Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes

Protein Engineering, Design and Selection

Volumn 17, Issue 5, 2004, Pages 463-472

  Livesay, Dennis R ^a,c   Subramaniam, Shankar ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c CALIFORNIA STATE POLYTECHNIC UNIVERSITY   (United States)

Author keywords

Antibody antigen complex; Antibody hapten complex; Immunoglobulin superfamily; Molecular recognition

Indexed keywords

ANTIBODY; ANTIGEN; ARGININE; HAPTEN; MUTANT PROTEIN; TYROSINE;

ANTIGEN ANTIBODY COMPLEX; ANTIGEN BINDING; ANTIGEN SPECIFICITY; ARTICLE; ELECTRICITY; HUMAN; MOLECULAR RECOGNITION; NONHUMAN; PHYLOGENY; PKA; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; ANTIBODIES; COMPUTATIONAL BIOLOGY; HAPTENS; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN BINDING; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 4644327096     PISSN: 17410126     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/gzh058     Document Type: Article

References (31)

1. Alegre, M.L., Collins, A.M., Pulito, V.L., Brosius, R.A., Olson, W.C., Zivin, R.A., Knowlew, R., Thislethwaite, J.R., Jolliffe, L.K. and Bluestone, J.A. (1992) J. Immunol., 148, 3461-3468.
2. Almagro, J.C. (2004) J. Mol. Recognit. 17, 132-143.
3. Antosiewicz, J., McCammon, J.A. and Gilson, M.K. (1994). J. Mol. Biol., 238, 415-436.
4. Bernstein, F.C., Koetzle, T.F., Williams, E.J.B., Meyer, E.F.J., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
5. Brooks, R.B., Burccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M. (1983)J. Comput. Chem. 4, 187-217.
6. Chacko, S., Silverton, E.W., Smith-Gill, S., Cohen, G. and Davies, D. (1995) J. Mol. Biol., 245, 261-274.
7. Chothia, C. and Lesk, A.M. (1987) J. Mol. Biol., 196, 901-917.
8. Collis, A.V., Brouwer, A.P. and Martin, A.C. (2003) J. Mol. Biol., 325, 337-354.
9. Davies, D.R. and Melzger, H.A. (1983) Annu. Rev. Immunol., 1, 87-117.
10. Gibas, C.J. and Subramaniam, S. (1996) Biophys J., 71, 138-147.
11. Gibas, C.J. and Subramaniam, S. (1997) Biochemistry, 36, 15599-15614.
12. Gibas, C.J., Jambeck, P. and Subramaniam, S. (2000) Methods, 20, 292-309.
13. Gilson, M.K. (1993) Proteins: Struct. Fund. Genet., 15, 266-282.
14. Ioerger, T.R., Du, C. and Linthicum, D.S. (1999) Mol. Immunol., 36, 373-386.
15. Jorgensen, W.L. and Tirado-Rives, J. (1988) J. Am. Chem. Soc., 110, 1657-1666.
16. Knossow, M., Daniels, R.S., Douglas, A.R., Skehel, J.J. and Wiley, D.E. (1984) Nature, 311, 678-680.
17. Livesay, D., Linthicum, S. and Subramaniam, S. (1999) Mol. Immunol., 36, 397-410.
18. Livesay, D.R., Jambeck, P., Rojnuckarin, A. and Subramaniam, S. (2003) Biochemistry, 42, 3464-3473.
19. MacCallum, R.M., Martin, A.C. and Thornton, J.M. (1996) J. Mol. Biol., 262, 732-45.
20. Madura, J.D. et al. (1995) Comput. Phys. Commun., 91, 57-95.
21. Martin, A.R. (1996) Proteins, 25, 130-133.
22. Padlan, E.A. (1994) Mol. Immunol., 31, 169-217.
23. Pellequer, J.L., Chen, S., Roberts, V.A., Tainer, J.A. and Getzoff, E.D. (1999) J. Mol. Recognit., 12, 267-275.
24. Poljak, R.J., Amzel, L.M., Chen, B.L., Phizackerley, R.P. and Saul, F. (1973) Proc. Natl Acad. Sci. USA, 70, 3305-3310.
25. Ramirez-Benitez, M.C. and Almagro, J.C. (2001) Proteins, 45, 199-206.
26. Shindyalov, I.N. and Bourne, P.E. (1998) Protein Eng., 11, 739-747.
27. Shrake, A. and Rupley, J.A. (1957)J. Mol. Biol., 79, 351-371.
28. Slagle, S.P., Kozack, R.E. and Subramaniam, S. (1994) J. Biomol. Struct. Dyn. 12, 439-456.
29. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Nucleic Acids Res., 22, 4673-4680.
30. Vargas-Madrazo, E., Lara-Ochoa,F. and Almagro J.C. (1995) J. Mol. Biol., 254, 497-504.
31. Wallace, A.C, Laskowski, R.A. and Thornton, J.M. (1995) Protein Eng., 8, 127-134.