Three-bead rotating chain model shows universality in the stretching of proteins

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Oct;72(4 Pt 1):041908. doi: 10.1103/PhysRevE.72.041908. Epub 2005 Oct 10.

Abstract

We introduce a model of proteins in which all of the key atoms in the protein backbone are accounted for, thus extending the freely rotating chain model. We use average bond lengths and average angles from the Protein Data Bank as input parameters, leaving the number of residues as a single variable. The model is used to study the stretching of proteins in the entropic regime. The results of our Monte Carlo simulations are found to agree well with experimental data, suggesting that the force extension plot is universal and does not depend on the side chains or primary structure of the proteins.

MeSH terms

  • Amino Acid Sequence
  • Computer Simulation
  • Elasticity
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Monte Carlo Method
  • Protein Conformation
  • Proteins / chemistry*
  • Rotation
  • Stress, Mechanical

Substances

  • Proteins