Contact Pair Dynamics During Folding of a Model Globular Protein, Hp-36
Abstract
The dynamics of contact pair formation between various hydrophobic residues during folding of a model protein Hp-36 is investigated by Brownian dynamics simulation. Hydropathy scale and non-local helix propensity of amino acids are used to model the complex interaction potential. The resulting structure of the model protein mimics the native state of the real protein with a of 4.5 \AA. A contact pair distance time correlation function (CPCF), , is introduced which shows multistage decay, including a {\it slow late stage dynamics} for a few specific pairs. {\it These pairs determine the long time folding rate}. Dynamics can be correlated with the landscape, relative contact order and topological contact.
Keywords
Cite
@article{arxiv.cond-mat/0212379,
title = {Contact Pair Dynamics During Folding of a Model Globular Protein, Hp-36},
author = {Arnab Mukherjee and Biman Bagchi},
journal= {arXiv preprint arXiv:cond-mat/0212379},
year = {2007}
}
Comments
4 pages including 4 figures. Submitted to the Phys. Rev. Lett