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

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 energy profile is detected for amino
acids far from the active site. The overall long-range impact is about
50 percent of the total. We also illustrate that the overall rate
is not necessarily determined by the highest free energy barrier along
the reaction path (with respect to the free enzyme and substrate)
and that the specificity is not necessarily determined by the same
reaction step that determines the rate.