Three-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 (Kd = 5 nM), which inhibits proteolytic activity of the enzyme (K(inh) = 35(+/-3)nM), has been studied by crystallographic methods. The three-dimensional structure of the complex between the Fab fragment and a synthetic peptide, spanning residues 36 to 46 of the protease, has been determined at 2.2 A resolution, and that of the Fab in the free state has been determined at 2.6 A 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-binding site. The peptide adopts a beta hairpin-like structure in which residues P38 to P42 form a type II beta-turn conformation. An intermolecular antiparallel beta-sheet is formed between the peptide and the CDR3-H loop of the antibody; additional polar interactions occur between main-chain atoms of the peptide and hydroxyl groups from tyrosine residues protruding from CDR1-L and CDR3-H. Three water molecules, located at the antigen-antibody interface, mediate polar interactions between the 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 regions, CDR1-L and CDR3-H, upon binding the peptide. The conformation of the bound peptide, which shows no overall structural similarity to the corresponding segment in HIV-1 protease, suggests that F11.2.32 might inhibit proteolysis by distorting the native structure of the enzyme.
Lescar
J
J
Unité d'Immunologie Structurale (URA 1961 CNRS), Département d'Immunologie, Institut Pasteur, Paris, France.
Stouracova
R
R
Riottot
M M
MM
Chitarra
V
V
Brynda
J
J
Fabry
M
M
Horejsi
M
M
Sedlacek
J
J
Bentley
G A
GA
D000595:Amino Acid Sequence; D000911:Antibodies, Monoclonal / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D003198:Computer Simulation; D003429:Cross Reactions; D018360:Crystallography, X-Ray; D016333:HIV Protease; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D006825:Hybridomas; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
D000911:Antibodies, Monoclonal; C105869:Fab F11.2.32; D017320:HIV Protease Inhibitors; D007140:Immunoglobulin Fab Fragments; D016333:HIV Protease