Structural evidence for induced fit as a mechanism for antibody-antigen recognition.

The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined by x-ray crystallographic techniques at 2.0 A, 2.9 A, and 3.1 A resolution, respectively. The nonapeptide antigen assumes a type I beta turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the beta turn of the peptide, allowing TyrP105 to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition.

[1]  J. L. Smith,et al.  Structure of myohemerythrin in the azidomet state at 1.7/1.3 A resolution. , 1987, Journal of molecular biology.

[2]  Barry C. Finzel,et al.  The use of an imaging proportional counter in macromolecular crystallography , 1987 .

[3]  T. A. Jones,et al.  A graphics model building and refinement system for macromolecules , 1978 .

[4]  I. Mian,et al.  Structure, function and properties of antibody binding sites. , 1991, Journal of molecular biology.

[5]  R. Poljak,et al.  Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution , 1986, Science.

[6]  T. Kieber‐Emmons,et al.  Idiotypic networks and nature of molecular mimicry: an overview. , 1989, Methods in enzymology.

[7]  M. Karplus,et al.  Dynamics of ligand binding to heme proteins. , 1979, Journal of molecular biology.

[8]  Talapady N. Bhat,et al.  OMITMAP: An electron density map suitable for the examination of errors in a macromolecular model , 1984 .

[9]  R. Lerner,et al.  Principles of antibody catalysis , 1988, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  Todd O. Yeates,et al.  Versatile Rigid-Body and Group Refinement in Real Space , 1988 .

[11]  J. N. Varghese,et al.  Three-dimensional structure of a complex of antibody with influenza virus neuraminidase , 1987, Nature.

[12]  R. Bruccoleri,et al.  Protein engineering of antibody binding sites: recovery of specific activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[13]  P E Wright,et al.  Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix. , 1988, Journal of molecular biology.

[14]  G. Cohen,et al.  Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Thornton,et al.  Beta-turns and their distortions: a proposed new nomenclature. , 1990, Protein engineering.

[16]  G. Air,et al.  Three-dimensional structures of influenza virus neuraminidase-antibody complexes. , 1989, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[17]  P. Colman.  Antigen-antigen receptor interactions , 1991 .

[18]  Andrew R. Cherenson,et al.  The structure of an antigenic determinant in a protein , 1984, Cell.

[19]  I. Wilson,et al.  Anti-peptide antibodies detect steps in a protein conformational change: low-pH activation of the influenza virus hemagglutinin , 1987, The Journal of cell biology.

[20]  I. Wilson,et al.  Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution , 1981, Nature.

[21]  George M. Church,et al.  A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters , 1977 .

[22]  P. Colman,et al.  Structure of antibody-antigen complexes: implications for immune recognition. , 1988, Advances in immunology.

[23]  A. Lesk,et al.  Canonical structures for the hypervariable regions of immunoglobulins. , 1987, Journal of molecular biology.

[24]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[25]  B C Finzel,et al.  Three-dimensional structure of an antibody-antigen complex. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[26]  A. Yonath,et al.  Cryocrystallography of ribosomal particles. , 1989, Acta crystallographica. Section B, Structural science.

[27]  I. Wilson,et al.  Changes in the conformation of influenza virus hemagglutinin at the pH optimum of virus-mediated membrane fusion. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[28]  I. Wilson,et al.  Preliminary crystallographic data, primary sequence, and binding data for an anti-peptide Fab and its complex with a synthetic peptide from influenza virus hemagglutinin. , 1988, The Journal of biological chemistry.

[29]  Michael L. Connolly,et al.  Depth-buffer algorithms for molecular modelling , 1985 .

[30]  R L Stanfield,et al.  Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A. , 1992, Science.

[31]  A. Edmundson,et al.  An autoantibody to single‐stranded DNA: Comparison of the three‐dimensional structures of the unliganded fab and a deoxynucleotide–fab complex , 1991, Proteins.

[32]  H. Hope.  Cryocrystallography of biological macromolecules: a generally applicable method. , 1988, Acta crystallographica. Section B, Structural science.

[33]  A. Lesk,et al.  Conformations of immunoglobulin hypervariable regions , 1989, Nature.

[34]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[35]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[36]  P. Fitzgerald.  MERLOT, an integrated package of computer programs for the determination of crystal structures by molecular replacement , 1988 .

[37]  R. Lerner,et al.  The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn , 1985, Nature.

[38]  Y. Satow,et al.  Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. , 1985, Journal of molecular biology.

[39]  E. Padlan.  On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands , 1990, Proteins.

[40]  T. N. Bhat,et al.  Small rearrangements in structures of Fv and Fab fragments of antibody D 1.3 on antigen binding , 1990, Nature.

[41]  S. Harrison.  A point-focusing camera for single-crystal diffraction , 1968 .