Microsecond Timescale Simulations at the Transition State of PmHMGR Predict Remote Allosteric Residues
2019
Understanding the mechanisms of enzymatic
catalysis requires a detailed understanding of the complex interplay of structure
and dynamics of large systems that is a challenge for both experimental and
computational approaches. QM/MM methods have been
extensively used to study these reactions, but the difficulties arising from
the hybrid treatment of the system are well documented. More importantly, the
computational demands of QM/MM simulations mean that the dynamics of the
reaction can only be considered on a timescale of nanoseconds even though the
conformational changes needed to react the catalytically active state happen on
a much slower timescale. Here we demonstrate an alternative
approach that uses transition state force fields (TSFFs) derived by the
quantum-guided molecular mechanics (Q2MM) method that provides a consistent
treatment of the entire system at the classical molecular mechanics level and
allows simulations at the microsecond timescale. Application of this approach
the second hydride transfer transition state of HMG-CoA reductase from Pseudomonas mevalonii (PmHMGR) identified three remote residues, R396 E399 and L407, (15-27 A away from the
active site) that have a remote dynamic effect on enzyme activity. The
predictions were subsequently validated experimentally via site-directed
mutagenesis. These results show that microsecond
timescale MD simulations of transition states are possible and can predict rather
than just rationalize remote allosteric residues.
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