title: αC helix as a switch in the conformational transition of Src/CDK-like kinase domains.
abstract: One mechanism of regulating the catalytic activity of protein kinases is through conformational transitions. Despite great diversity in the structural changes involved in the transitions, a certain set of changes within the kinase domain (KD) has been observed for many kinases including Src and CDK2. We investigated this conformational transition computationally to identify the topological features that are energetically critical to the transition. Results from both molecular dynamics sampling and transition path optimization highlight the displacement of the αC helix as the major energy barrier, mediating the switch of the KD between the active and down-regulated states. The critical role of the αC helix is noteworthy by providing a rationale for a number of activation and deactivation mechanisms known to occur in cells. We find that kinases with the αC helix displacement exist throughout the kinome, suggesting that this feature may have emerged early in evolution.
authors.affiliation: Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology and Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, United States.
authors.forename: He
authors.initials: H
authors.lastname: Huang
authors.forename: Ruijun
authors.initials: R
authors.lastname: Zhao
authors.forename: Bradley M
authors.initials: BM
authors.lastname: Dickson
authors.forename: Robert D
authors.initials: RD
authors.lastname: Skeel
authors.forename: Carol Beth
authors.initials: CB
authors.lastname: Post
mesh_terms: D055162:Biocatalysis; D018844:Cyclin-Dependent Kinases / Q000737:chemistry*; D019143:Evolution, Molecular; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D018909:src Homology Domains
chemical_list: D018844:Cyclin-Dependent Kinases