title: Molecular dynamics and docking simulation of a natural variant of Activated Protein C with impaired protease activity: implications for integrin-mediated antiseptic function.
abstract: Activated Protein C (APC) is a multifunctional serine protease, primarily known for its anticoagulant function in the coagulation system. Several studies have already elucidated its role in counteracting apoptosis and inflammation in cells, while significant effort is still ongoing for defining its involvement in sepsis. Earlier literature has shown that the antiseptic function of APC is mediated by its binding to leukocyte integrins, which is due to the presence of the integrin binding motif Arg-Gly-Asp at the N-terminus of the APC catalytic chain. Many natural mutants have been identified in patients with Protein C deficiency diagnosis including a variant of specificity pocket (Gly216Asp). In this work, we present a molecular model of the complex of APC with αVβ3 integrin obtained by protein-protein docking approach. A computational analysis of this variant is hereby presented, based on molecular dynamics and docking simulations, aiming at investigating the effects of the Gly216Asp mutation on the protein conformation and inferring its functional implications. Our study shows that such mutation is likely to impair the protease activity while preserving the overall protein fold. Moreover, superposition of the integrin binding motifs in wild-type and mutant forms suggests that the interaction with integrin can still occur and thus the mutant is likely to retain its antiseptic function related to the neutrophyl integrin binding. Therapeutic applications could result in this APC mutant which retains antiseptic function without anticoagulant side effects.
authors.affiliation: a Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche , 20090 Segrate , Italy.
authors.forename: Pasqualina
authors.initials: P
authors.lastname: D'Ursi
authors.forename: Alessandro
authors.initials: A
authors.lastname: Orro
authors.forename: Giulia
authors.initials: G
authors.lastname: Morra
authors.forename: Marco
authors.initials: M
authors.lastname: Moscatelli
authors.forename: Gabriele
authors.initials: G
authors.lastname: Trombetti
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
authors.forename: Ermanna
authors.initials: E
authors.lastname: Rovida
mesh_terms: D000891:Anti-Infective Agents, Local / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D006801:Humans; D039302:Integrin alphaVbeta3 / Q000737:chemistry* / Q000378:metabolism; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense; D010447:Peptide Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011486:Protein C / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018046:Protein C Inhibitor / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017434:Protein Structure, Tertiary
chemical_list: D000891:Anti-Infective Agents, Local; D039302:Integrin alphaVbeta3; D011486:Protein C; D018046:Protein C Inhibitor; D010447:Peptide Hydrolases
keywords: Activated Protein C (APC); integrin; molecular docking; molecular dynamics; sepsis