As
an important member of cytochrome P450 (CYP) enzymes, CYP17A1
is a dual-function monooxygenase with a critical role in the synthesis
of many human steroid hormones, making it an attractive therapeutic
target. The emerging structural information about CYP17A1 and the
growing number of inhibitors for these enzymes call for a systematic
strategy to delineate and classify mechanisms of ligand transport
through tunnels that control catalytic activity. In this work, we
applied an integrated computational strategy to different CYP17A1
systems with a panel of ligands to systematically study at the atomic
level the mechanism of ligand-binding and tunneling dynamics. Atomistic simulations and
binding free energy computations identify the dynamics of dominant
tunnels and characterize energetic properties of critical residues
responsible for ligand binding. The common transporting pathways including
S, 3, and 2c tunnels were identified in CYP17A1 binding systems, while
the 2c tunnel is a newly formed pathway upon ligand binding. We employed
and integrated several computational approaches including the analysis
of functional motions and sequence conservation, atomistic modeling
of dynamic residue interaction networks, and perturbation response
scanning analysis to dissect ligand tunneling mechanisms. The results
revealed the hinge-binding and sliding motions as main functional
modes of the tunnel dynamic, and a group of mediating residues as
key regulators of tunnel conformational dynamics and allosteric communications.
We have also examined and quantified the mutational effects on the
tunnel composition, conformational dynamics, and long-range allosteric
behavior. The results of this investigation are fully consistent with
the experimental data, providing novel rationale to the experiments
and offering valuable insights into the relationships between the
structure and function of the channel networks and a robust atomistic
model of activation mechanisms and allosteric interactions in CYP
enzymes.
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