Molecular simulation of the reversible mechanical unfolding of proteins.
In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations.
Rathore
Nitin
N
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Yan
Qiliang
Q
de Pablo
Juan J
JJ
D000409:Alanine / Q000737:chemistry; D003198:Computer Simulation; D008433:Mathematics; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D009842:Oligopeptides; D011506:Proteins; D000409:Alanine