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American Physical Society, Physical Review Letters, 19(95)

DOI: 10.1103/physrevlett.95.198103

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Allostery in a Coarse-Grained Model of Protein Dynamics

Journal article published in 2005 by Dengming Ming, Michael E. Wall ORCID
This paper is available in a repository.
This paper is available in a repository.

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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.