3-DIMENSIONAL STRUCTURE OF AN FAB-PEPTIDE COMPLEX - STRUCTURAL BASIS OF HIV-1 PROTEASE INHIBITION BY A MONOCLONAL-ANTIBODY

F11.2.32, a monoclonal antibody raised against HIV-1 protease (K-d = 5 nM), which inhibits proteolytic activity of the enzyme (K-inh = 35(+/ -3) nM), has been studied by crystallographic methods. The three-dimen sional structure of the complex between the Fab fragment and a synthet ic peptide, spanning residues 36 to 46 of the protease, has been deter mined at 2.2 Angstrom resolution, and that of the Fab in the free stat e has been determined at 2.6 Angstrom resolution. The refined model of the complex reveals ten well-ordered residues of the peptide (P36 to P45) bound in a hydrophobic cavity at the centre of the antigen-bindin g site. The peptide adopts a beta hairpin-like structure in which resi dues P38 to P42 form a type II beta-turn conformation. An intermolecul ar antiparallel beta-sheet is formed between the peptide and the CDR3- H loop of the antibody; additional polar interactions occur between ma in-chain atoms of the peptide and hydroxyl groups from tyrosine residu es protruding from CDR1-L and CDR3-H. Three water molecules, located a t the antigen-antibody interface, mediate polar interactions between t he peptide and the most buried hypervariable loops, CDR3-L and CDR1-H. A comparison between the free and complexed Fab fragments shows that significant conformational changes occur in the long hypervariable reg ions, CDR1-L and CDR3-H, upon binding the peptide. The conformation of the bound peptide, which shows no overall structural similarity to th e corresponding segment in HIV-1 protease, suggests that F11.2.32 migh t inhibit proteolysis by distorting the native structure of the enzyme . (C) 1997 Academic Press Limited.