ABSTRACT
Cytochrome P450, the ubiquitous metalloenzyme involved in detoxification of foreign components, has remained one of the most popular systems for substrate-recognition process. However, despite being known for its high substrate specificity, the mechanistic basis of substrate-binding by archetypal system cytochrome P450cam has remained at odds with the contrasting reports of multiple diverse crystallographic structures of its substrate-free form. Here we address this issue by elucidating the probability of mutual dynamical transition to the other crystallographic pose of cytochrome P450cam and vice versa via unbiased all-atom computer simulation. A robust Markov state model (MSM), constructed using adaptively sampled 84 microsecond-long Molecular dynamics simulation trajectories, maps the broad and heterogenous P450cam conformational landscape into five key sub-states. In particular, the MSM identifies an intermediate-assisted dynamic equilibrium between a pair of conformations of P450cam, in which the substrate-recognition sites remain ‘closed’ and ‘open’ respectively. However, the estimate of a significantly high stationary population of closed conformation, coupled with faster rate of open → closed transition than its reverse process, dictates that the net conformational equilibrium would be swayed in favour of ‘closed’ conformation. Together, the investigation quantitatively infers that while a potential substrate of cytochrome P450cam would in principle explore a diverse array of conformations of substrate-free protein, it would mostly encounter a ‘closed’ or solvent-occluded conformation and hence would follow an induced-fit based recognition process. Overall, the work reconciles multiple precedent crystallographic, spectroscopic investigations and establishes how a statistical elucidation of conformational heterogeneity in protein would provide crucial insights in the mechanism of potential substrate-recognition process.
STATEMENT OF SIGNIFICANCE Conformational heterogeneity plays an important role in defining the structural and functional dynamics of the enzymes. While the static three-dimensional crystallographic structures of enzymes solved in different conditions and/or environments are crucial to provide the conformational sub-states of enzymes, these are not sufficient to understand the kinetics and thermodynamics of these sub-states and their role in substrate recognition process. Cytochrome P450cam, the archtypal metalloenzyme, presents such a complex scenario due to prevalent reports of contrasting crystallographic structures of its substrate-free form. This work quantifies the conformational heterogeneity of substrate-free P450cam by exploring the possibility of mutual transition among the crystallographic poses at an atomic resolution and in the process elucidates its possible substrate-recognition mechanism.
Competing Interest Statement
The authors have declared no competing interest.
