SURPASS Low-Resolution Coarse-Grained Protein Modeling

J Chem Theory Comput. 2017 Nov 14;13(11):5766-5779. doi: 10.1021/acs.jctc.7b00642. Epub 2017 Oct 23.

Abstract

Coarse-grained modeling of biomolecules has a very important role in molecular biology. In this work we present a novel SURPASS (Single United Residue per Pre-Averaged Secondary Structure fragment) model of proteins that can be an interesting alternative for existing coarse-grained models. The design of the model is unique and strongly supported by the statistical analysis of structural regularities characteristic for protein systems. Coarse-graining of protein chain structures assumes a single center of interactions per residue and accounts for preaveraged effects of four adjacent residue fragments. Knowledge-based statistical potentials encode complex interaction patterns of these fragments. Using the Replica Exchange Monte Carlo sampling scheme and a generic version of the SURPASS force field we performed test simulations of a representative set of single-domain globular proteins. The method samples a significant part of conformational space and reproduces protein structures, including native-like, with surprisingly good accuracy. Future extension of the SURPASS model on large biomacromolecular systems is briefly discussed.

MeSH terms

  • Models, Biological*
  • Molecular Dynamics Simulation*
  • Monte Carlo Method
  • Protein Structure, Secondary
  • Proteins / chemistry*

Substances

  • Proteins