All-atom ab initio folding of a diverse set of proteins

Structure. 2007 Jan;15(1):53-63. doi: 10.1016/j.str.2006.11.010.

Abstract

Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio folding of a representative diverse set of proteins by using a minimalist transferable-energy model that consists of two-body atom-atom interactions, hydrogen bonding, and a local sequence-energy term that models sequence-specific chain stiffness. Starting from a random coil, the native-like structure was observed during replica exchange Monte Carlo (REMC) simulation for most proteins regardless of their structural classes; the lowest energy structure was close to native-in the range of 2-6 A root-mean-square deviation (rmsd). Our results demonstrate that the successful folding of a protein chain to its native state is governed by only a few crucial energetic terms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Molecular*
  • Monte Carlo Method
  • Protein Folding*
  • Protein Structure, Secondary*