title: Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase.
abstract: Understanding the differences between murine (m) and human (h) proteinase 3 (PR3) and neutrophil elastase (NE) is crucial for the interpretation of in vivo studies of inflammatory processes. We built structural models of mPR3 and mNE and analyzed their surface properties. We performed molecular dynamics (MD) simulations on several enzyme-peptide complexes to investigate their interaction patterns. The analysis of trajectories confirms that murine and human complexes have different interaction patterns with peptidic substrates. We provide a map of the binding sites of the murine proteases and suggest sequence motifs that we predict to be specific for mPR3 or mNE.
authors.affiliation: Computational Biology Unit, Bergen Center for Computational Science, BCCS, University of Bergen, Thormohlensgt 55, N-5008, Bergen, Norway.
authors.forename: Eric
authors.initials: E
authors.lastname: Hajjar
authors.forename: Brice
authors.initials: B
authors.lastname: Korkmaz
authors.forename: Nathalie
authors.initials: N
authors.lastname: Reuter
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D006801:Humans; D019272:Leukocyte Elastase / Q000737:chemistry* / Q000378:metabolism; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D053146:Myeloblastin / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity; D013499:Surface Properties
chemical_list: D019272:Leukocyte Elastase; D053146:Myeloblastin