association free energy (potential of mean force) in water compared to those from AA MD. A series of peptides/proteins adsorbed onto or penetrated into the membrane simulated by the CG MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins as comparable to those in the orientations of proteins in membranes (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated the good performance of the SPICA FF.

Original languageEnglish
JournalJournal of Chemical Theory and Computation
DOIs
Publication statusAccepted/In press - 2021

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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