Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

Biophys J. 2005 Apr;88(4):2472-93. doi: 10.1529/biophysj.104.051938. Epub 2005 Jan 21.

Abstract

The ensemble folding of two 21-residue alpha-helical peptides has been studied using all-atom simulations under several variants of the AMBER potential in explicit solvent using a global distributed computing network. Our extensive sampling, orders of magnitude greater than the experimental folding time, results in complete convergence to ensemble equilibrium. This allows for a quantitative assessment of these potentials, including a new variant of the AMBER-99 force field, denoted AMBER-99 phi, which shows improved agreement with experimental kinetic and thermodynamic measurements. From bulk analysis of the simulated AMBER-99 phi equilibrium, we find that the folding landscape is pseudo-two-state, with complexity arising from the broad, shallow character of the "native" and "unfolded" regions of the phase space. Each of these macrostates allows for configurational diffusion among a diverse ensemble of conformational microstates with greatly varying helical content and molecular size. Indeed, the observed structural dynamics are better represented as a conformational diffusion than as a simple exponential process, and equilibrium transition rates spanning several orders of magnitude are reported. After multiple nucleation steps, on average, helix formation proceeds via a kinetic "alignment" phase in which two or more short, low-entropy helical segments form a more ideal, single-helix structure.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Biophysics / methods*
  • Cluster Analysis
  • Computer Simulation
  • Diffusion
  • Hot Temperature
  • Kinetics
  • Markov Chains
  • Models, Molecular
  • Models, Statistical
  • Molecular Conformation
  • Peptides / chemistry
  • Polymers / chemistry
  • Protein Folding
  • Protein Structure, Secondary
  • Software
  • Temperature
  • Thermodynamics
  • Time Factors

Substances

  • Peptides
  • Polymers
  • polyproline
  • polyalanine