Simulating the Serpin Latency Transition at Atomic Resolution

Abstract

Protease inhibition by serpins requires a massive conformational transition from an active, metastable state to an inactive, stable state. Similar reactions can also occur in the absence of proteases, and these latency transitions take hours, making their time scales many orders of magnitude larger than are currently accessible using conventional molecular dynamics simulations. Using a path integral based variational framework termed the Dominant Reaction pathways (DRP) method, we have successfully simulated the latency transition for several serpins in all atom detail using a physics based force field. The DRP method can clearly distinguish serpins which spontaneously perform the latency transition from those that do not. Additionally, the DRP simulations successfully reproduce the effects of mutations on the rate of the latency transition. For the serpin plasminogen activator inhibitor 1 (PAI-1) we find a long lived intermediate state along the active to latent pathway. This state shares several features that characterize a so called pre-latent state that has been detected experimentally, including partial insertion of the reactive center loop into beta-sheet A and removal of strand one from sheet C, and we propose that our intermediate represents the pre-latent state. Analysis of the energetics of the transition identifies a small subset of residues that provide the bulk of the energy change during the transition, and these residues include many known sites of disease associated mutations. Docking a known PAI-1 inhibitor to our pre-latent state identifies a pocket that it shares with the latent structure and which may provide a target site for computational drug screening. Comparison of the latency transitions in different serpins reveals how sequence variation has modulated conformational plasticity in this family of unusually labile proteins. The DRP method should prove applicable to conformational changes in other large proteins.