Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase‑1

Collagen hydrolysis, catalyzed by Zn­(II)-dependent matrix
metalloproteinases
(MMPs), is a critical physiological process. Despite previous computational
investigations into the catalytic mechanisms of MMP-mediated collagenolysis,
a significant knowledge gap in understanding remains regarding the
influence of conformational sampling and entropic contributions at
physiological temperature on enzymatic collagenolysis. In our comprehensive
multilevel computational study, employing quantum mechanics/molecular
mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge
this gap and provide valuable insights into the catalytic mechanism
of MMP-1. Specifically, we compared the full enzyme–substrate
complex in solution, clusters in solution, and gas-phase to elucidate
insights into MMP-1-catalyzed collagenolysis. Our findings reveal
significant differences in the catalytic mechanism when considering
thermal effects and the dynamic evolution of the system, contrasting
with conventional static potential energy surface QM/MM reaction path
studies. Notably, we observed a significant stabilization of the critical
tetrahedral intermediate, attributed to contributions from conformational
flexibility and entropy. Moreover, we found that protonation of the
scissile bond nitrogen occurs via proton transfer from a Zn­(II)-coordinated
hydroxide rather than from a solvent water molecule. Following C–N
bond cleavage, the C-terminus remains coordinated to the catalytic
Zn­(II), while the N-terminus forms a hydrogen bond with a solvent
water molecule. Subsequently, the release of the C-terminus is facilitated
by the coordination of a water molecule. Our study underscores the
pivotal role of protein conformational dynamics at physiological temperature
in stabilizing the transition state of the rate-limiting step and
key intermediates, compared to the corresponding reaction in solution.
These fundamental insights into the mechanism of collagen degradation
provide valuable guidance for the development of MMP-1-specific inhibitors.