Efficient Expansion, Folding, and Unfolding of Proteins

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Nov;70(5 Pt 1):051906. doi: 10.1103/PhysRevE.70.051906. Epub 2004 Nov 15.

Abstract

We consider a nonstatistical, computationally fast experiment to identify important topological constraints in folding small globular proteins of about 100-200 amino acids. In this experiment, proteins are expanded mechanically along a path of steepest increase in the free space around residues. The pathways are often consistent with folding scenarios reported in kinetics experiments and most accurately describe obligatory or mechanic folding proteins. The results suggest that certain topological "defects" in proteins lead to preferred, entropically favorable channels down their free energy landscapes.

Publication types

  • Comparative Study
  • Evaluation Study
  • Validation Study

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Computer Simulation
  • Elasticity
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Denaturation*
  • Protein Folding*
  • Proteins / analysis
  • Proteins / chemistry*
  • Structure-Activity Relationship

Substances

  • Amino Acids
  • Proteins