Exploring the energy landscape of model proteins: a metric criterion for the determination of dynamical connectivity

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov;72(5 Pt 1):051929. doi: 10.1103/PhysRevE.72.051929. Epub 2005 Nov 29.

Abstract

A method to reconstruct the energy landscape of small peptides is presented with reference to a two-dimensional off-lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly connected pairs (DCP). As the mutual distance of DCP is typically much smaller than that of generic pairs, a metric criterion can be established to identify the great majority of DCP. Advantages and limits of this approach are thoroughly analyzed for three different heteropolymeric chains. A funnel-like structure of the energy landscape is found in all of the three cases, but the escape rates clearly reveal that the native configuration is more easily accessible (and is significantly more stable) for the sequence that is expected to behave as a real protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Computer Simulation
  • Energy Transfer
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Denaturation
  • Protein Folding
  • Proteins / chemistry*
  • Sequence Analysis, Protein / methods*
  • Thermodynamics

Substances

  • Proteins