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Use of deuterium labelling in NMR studies of antibody combining site structure

Published online by Cambridge University Press:  17 March 2009

Jacob Anglister
Jacob Anglister
Affiliation:
Department of Polymer Research, The Weizmann Institute of Science, Rehovot 76100, Israel
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Extract

Antibody molecules secreted by B-lymphocytes play a central role in the immune defense systems of higher organisms. The major function of the antibody molecule is to bind specifically to foreign molecules (antigens) and to effect their inactivation and/or removal. Antibody molecules exist in millions of different forms, each with a unique amino acid sequence and combining site structure. Collectively called immunoglobulins (abbreviated as Ig), they form one of the major classes of proteins present in the blood, constituting 20% of the total plasma protein by weight.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 23 , Issue 2 , May 1990 , pp. 175 - 203
Copyright
Copyright © Cambridge University Press 1990

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References

REFERENCES

Ada, G. (1989). Prospects for a vaccine against HIV. Nature 339, 331–332.CrossRefGoogle Scholar
Albrand, J. P., Birdsall, B., Feeney, J., Roberts, G. C. K. & Burgen, A. S. V. (1979). The use of transferred nuclear Overhauser effects in the study of the conformations of small molecules bound to proteins. Int. J. Biolog. Macromolecules 1, 37–41.CrossRefGoogle Scholar
Alzari, P. M., Lascombe, M.-B. & Poljak, R. J. (1988). Three-dimensional structure of antibodies. Ann. Rev. Immunol. 6, 555–580.CrossRefGoogle ScholarPubMed
Amit, A. G., Mariuzza, R. A., Phillips, S. E. V. & Poljak, R. J. (1986). The three-dimensional structure of an antigen-antibody complex at 2.8 Å resolution. Science 223, 747–753.CrossRefGoogle Scholar
Amzel, L. M. & Poljak, R. J. (1979). Three-dimensional structure of immunoglobulins. Ann. Rev. Biochem. 48, 961–967.CrossRefGoogle ScholarPubMed
Anglister, J., Frey, T. & McConnell, H. M. (1984 a). Magnetic resonance of a monoclonal anti-spin-label antibody. Biochemistry 23, 1138–1142.CrossRefGoogle Scholar
Anglister, J., Frey, T. & McConnell, H. M. (1984 b). Distances of tyrosine residues from a spin-label hapten in the combining site of specific monoclonal antibody. Biochemistry 23, 5372–5375.CrossRefGoogle ScholarPubMed
Anglister, J., Frey, T. & McConnell, H. M. (1985). NMR technique for assessing contributions of heavy and light chains to an antibody combining site. Nature 315, 65–67.CrossRefGoogle Scholar
Anglister, J., Bond, M. W., Frey, T., Leahy, D., Levitt, M., McConnell, H. M., Rule, S. G., Tomasello, J. & Whittaker, M. (1987). contribution of tryptophan residues to the combining site of a monoclonal anti dinitrophenyl spin-label-antibody. Biochemistry 26, 6058–6064.CrossRefGoogle Scholar
Anglister, J., Jacob, C., Assulin, O., Ast, G., Pinker, R. & Arnon, R. (1988). NMR study of the complexes between a synthetic peptide derived from the B subunit of cholera toxin and three monoclonal antibodies against it. Biochemistry 27, 717–724.CrossRefGoogle Scholar
Anglister, J., Levy, R. & Scherf, T. (1989). Interactions of antibody aromatic residues with a peptide of cholera toxin observed by two-dimensional transferred nuclear Overhauser effect difference spectroscopy. Biochemistry 28, 3360–3365.CrossRefGoogle ScholarPubMed
Anglister, J. & Zilber, B. Antibodies against a peptide of cholera toxin differing in cross-reactivity with the toxin differ in their specific interactions with the peptide as observed by 1H NMR spectroscopy. (in press.).Google Scholar
Arnon, R. (1986). Synthetic peptides as the basis for future vaccines. Trends Biochem. Sci. 11, 521–524.CrossRefGoogle Scholar
Balakrishnan, K., Hsu, F. J., Hafeman, D. G. & McConnell, H. M. (1982). Monoclonal antibodies to a nitroxide lipid hapten. Biochimica et Biophysica Acta 721, 30–38.CrossRefGoogle ScholarPubMed
Bax, A., Griffey, R. H. & Hawkins, B. L. (1983). Sensitivity-enhanced correlation of 15N and 1H chemical shifts in natural-abundance samples via multiple quantum coherence. J. Am. Chem. Soc. 105, 7188–7190.CrossRefGoogle Scholar
Bird, R. E., Hardman, K. D., Jacobson, J. W., Johnson, S., Kaufman, B. M., Lee, S.-M., Lee, T., Pope, S. H., Riordan, G. S. & Whitlow, M. (1988). Single-chain antigen-binding proteins. Science 242, 423–426.CrossRefGoogle ScholarPubMed
Bothner-By, A. A. & Gassend, R. (1972). Binding of small molecules to proteins. Ann. N. Y. Acad. Sci. 222, 668–676.CrossRefGoogle Scholar
Boulianne, L. G., Hozumi, N. & Shulman, M. J. (1984). Production of functional chimaeric mouse/human antibody. Nature 312, 643–646.CrossRefGoogle ScholarPubMed
Bruccoleri, R. E., Haber, E. & Novotny, J. (1988). Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 335, 564–568.CrossRefGoogle ScholarPubMed
Campbell, I. D., Dobson, C. M. & Williams, R. J. P. (1975). Assignment of the 1H n.m.r. spectra of proteins. Proc. R. Soc. Land. A 345, 23–40.Google Scholar
Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901–917.CrossRefGoogle ScholarPubMed
Chothia, C., Lesk, A. M., Levitt, M., Amit, A. G., Mariuzza, R. A., Phillips, S. E. V. & Poljak, R. J. (1986). The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science 233, 755–758.CrossRefGoogle ScholarPubMed
Clore, G. M. & Gronenborn, A. M. (1982). Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J. magn. Reson. 48, 402–417.Google Scholar
Clore, G. M. & Gronenborn, A. M. (1983). Theory of the time dependent transferred nuclear Overhauser effect: Applications to structural analysis of ligand-protein complexes in solution. J. magn. Reson. 53, 423–442.Google Scholar
Clore, G. M., Gronenborn, A. M. & McLaughlin, L. W. (1984). Structure of the ribotrinucleoside diphosphate codon UpUpC bound to tRNAphe from yeast. A time-dependent transferred nuclear Overhauser enhancement study. J. Mol. Biol. 174, 163–173.CrossRefGoogle ScholarPubMed
Clore, G. M., Gronenborn, A. M., Carlson, G. & Meyer, E. F. (1986). Stereochemistry of binding of the tetrapeptide Acetyl-Pro-Ala-Pro-Tyr-NH2 to porcine pancreatic elastase. Combined use of two-dimensional transferred nuclear Overhauser enhancement measurements, restrained molecular dynamics, X-ray crystallography and molecular modelling. J. Mol. Biol. 190, 259–267.CrossRefGoogle ScholarPubMed
Colman, P. M., Layer, W. G., Varghese, J. N., Baker, A. T., Tulloch, P. A., Air, G. M. & Webster, R. G. (1987). Three-dimensional structure of a complex of antibody with influenza virus neuraminidase. Nature 326, 358–363.CrossRefGoogle ScholarPubMed
Davies, D. R. & Metzger, H. (1983). Structural basis of antibody function. Ann. Rev. Immunol. 1, 87–117.CrossRefGoogle ScholarPubMed
Deverson, E., Berek, C., Taussig, M. & Feinstein, A. (1987). Monoclonal BALB/c anti-progesterone antibodies use family IX variable region heavy chain genes. Eur. J. Immunol. 17, 9–13.CrossRefGoogle ScholarPubMed
Dower, S. K. & Dwek, R. A. (1979). An antibody binding site: a combined magnetic resonance and crystallographic approach. In Biological Applications of Magnetic Resonance (ed. Shulman, R. G.). 271–303, New York: Academic Press.CrossRefGoogle Scholar
Dower, S. K., Wain-Hobson, S., Gettins, P., Givol, D., Roland, W., Jackson, C., Perkins, S. J., Sunderland, C. A., Sutton, B. J., Wright, C. E. & Dwek, R. A. (1977). The combining site of the dinitrophenyl-binding immunoglobulin A myeloma protein MOPC 315. Biochemical J. 165, 207–225.CrossRefGoogle ScholarPubMed
Dwek, R. A., Knott, J. C. A., Marsh, D., McLaughlin, A. C., Press, E. M., Price, N. C. & White, A. I. (1975). Structural studies on the combining site of the myeloma protein MOPC 315. Eur. J. Biochem. 53, 25–39.CrossRefGoogle Scholar
Dwek, R. A., Wain-Hobson, S., Dower, S., Gettins, P., Sutton, B., Perkins, S. J. & Givol, D. (1977). Structure of an antibody combining site by magnetic resonance. Nature 266, 31–37.CrossRefGoogle ScholarPubMed
Dyson, J. H., Lerner, R. A. & Wright, P. E. (1988). The physical basis for induction of protein-reactive antipeptide antibodies. Ann. Rev. Biophys. Biophys. Chem. 17, 305–324.CrossRefGoogle ScholarPubMed
Eisen, H. N., Simms, E. S. & Potter, M. (1968). Mouse myeloma proteins with antihapten antibody activity. The protein produced by plasma cell tumor MOPC-315. Biochemistry 7, 4126.CrossRefGoogle Scholar
Fesik, S. W. & Zuiderweg, E. R. P. (1989). An approach for studying the active site of enzyme/inhibitor complexes using deuterated ligands and 2D NOE difference spectroscopy. J. Amer. Chem. Soc. (In the Press.)CrossRefGoogle Scholar
Franek, F. & Nezlin, R. S. (1963). Recovery of antibody combining activity by interaction of different peptide chains isolated from purified horse antitoxins. Folia Microbiologica 8, 128–130.CrossRefGoogle ScholarPubMed
Frey, T., Anglister, J. & McConnell, H. M. (1984). Nonaromatic amino acids in the combining site region of a monoclonal anti-spin-label antibody. Biochemistry 23, 6470–6473.CrossRefGoogle ScholarPubMed
Frey, T., Anglister, J. & McConnell, H. M. (1988). Line-shape analysis of NMR difference spectra of an anti-spin-label antibody. Biochemistry 27, 5161–5165.CrossRefGoogle ScholarPubMed
Griffey, H. R. & Redfield, A. G. (1987). Proton-detected heteronuclear edited and correlated nuclear magnetic resonance and nuclear Overhauser effect in solution. Quarterly Reviews of Biophysics 19, 51–82.CrossRefGoogle ScholarPubMed
Gronenborn, A. M., Clore, G. M. & Jeffery, J. (1984 a). An unusual conformation of NAD+ bound to sorbitol dehydrogenase? A time-dependent transferred nuclear Overhauser effect study. J. Mol. Biol. 172, 559–572.CrossRefGoogle ScholarPubMed
Gronenborn, A. M., Clore, G. M., Hobbs, L. & Jeffery, J. (1984 b). Glucose-6-phosphate dehydrogenase. A transferred nuclear Overhauser enhancement study of NADP+ conformations in enzyme-coenzyme binary complexes. Eur.J. Biochem. 145, 365–371.CrossRefGoogle ScholarPubMed
Gronenborn, A. M., Clore, M. G., McLaughlin, L. W., Graeser, E., Lorber, B. & Giege, R. (1984 c). Yeast tRNAAsp: codon and wobble codon-anticodon interactions. A transferred nuclear Overhauser enhancement study. Eur. J. Biochem. 145, 359–364.CrossRefGoogle ScholarPubMed
Hayashi, F., Endo, S., Arata, Y., Shimizu, A. & Kyogoku, Y. (1989). Photo-CIDNP studies of Bence Jones proteins, immunoglobulins, and their proteolytic fragments. Biochemistry 28, 3976–3981.CrossRefGoogle ScholarPubMed
Hochman, J., Inbar, D. & Givol, D. (1973). An active antibody fragment (Fv) composed of the variable portions of heavy and light chains. Biochemistry 12, 1130–1135.CrossRefGoogle ScholarPubMed
Houghton, A. N. (1988). Building a better monoclonal antibody. Immunology Today 9, 265–267.CrossRefGoogle ScholarPubMed
Jacob, C. O., Sela, M. & Arnon, R. (1983). Antibodies against synthetic peptides of the B subunit of cholera toxin: Crossreaction and neutralization of the toxin. Proc. Natl. Acad. Sci. USA 80, 7611–7615.CrossRefGoogle Scholar
Jacob, C. O., Sela, M., Pines, M., Hurwitz, S. & Arnon, R. (1984). Both cholera toxin-induced adenylate cyclase activation and cholera toxin biological activity are inhibited by antibodies against related synthetic peptides. Proc. Natl. Acad. Sci. USA 81, 7893–7896.CrossRefGoogle ScholarPubMed
James, T. L. & Cohn, M. (1974). The role of the lysyl residue at the active site of creatine kinase. Nuclear Overhauser effect studies. J. Biol. Chem. 249, 2599–2604.CrossRefGoogle ScholarPubMed
Jones, P. T., Dear, P. H., Jefferson, F., Neuberger, S. M. & Winter, G. (1986). Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature 321, 522–525.CrossRefGoogle Scholar
Kato, K., Nishimura, Y., Waelchli, M. & Arata, Y. (1989). Proton nuclear magnetic resonance study of a selectively deuterated mouse monoclonal antibody: Use of two-dimensional homonuclear Hartmann-Hahn spectroscopy. J. Biochem. (In the Press.)CrossRefGoogle Scholar
Köhler, G. & Milstein, C. (1975). Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 256, 495–498.CrossRefGoogle ScholarPubMed
Leahy, D. J., Rule, G. S., Whittaker, M. M. & McConnell, H. M. (1988). Sequences of 12 monoclonal anti-dinitrophenyl spin-label antibodies for NMR studies. Proc. Natl. Acad. Sci. USA 85, 3661–3665.CrossRefGoogle ScholarPubMed
Levy, R., Assulin, O., Scherf, T., Levitt, M. & Anglister, J. (1989). Probing antibody diversity by 2D NMR: comparison of amino acid sequences, predicted structures and observed antibody-antigen interactions in complexes of two antipeptide antibodies. Biochemistry 28, 7168–7175CrossRefGoogle ScholarPubMed
Little, J. R. & Eisen, H. N. (1967). Evidence for tryptophan in the active sites of antibodies to polynitrobenzenes. Biochemistry 6, 3119–3125.CrossRefGoogle ScholarPubMed
Marion, D., Driscoll, P. C., Kay, L. E., Wingfield, P. T., Bax, A., Gronenborn, A. M. & Clore, G. M. (1989). Overcoming the overlap problem in the assignment of 1H NMR spectra of large proteins by use of three-dimensional heteronuclear 1H-15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: Application to interleukin 1β. Biochemistry 28, 6150–6156.CrossRefGoogle Scholar
Meek, K., Jeske, D., Slaoui, M., Leo, O., Urbain, J. & Capra, D. (1984). Complete amino acid sequence of heavy chain variable regions derived from two monoclonal anti-ρ-azophenylarsonate antibodies of Balb/c mice expressing the major cross-reactive idiotype of the A/J strain. J. Exp. Med. 160, 1070–1086.CrossRefGoogle Scholar
Metzger, H. & Mannik, M. (1964). Recombination of antibody polypeptide chains in the presence of antigen. J. Exp. Med. 120, 765–782.CrossRefGoogle ScholarPubMed
Moynet, D., MacLean, J. S., Ng, K., Anctil, D. & Gibson, M. D. (1985). Polymorphism of κ variable region (Vκ- 1) genes in inbred mice: relationship to the Igk-Ef2 serum light chain marker. Eur. J. Immunol. 134, 3455–3460.CrossRefGoogle Scholar
Noggle, J. H. & Schirmer, R. E. (1971). The Nuclear Overhauser Effect: Chemical Applications. New York: Academic Press.Google Scholar
Padlan, E. A., Davies, D. R., Pecht, I., Givol, D. & Wright, C. (1976). Model-building studies of antigen-binding sites: The hapten-binding site of MOPC-315. Cold Spring Harbor Symposium on Quantitative Biology XLI, 627–637.Google Scholar
Palker, T. J., Clark, M. E., Langlois, A. J., Matthews, T. J., Weinhold, K. J., Randall, R. R., Bolognesi, D. P. & Haynes, B. F. (1988). Type-specific neutralization of the human immunodeficiency virus with antibodies to env-encoded synthetic peptides. Proc. Natl. Acad. Sci. USA 85, 1932–1936.CrossRefGoogle ScholarPubMed
De La Paz, P., Sutton, B. J., Darsley, M. J. & Rees, A. R. (1986). Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope. Embo J. 3, 415–425.CrossRefGoogle Scholar
Ramakrishnan, C. & Ramachandran, G. N. (1965). Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909.CrossRefGoogle ScholarPubMed
Redfield, A. G. (1983). Stimulated echo NMR spectra and their use for heteronuclear two-dimensional shift correlation. Chem. Phys. Lett. 96, 537–540.CrossRefGoogle Scholar
Rees, A. R. & De La Paz, P. (1986). Investigating antibody specificity using computer graphics and protein engineering. Trends Biochem. Sci. 11, 144–148.CrossRefGoogle Scholar
Regenmortel, Van. M. H. V. (1987). Antigenic cross-reactivity between proteins and peptides: new insights and applications. Trends Biochem. Sci. 12, 237–240.CrossRefGoogle Scholar
Regenmortel Van, M. H. V. (1989). Structural and functional approaches to the study of protein antigenicity. Immunology Today 10, 266–272.CrossRefGoogle Scholar
Roberts, S., Cheetham, J. C. & Rees, A. R. (1987). Generation of an antibody with enhanced affinity and specificity for its antigen by protein engineering. Nature 328, 731–734.CrossRefGoogle ScholarPubMed
Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smith-Gill, S. J., Finzel, B. C. & Davies, D. R. (1987). Three-dimensional structure of an antibody-antigen complex. Proc. Natl. Acad. Sci. USA 84, 8075–8079.CrossRefGoogle ScholarPubMed
Shokat, K. M., Leumann, C. J., Sugasawara, R. & Schultz, P. G. (1989). A new strategy for the generation of catalytic antibodies. Nature 338, 269–271.CrossRefGoogle ScholarPubMed
Skerra, A. & Plückthun, A. (1988). Assembly of a functional immunoglobulin Fv fragment in Escherichia coli. Science 240, 1038–1041.CrossRefGoogle ScholarPubMed
Steward, M. W. & Howard, C. R. (1987). Synthetic peptides: a next generation of vaccines? Immunology Today 8, 51–58.CrossRefGoogle ScholarPubMed
Tanaka, T., Hanzawa, H., Igarashi, T. & Arata, Y. (1989). 1H NMR study of antigen-antibody interactions. 7th International Congress of Immunology, Berlin. page 6, abstract 1–36.Google Scholar
Torchia, D. A., Sparks, S. W. & Bax, A. (1989). Staphylococcal nuclease: Sequential assignments and solution structure. Biochemistry 28, 5509–5524.CrossRefGoogle ScholarPubMed
Tramontano, A., Janda, K. D. & Lerner, R. A. (1986). Catalytic Antibodies. Science 234, 1566–1573.CrossRefGoogle ScholarPubMed
Verhoeyen, M., Milstein, C. & Winter, G. (1988). Reshaping human antibodies: Grafting an antilysozyme activity. Science 239, 1534–1536.CrossRefGoogle ScholarPubMed
Wien, W. R., Morrisett, J. D. & McConnell, H. M. (1972). Spin-label-induced nuclear relaxation. Distances between bound saccharides, histidine-15, and tryptophan-123 on lysozyme in solution. Biochemistry 11, 3707–3716.CrossRefGoogle ScholarPubMed
Wu, T. T. & Kabat, A. E. (1970). An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med. 132, 211–250.CrossRefGoogle ScholarPubMed
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. New York: Wiley Publ.CrossRefGoogle Scholar
Wüthrich, K. (1989). The development of nuclear magnetic resonance spectroscopy as a technique for protein structure determination. Acc. Chem. Res. 22, 36–44.CrossRefGoogle Scholar