Computer simulations of de novo designed helical proteins

Biophys J. 1998 Jul;75(1):92-105. doi: 10.1016/S0006-3495(98)77497-1.

Abstract

In the context of reduced protein models, Monte Carlo simulations of three de novo designed helical proteins (four-member helical bundle) were performed. At low temperatures, for all proteins under consideration, protein-like folds having different topologies were obtained from random starting conformations. These simulations are consistent with experimental evidence indicating that these de novo designed proteins have the features of a molten globule state. The results of Monte Carlo simulations suggest that these molecules adopt four-helix bundle topologies. They also give insight into the possible mechanism of folding and association, which occurs in these simulations by on-site assembly of the helices. The low-temperature conformations of all three sequences have the features of a molten globule state.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Biophysical Phenomena
  • Biophysics
  • Computer Simulation*
  • Dimerization
  • Drug Design
  • Hydrogen Bonding
  • Models, Molecular*
  • Molecular Sequence Data
  • Monte Carlo Method
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Thermodynamics

Substances

  • Proteins