Backbone and side-chain ordering in a small protein.
We investigate the relation between backbone and side-chain ordering in a small protein. For this purpose, we have performed multicanonical simulations of the villin headpiece subdomain HP-36, an often used toy model in protein studies. Concepts of circular statistics are introduced to analyze side-chain fluctuations. In contrast to earlier studies on homopolypeptides [Wei et al., J. Phys. Chem. B 111, 4244 (2007)], we do not find collective effects leading to a separate transition. Rather, side-chain ordering is spread over a wide temperature range. Our results indicate a thermal hierarchy of ordering events, with side-chain ordering appearing at temperatures below the helix-coil transition but above the folding transition. We conjecture that this thermal hierarchy reflects an underlying temporal order, and that side-chain ordering facilitates the search for the correct backbone topology.
Wei
Yanjie
Y
Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA.
Nadler
Walter
W
Hansmann
Ulrich H E
UH
D003198:Computer Simulation; D008958:Models, Molecular; D016900:Neurofilament Proteins / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D016900:Neurofilament Proteins; D010446:Peptide Fragments; C115223:villin headpiece subdomain peptide