Sampling realistic protein conformations using local structural bias

PLoS Comput Biol. 2006 Sep 22;2(9):e131. doi: 10.1371/journal.pcbi.0020131. Epub 2006 Aug 21.

Abstract

The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computational Biology*
  • Computer Simulation
  • Models, Molecular
  • Probability
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry*

Substances

  • Proteins