In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field

Phys Rev Lett. 2005 Jan 14;94(1):018101. doi: 10.1103/PhysRevLett.94.018101. Epub 2005 Jan 5.

Abstract

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computer Simulation
  • Energy Transfer
  • HIV / metabolism*
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Structure, Secondary
  • Stress, Mechanical
  • Structure-Activity Relationship
  • Viral Proteins / analysis
  • Viral Proteins / chemistry*

Substances

  • Viral Proteins