Investigation on the Substrate Specificity of Serine Protease Neuropsin by Molecular Dynamics Simulation and Marmoset Gene Atlas (MGA)

Serine protease neuropsin is highly expressed in the central nervous system, which regulates brain cognitive function through its proteolytic activity. Neuropsin cleaves heparan sulfate proteoglycan bound to neuregulin-1 (NRG-1) at three specific sites, liberating the ligand domain of NRG-1, which, in turn, induces activation of ErbB4 to release GABA from parvalbumin-expressing interneurons. Little, however, is known about the selective substrate-cleavage mechanism of neuropsin. We investigated the substrate specificity of neuropsin by using molecular dynamics (MD) simulations and a secreted-peptide database since neuropsin recognizes only a few-residue sequences, and such short sequences are found in multiple proteins of the human proteome. The substrate specificity and catalytic activity of neuropsin depended on multiple factors that are related to the stabilization of the transition state in the enzyme reaction. Namely, the factors are the formation of a salt bridge between neuropsin and the substrate, catalytic triad, reactive conformation, and oxyanion hole. Our MD simulation analysis showed that the SLRFKW sequence is the most favorable sequence to stabilize the transition state. The Marmoset Gene Atlas, which is a database of gene expression in the brain, showed that only a few peptides including NRG-1 have scissoring sites by neuropsin.