Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent

J Chem Theory Comput. 2015 Dec 8;11(12):5573-7. doi: 10.1021/acs.jctc.5b00954. Epub 2015 Nov 13.

Abstract

The REST2 method is successfully applied to investigate the thermal stability of chignolin CLN025 and of Trp-cage. As opposed to temperature replica exchange, REST2 relies on the rescaling of the protein potential energy, which allows a smaller number of replicas. The shape of the stability curve reconstructed on the basis of the corresponding-state principle is in very good agreement with experimental data; for chignolin, the effect of mutations is also recovered.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Molecular Dynamics Simulation
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Protein Stability
  • Protein Structure, Secondary
  • Solvents / chemistry*
  • Temperature
  • Thermodynamics

Substances

  • Oligopeptides
  • Solvents
  • chignolin