Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity

Abstract

Different forms of carboxypeptidase proenzymes (zymogens) are observed experimentally to show different behavior: procarboxypeptidase A (proCPA, forms proCPA1 and proCPA2) exhibit some activity against small substrates, but proCPB does not. In this work, these three zymogen forms (subtypes A1, A2 and B) are investigated by means of 15-ns molecular dynamics simulations and principal component analysis to shed light on their dynamic/conformational behaviors that may be relevant to those experimental observations. The simulations revealed that proCPA (both A1 and A2) shows different conformational behavior from proCPB: the former undergoes a major conformational change (opening and closing), and the latter exhibits only a minor conformational change (remaining closed throughout the simulation). Differences center on the interface between the globular moiety of the pro-segment and the catalytic domain. Analysis of the trajectories demonstrates the importance of hydrogen bonds and salt-bridges in stabilizing the zymogen structures and shows different hydrogen-bond patterns between proCPA and proCPB: the former shows fewer strong H-bonds formed between the globular domain and the catalytic domain. The observed difference in conformational behavior between proCPA and proCPB may explain why small substrates and inhibitors can access the active sites of proCPA1 and proCPA2 but not of proCPB.