Folding behaviors of lattice model proteins with three kinds of contact potentials

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jun;67(6 Pt 1):061905. doi: 10.1103/PhysRevE.67.061905. Epub 2003 Jun 18.

Abstract

The interaction potentials between the amino acids are very important in the study of protein folding and design. In this work, the folding behaviors of lattice model protein chains are studied using three kinds of contact potentials between the beads. For these three cases, a number of sequences are designed using the Z-score method, and then their folding behaviors are obtained via Monte Carlo simulations for different sizes of the chains. It is found that the proper weakening of hydrophobicity may speed up the folding and the elimination of the mixing interaction terms may deteriorate the foldability. The different features of the foldability are discussed by comparing the characteristics of the energy landscapes of these model chains. The formations of various contacts are also analyzed, which provide us with some microscopic information on the model systems and interaction potentials.

MeSH terms

  • Biophysics / methods*
  • Hot Temperature
  • Kinetics
  • Models, Molecular
  • Models, Statistical
  • Monte Carlo Method
  • Protein Conformation
  • Protein Denaturation
  • Protein Folding*
  • Proteins / chemistry*
  • Temperature
  • Thermodynamics
  • Time
  • Time Factors

Substances

  • Proteins