Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition.

ABSTRACT: Atomically detailed simulations of HIV RT are performed to investigate the contributions of the conformational transition to the overall rate and specificity of enzyme catalysis. A number of different scenarios are considered within Milestoning theory to provide a more complete picture of the process of opening and closing the enzyme. We consider the open to closed transition in the absence of and with the correct and incorrect substrates. We also consider the free energy profile and the kinetics of the conformational change after the chemistry step in which a new base was added to the DNA, but the DNA was not yet displaced. We partition the free energy along the reaction coordinate and analyze the importance of different protein domains. Strikingly, significant influence on the free energ

SUBMITTER: Kirmizialtin S 

PROVIDER: S-EPMC4623308 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature