Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction

Journal of Molecular Biology

Volumn 279, Issue 5, 1998, Pages 1193-1210

  Oliva, Baldomero ^a,b   Bates, Paul A ^b   Querol, Enrique ^a   Avilés, Francesc X ^a   Sternberg, Michael J E ^b  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Analysis; Antibody structure; Bioinformatics; Combining site; Protein modelling

Indexed keywords

IMMUNOGLOBULIN HEAVY CHAIN;

ALGORITHM; ANTIBODY STRUCTURE; ARTICLE; COMPLEMENTARITY DETERMINING REGION; CONSENSUS SEQUENCE; DATA BASE; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

EID: 0032568959     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1847     Document Type: Article

References (35)

1. Al-Lazikani B., Lesk A.M., Chothia C. Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273:1997;927-948
2. Barton G.J., Sternberg M.J.E. Flexible protein sequence patterns a sensitive method to detect weak structural similarities. J. Mol. Biol. 212:1990;389-402
3. Bernstein F.C., Koetzle T.F., Williams G., Meyer D.J., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542
4. Bruccoleri R.E., Haber E., Novotny J. Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature. 335:1988;564-568
5. Chothia C., Lesk A.M. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196:1987;901-918
6. Chothia C., Lesk A.M., Levitt M., Amit A.G., Mariuzza R.A., Phillips S.E., Poljak R.J. The predicted structure of immunoglobulin D1. 3 and its comparison with the crystal structure. Science. 233:1986;755-758
7. Chothia C., Lesk A.M., Tramontano A., Levitt M., Smith-Gill S.J., Air G., Sheriff S., Padlan E.A., Davies D., Tulip W.R., Colman P.M., Spinelli S., Alzari P.M., Poljak R.J. Conformations of immunoglobulin hypervariable regions. Nature. 342:1989;877-883
8. H segments. J. Mol. Biol. 227:1992;799-817
9. Donate L.E., Rufino S.D., Canard L.H.J., Blundell T.L. Conformational analysis and clustering of short and medium loops connecting regular secondary structures a database for modeling and prediction. Protein Sci. 5:1996;2600-2616
10. Everitt B. Cluster Analysis. 1974;Heineman Educational Books Ltd, London. chapt. 3
11. Fidelis K., Stern P.S., Bacon D., Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7:1994;953-960
12. Gribskov M., McLachlan A.D., Eisenberg D. Profile analysis detection of distantly related proteins. Proc. Natl Acad. Sci. USA. 84:1987;4355-4358
13. Havel T.F., Wüthrich K. An evaluation of the combined use of nuclear magnetic resonance and distance geomety for the determination of protein conformation in solution. J. Mol. Biol. 182:1985;281-294
14. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA. 89:1992;10915-10919
15. Jones P.T., Dear P.H., Foote J., Neuberger M.S., Winter G. Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature. 321:1986;522-525
16. Kabat E.A., Wu E.T., Perry H.M., Gottesman K.S., Foeller C. Sequences of Proteins of Immunological Interest. 1991;US Department of Health and Human Services NIH, Bethesda, MD
17. Kwasigroch J.M., Chomilier J., Mornon J.P. A global taxonomy of loops in globular proteins. J. Mol. Biol. 259:1996;855-872
18. Martin A.C.R., Thornton J.M. Structural families in loops of homologous proteins automatic classification, modelling and application to antibodies. J. Mol. Biol. 263:1996;800-815
19. Martin A.C.R., Cheetham J.C., Rees A.R. Modeling antibody hypervariable loops a combined algorithm. Proc. Natl Acad. Sci. USA. 86:1989;9268-9272
20. Morea V., Tramontano A., Rustici M., Chothia C., Lesk A.M. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J. Mol. Biol. 275:1998;269-294
21. Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:1970;443-453
22. Oliva B., Bates P.A., Querol E., Avilés F.X., Sternberg M.J.E. An automatic classification of the structure of protein loops. J. Mol. Biol. 266:1997;814-830
23. Pascual V., Capra J.D. Human immunoglobulin heavy chain variable region genes organisation, polymorphism, and expression. Advan. Immunol. 49:1991;1-74
24. Rees A.R., Staunton D., Webster D.M., Searle S.J., Henry A.H., Pedersen J.T. Antibody design beyond the natural limits. Trends Biotechmol. 12:1994;199-206
25. Rees A.R., Searle S.J., Henry A.H., Whitelegg N., Pedersen J. Antibody combining sites structure and prediction. Sternberg M.J.E. Protein Structure Prediction: A Practical Approach. 1996;141-172 Oxford University Press, Oxford
26. Ring C.S., Kneller D.G., Langridge R., Cohen F.E. Taxonomy and conformational analysis of loops in proteins. J. Mol. Biol. 224:1992;685-699
27. Rufino S.D., Donate L.E., Canard L.H.J., Blundell T.L. Predicting the conformational class of short and medium size loops connecting regular secondary structures application to comparative modelling. J. Mol. Biol. 267:1997;1-16
28. Shenkin P.S., Yarmush D.L., Fine R.M., WanG H., Levinthal C. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers. 26:1998;2053-2058
29. Shirai H., Kidera A., Nakamura H. Structural classification of H3 in antibodies. FEBS Letters. 399:1996;1-8
30. Tomlinson I.M., Cox J.P.L., Gherardi E., Lesk A.M., Chothis C. The structural repertoire of the human Vk domain. EMBO J. 14:1995;4628-4638
31. Tonegawa S. Somatic generation of antibody diversity. Nature. 302:1983;575-581
32. Tramontano A., Chothia C., Lesk A.M. Structural determinants of the conformations of medium-sized loops in proteins. Proteins: Struct. Funct. Genet. 6:1990;382-394
33. van Vlijmen H.W.T., Karplus M. PDB-based protein loop prediction parameters for selection and methods for optimization. J. Mol. Biol. 267:1997;975-1001
34. Wilmot C.M., Thornton J.M. β-Turns and their distorsions a proposed new nomenclature. Protein Eng. 3:1990;479-493
35. Wintjens R.T., Rooman M.J., Wodak S.J. Automatic clasification of αα-turn motifs in proteins. J. Mol. Biol. 255:1996;235-253