Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations

Peptidylarginine
deiminase 2 (PAD2) is a Ca2+-dependent
enzyme that catalyzes the conversion of protein arginine residues
to citrulline. This kind of structural modification in histone molecules
may affect gene regulation, leading to effects that may trigger several
diseases, including breast cancer, which makes PAD2 an attractive
target for anticancer drug development. To design new effective inhibitors
to control activation of PAD2, improving our understanding of the
molecular mechanisms of PAD2 using up-to-date computational techniques
is essential. We have designed five different PAD2–substrate
complex systems based on varying protonation states of the active
site residues. To search the conformational space broadly, multiple
independent molecular dynamics simulations of the complexes have been
performed. In total, 50 replica simulations have been performed, each
of 1 μs, yielding a total simulation time of 50 μs. Our
findings identify that the protonation states of Cys647, Asp473, and
His471 are critical for the binding and localization of the N-α-benzoyl-l-arginine ethyl ester substrate
within the active site. A novel mechanism for enzyme activation is
proposed according to near attack conformers. This represents an important
step in understanding the mechanism of citrullination and developing
PAD2-inhibiting drugs for the treatment of breast cancer.