Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.

ABSTRACT: Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological ope

SUBMITTER: Li D 

PROVIDER: S-EPMC4572606 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature