A single amino acid change in the binding pocket alters specificity of an anti-integrin antibody AP7.4 as revealed by its crystal structure

Blood Cells, Molecules, and Diseases

Volumn 32, Issue 1, 2004, Pages 176-181

  Vasudevan, Sona ^a,b   Celikel, Reha ^a   Ruggeri, Zaverio M ^a   Varughese, Kottayil I ^a   Kunicki, Thomas J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Amino acid; Anti integrin antibody; Crystal structure

Indexed keywords

2 AMINO 7 PHOSPHONOHEPTANOIC ACID; AMINO ACID; AMINO ACID DERIVATIVE; BINDING PROTEIN; IMMUNOGLOBULIN F(AB) FRAGMENT; INTEGRIN; LIGAND; MONOCLONAL ANTIBODY;

ACCURACY; ALPHA CHAIN; AMINO ACID SEQUENCE; ARTICLE; CELL VOLUME; CRYSTAL STRUCTURE; DNA FLANKING REGION; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; STRUCTURE ANALYSIS;

ESCHERICHIA COLI;

EID: 0742306872     PISSN: 10799796     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bcmd.2003.04.001     Document Type: Article

References (29)

1. Hynes R.O. Integrins: versatility, modulation, and signaling in cell adhesion. Cell. 69:1992;11-25.
2. Hynes R.O. Integrins: a family of cell surface receptors. Cell. 48:1987;549-554.
3. Hemler M.E. VLA proteins in the integrin family: structures, functions, and their role on leukocytes. Annu. Rev. Immunol. 8:1990;365-400.
4. Ruoslahti E. Integrins. J. Clin. Invest. 87:1991;1-5.
5. Springer T.A. Adhesion receptors of the immune system. Nature. 346:1990;425-434.
6. Albelda S.M., Buck C.A. Integrins and other cell adhesion molecules. FASEB J. 4:1990;2868-2880.
7. Arnaout M.A. Structure and function of the leukocyte adhesion molecules CD11/CD18. Blood. 75:1990;1037-1050.
8. Ruoslahti E., Pierschbacher M.D. New perspectives in cell adhesion: RGD and integrins. Science. 238:1987;491-497.
9. Pierschbacher M.D., Ruoslahti E. Cell attachment activity of fibronectin can be duplicated by small synthetic fragments of the molecule. Nature. 309:1984;30-33.
10. Pierschbacher M.D., Ruoslahti E. Influence of stereachemistry of the sequence Arg-Gly-Asp-Xaa on binding specificity in cell adhesion. J. Biol. Chem. 262:1987;17294-17298.
11. 3 antagonists. J. Med. Chem. 37:1994;1-8.
12. Busk M., Pytela R., Sheppard D. Characterization of the integrin alpha v beta 6 as a fibronectin-binding protein. J. Biol. Chem. 267:1992;5790-5796.
13. 8. Mol. Biol. Cell. 4:1993;285. (Suppl.).
14. Kodandapani R., Veerapandian B., Kunicki T.J., Ely K.R. Crystal structure of the OPG2 Fab: an anti-receptor antibody that mimics an RGD cell adhesion site. J. Biol. Chem. 270:1995;2268-2273.
15. Kodandapani R., Veerapandian L., Ni C.-Z., Chiou C.-K., Whittal R.M., Kunicki T.J., Ely K.R. Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a β3 peptide. Biochem. Biophys. Res. Commun. 251:1998;61-66.
16. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., Warren G.L. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D. 54:1998;905-921.
17. Evans S.V. SETOR: hardware-lighted three-dimensional solid model representations of macromolecules. J. Mol. Graphics. 11:1993;134-138.
18. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., Sect. A. 46:1991;585-593.
19. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:1993;283-291.
20. E.A. Kabat, T.T. Wu, H. Bilofsky, Sequences of Immunoglobulin Chains, NIH publication National Institutes of Health, 1979, pp. 80-2008.
21. Satow Y., Cohen G.H., Padlan E.A., Davies D.R. Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A. J. Mol. Biol. 190:1986;593-604.
22. Chothia C., Lesk A.M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196:1987;901-917.
23. Vargas-Madrazo E., Paz-Garcia E. Modifications to canonical structure sequence patterns: analysis for L1 and L3. Proteins. 47:2002;250-254.
24. Shirai H., Kidera A., Nakamura H. Structural classification of CDR-H3 in antibodies. FEBS Lett. 399:1996;1-8.
25. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 28:2000;235-242.
26. Wu T.T., Johnson G., Kabat E.A. Length distribution of CDRH3 in antibodies. Proteins. 16:1993;1-7.
27. Johnson G., Wu T.T. Preferred CDRH3 lengths for antibodies with defined specificities. Int. Immunol. 10:1998;1801-1805.
28. Blobel C.P., White J.M. Structure, function and evolutionary relationship of proteins containing a disintegrin domain. Curr. Opin. Cell Biol. 4:1992;760-765.
29. 3 integrins. FEBS Lett. 391:1996;138-143.