title: Unraveling the allosteric mechanism of serine protease inhibition by an antibody.
abstract: Recent structural studies have outlined the mechanism of protease inhibition by active site-directed antibodies. However, the molecular basis of allosteric inhibition by antibodies has been elusive. Here we report the 2.35 A resolution structure of the trypsin-like serine protease hepatocyte growth factor activator (HGFA) in complex with the allosteric antibody Ab40, a potent inhibitor of HGFA catalytic activity. The antibody binds at the periphery of the substrate binding cleft and imposes a conformational change on the entire 99-loop (chymotrypsinogen numbering). The altered conformation of the 99-loop is incompatible with substrate binding due to the partial collapse of subsite S2 and the reorganization of subsite S4. Remarkably, a single residue deletion of Ab40 abolished inhibition of HGFA activity, commensurate with the reversal of the 99-loop conformation to its "competent" state. The results define an "allosteric switch" mechanism as the basis of protease inhibition by an allosteric antibody.
authors.affiliation: Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Rajkumar
authors.initials: R
authors.lastname: Ganesan
authors.affiliation: Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA; Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Eigenbrot
authors.affiliation: Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Wei-Ching
authors.initials: WC
authors.lastname: Liang
authors.affiliation: Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Shia
authors.affiliation: Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Lipari
authors.affiliation: Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA. Electronic address: dak@gene.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: Kirchhofer
mesh_terms: D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry / Q000494:pharmacology*; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid; D057057:Serine Proteases / Q000276:immunology* / Q000378:metabolism; D015842:Serine Proteinase Inhibitors / Q000494:pharmacology*
chemical_list: D000906:Antibodies; D015842:Serine Proteinase Inhibitors; D057057:Serine Proteases