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Exploring Reactive Conformations of Coenzyme A during Binding and Unbinding to Pyruvate Formate–Lyase
journal contribution
posted on 2019-10-17, 13:06 authored by Marko Hanževački, Radha Dilip Banhatti, Karmen Čondić-Jurkić, Ana-Sunčana Smith, David M. SmithPyruvate formate–lyase
(PFL) is a glycyl radical enzyme
that converts pyruvate and coenzyme A (CoA) into formate and acetyl-CoA
in two half-reactions. Recently, we showed that the acetylation of
the PFL active site in the first half-reaction induces subtle conformational
changes, leading to the opening of a potential channel for CoA entry.
Entry of CoA into the active site is crucial for the second half-reaction,
involving the acetyl transfer to CoA, and the completion of the catalytic
cycle. Using steered molecular dynamics (SMD) simulations, performed
on acetylated and nonacetylated monomeric PFL model systems, we first
of all investigate the possible entry/exit pathways of CoA with respect
to the active site through the previously identified channel. We then
perform umbrella sampling simulations on multiple snapshots from SMD
trajectories as well as unrestrained molecular dynamics simulations
starting from the final structures obtained from entry SMD, with a
view to identifying possible bound states of CoA in the near vicinity
of the active site. Detailed study of the unrestrained dissociation
processes reveals the presence of stable and reactive bound states
of CoA close to the active site, one of which is in an ideal position
for triggering the second half-reaction. Examination of the spatial
distributions associated with the reactive bound states allows us
to discuss the free energy barriers. Umbrella sampling, performed
on snapshots from unrestrained dynamics confirms the above findings.
The significance of the results for the catalysis are discussed for
both acetylated and nonacetylated systems.