Allostery in a Coarse-Grained Model of Protein Dynamics
Abstract
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM disagrees with the bimodal distribution obtained from an all-atom model; however, the bimodal distribution is recovered by strengthening interactions between atoms that are backbone neighbors. We use the backbone-enhanced model to analyze allosteric mechanisms of trypsinogen, and find relatively strong communication between the regulatory and active sites.
Keywords
Cite
@article{arxiv.q-bio/0506031,
title = {Allostery in a Coarse-Grained Model of Protein Dynamics},
author = {Dengming Ming and Michael Wall},
journal= {arXiv preprint arXiv:q-bio/0506031},
year = {2009}
}
Comments
11 pages, 3 figures; Fixed typo in Eq. (4); Changed local report number; Renormalized Fig. 1 to # of non-zero modes; Fixed scales of MSDs in Fig. 2; shortened manuscript; changed author list; fixed error in reference to active and regulatory sites of trypsinogen; added journal reference and DOI