title: Study of recombinant antibody fragments and PAI-1 complexes combining protein-protein docking and results from site-directed mutagenesis.
abstract: Elevated plasma levels of plasminogen activator inhibitor-1 (PAI-1) have been correlated with cardiovascular diseases such as myocardial infarction and venous thrombosis. PAI-1 has also been shown to play an important role in tumor development, diabetes, and obesitas. Monoclonal antibodies MA-8H9D4 and MA-56A7C10, and their single-chain variable fragments (scFv), exhibit PAI-1-neutralizing properties. In this study, a rigid-body docking approach is used to predict the binding geometry of two distinct conformations of PAI-1 (active and latent) in complex with these antibody fragments. Resulting models were initially refined by using the dead-end elimination algorithm. Different filtering criteria based on the mutagenesis studies and structural considerations were applied to select the final models. These were refined by using the slow-cooling torsion-angle dynamic annealing protocol. The docked structures reveal the respective epitopes and paratopes and their potential interactions. This study provides crucial information that is necessary for the rational development of low-molecular weight PAI-1 inhibitors.
authors.affiliation: Laboratory for Biocrystallography, Katholieke Universiteit Leuven, O & N2 Campus Gasthuisberg, Herestraat 49, B-3000 Leuven, Belgium.
authors.forename: Hector
authors.initials: H
authors.lastname: Novoa de Armas
authors.forename: Maarten
authors.initials: M
authors.lastname: Dewilde
authors.forename: Koen
authors.initials: K
authors.lastname: Verbeke
authors.forename: Marc
authors.initials: M
authors.lastname: De Maeyer
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Declerck
mesh_terms: D007128:Immunoglobulin Fragments / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D017395:Plasminogen Activator Inhibitor 1 / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D007128:Immunoglobulin Fragments; D017395:Plasminogen Activator Inhibitor 1; D011994:Recombinant Proteins