Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling

The microbial enzyme diaminopimelate epimerase (DapF),
a vital
enzyme in the lysine biosynthetic pathway, catalyzes the conversion
of L, L-diaminopimelate (L, L-DAP)
to D, L-diaminopimelate (D, L-DAP)
using a catalytic cysteine dyad with one cysteine in thiol state and
another in thiolate. Under oxidizing conditions, the catalytic cysteines
of apo DapF form a disulfide bond that alters the structure and function
of DapF. Given its potential as a target for antimicrobial resistance
treatments, understanding DapF’s functional dynamics is imperative.
In the present work, we employ microsecond-scale all-atom molecular
dynamics simulations of product-bound DapF and apo-DapF under oxidized
and reduced conditions. We employ a polarized charge model for the
ligand and the active site residues, which was necessary to preserve
the electrostatic environment in the active site and retain the ligand
in the active site. The product-bound DapF and apo-DapF in oxidized
and reduced conditions exhibit a closed, semi-open, and open conformation,
respectively, as identified using the internal coordinates of the
dimeric enzyme and the principal component analysis. The conformational
switch is guided by the dynamic catalytic (DC) loop, loop II, and
loop III movements in the active site. The time scale of the close-to-open
conformational transition is estimated to be 0.8 μs through
Markov state modeling (MSM) and transition path theory (TPT). The
present study explains the role of various active site residues and
loops in ligand binding and protein dynamics in the DapF enzyme under
different redox conditions. Such information will be helpful in future
inhibitor design studies targeting the DapF enzyme.