posted on 2018-05-31, 00:00authored byIsela Rodriguez-Bussey, Xin-Qiu Yao, Abdullah Danish Shouaib, Jonathan Lopez, Donald Hamelberg
Conformational dynamics
plays the key role in allosteric regulation
of enzymes. Despite numerous experimental and computational efforts,
the mechanism of how dynamics couple enzymatic function is poorly
understood. Here, we introduce a new approach to exploring the dynamics-function
relationship combining computational mutagenesis, microsecond-long
molecular dynamics simulations, and side-chain torsion angle analyses.
We apply our approach to elucidate the allosteric mechanism in cyclophilin
A (CypA), a peptidyl-prolyl cis–trans isomerase known to participate
in diverse biological processes and be associated with many diseases
including cancer. Multiple single mutations are performed in CypA
at previously discovered hotspot residues distal from the active site,
and residues displaying significant dynamical changes upon mutations
are then identified. The mutation-responsive residues delineate three
distinct pathways potentially mediating allosteric communications
between distal sites: two pathways resemble the allosteric networks
identified in a recent experimental study, whereas the third represents
a novel pathway. A residue–residue contact analysis is also
performed to complement the findings. Furthermore, a recently developed
difference contact network analysis is employed to explain mutation-specific
allosteric effects. Our results suggest that comparing multiple conformational
ensembles generated under various mutational conditions is a powerful
tool to gain novel insights into enzymatic functions that are difficult
to obtain through examining a single system such as the wild-type.
Our approach is easy to extend for other systems. The results can
also be utilized to facilitate the design of potent therapeutics targeting
CypA.