Predicting Membrane Protein Expression in Yeast from Sequence-Derived Features

Abstract

Neurolysin is a zinc metallopeptidase involved in neuropeptide degradation and modification by cleaving a number of bioactive peptides. In vivo, neurolysin hydrolyzes the short neuropeptide neurotensin, to create inactive shorter fragments. Neurolysin is of interest as a therapeutic target since a change in neurotensin level may cause a range of disorders such as pain perception, schizophrenia, addiction, cardiovascular disorders, and Huntington and Parkinson diseases. Neurolysin has a prolate ellipsoid shape with a deep channel that runs almost the entire length of the molecule. Although other metallopeptidases show a hinge-like motion, available crystal structures of neurolysin do not reveal any significant conformational changes. Thus, elucidation of its internal dynamics and how they are affected by ligand binding can aid in further design of potent ligands that either activate or inhibit neurolysin function. For this purpose, we combine two different computational techniques, namely WExplore and Elastic Network Modeling (ENM), to examine possible ligand binding sites and their effect on large-scale motions in neurolysin. WExplore uses the weighted ensemble algorithm and generates full-atomistic conformational ensembles that can span large free energy barriers. In this study, we use WExplore to generate a network of binding sites in the neurolysin channel, and predict their relative probabilities. ENM analysis, which is a fast coarse-grained normal mode analysis that provides collective deformations of proteins, reveals the hidden hinge-like motion of neurolysin, where the two domains rotate toward each other by narrowing the channel. The differences observed during hinge-like motion in apo and ligand bound forms of neurolysin pinpoint specific binding regions that affect low-frequency motions in an allosteric manner. This combined multiscale approach helps elucidate the coupling between ligand binding, hinge motion and neurolysin catalytic activity.