Allostery in a coarse-grained model of protein dynamics.
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.
Ming
Dengming
D
Computer and Computational Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
Wall
Michael E
ME
D000465:Algorithms; D000818:Animals; D002244:Carbon / Q000737:chemistry; D002417:Cattle; D004548:Elasticity; D004735:Energy Transfer; D008958:Models, Molecular; D015233:Models, Statistical; D011312:Pressure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000502:physiology*; D014362:Trypsinogen / Q000737:chemistry
D011506:Proteins; D002244:Carbon; D014362:Trypsinogen