Microsecond timescale MD simulations at the transition state of PmHMGR predict remote allosteric residues.

ABSTRACT: 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. 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 reach 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 microseco

SUBMITTER: Quinn TR 

PROVIDER: S-EPMC8115266 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature