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.

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

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