Unraveling Allosteric Mechanisms of Enzymatic Catalysis with an Evolutionary Analysis of Residue–Residue Contact Dynamical Changes

The evolution of protein conformational dynamics contains important information about protein function and regulation. Here, we describe an approach to dynamical-evolution analysis based on multiple microsecond molecular dynamics simulations and residue–residue contact analysis. We illustrate our approach by comparing three human cyclophilin isoforms, cyclophilin A, D, and E, which belong to a family of enzymes catalyzing peptidyl-prolyl cis–trans isomerization. Our results reveal that despite distinct overall equilibrium conformations between cyclophilins under substrate-free conditions, functional dynamical changes resembling substrate-binding and catalytic processes tend to be conserved. Key residues displaying either concerted or specific dynamical changes among isoforms during the reactions are identified, which delineate two distinct allosteric pathways for cyclophilin function consistent with recent nuclear magnetic resonance experiments. A sequence-based coevolution analysis is also employed for further understanding dynamical consequences. Our results collectively provide a framework where both common and specific functional mechanisms of a protein family can be elucidated.