Structural determinants in the sequences of immunoglobulin variable domain

Journal of Molecular Biology

Volumn 278, Issue 2, 1998, Pages 457-479

  Chothia, Cyrus ^a   Gelfand, Israel ^b   Kister, Alexander ^b  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

Conserved core; Deep structure; Residue classification

Indexed keywords

CD2 ANTIGEN; CD4 ANTIGEN; CD8 ANTIGEN; IMMUNOGLOBULIN;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; HYDROGEN BOND; HYDROPHOBICITY; IMMUNOGLOBULIN VARIABLE REGION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE;

EID: 0032080047     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1653     Document Type: Article

References (67)

1. Axe, D. D., Foster, N. W. & Fersht, A. R. (1996). Active barnase variants with completely random hydrophobic cores. Proc. Natl Acad. Sci. USA, 93, 5590-5594.
2. Barré, S., Greenberg, A. S., Flajnik, M. F. & Chothia, C. (1994). Structural conservation of hypervariable regions in the evolution of the immunoglobulins. Nature Struct. Biol. 1, 915-920.
3. Bashford, D., Chothia, C. & Lesk, A. M. (1987). Determinants of a protein fold: unique features of the globin amino acid sequences. J. Mol. Biol. 196, 199-216.
4. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macro-molecular structures. J. Mol. Biol. 112, 535-542.
5. Bowie, J. U. & Sauer, R. T. (1989). Identification determinants of folding and activity for a protein of unknown structure. Proc. Natl Acad. Sci. USA, 86, 2152-2156.
6. Brady, R. L., Dodson, E. J., Dodson, G. G., Lange, G., Davis, S. J., Williams, A. F. & Barclay, A. N. (1993). Crystal structure of domains 3 and 4 of rat CD4: relation to the amino-terminal domains. Science, 260, 979-983.
7. Buckle, A. M., Schreiber, G. & Fersht, A. R. (1994). Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0 Å resolution. Biochemistry, 33, 8878-8889.
8. Buckle, A. M., Cramer, P. & Fersht, A. R. (1996). Structural and energetic responses to cavity creating mutations in hydrophobic cores. Biochemistry, 35, 4298-4305.
9. Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105, 1-14.
10. Chothia, C. & Gerstein, M. (1997). How far can sequences diverge. Nature, 385, 379-380.
11. Chothia, C. & Janin, J. (1981). Relative orientation of close-packed β-pleated sheets in proteins. Proc. Natl Acad. Sci. USA, 78, 4146-4150.
12. Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-916.
13. Chothia, C., Novotny, J., Bruccoleri, R. & Karplus, M. (1985). Domain associations in immunoglobulin molecules. I. The packing of variable domains. J. Mol. Biol. 186, 651-663.
14. Chothia, C., Boswell, D. R. & Lesk, A. M. (1988). The outline structure of the T cell αβ receptor. EMBO J. 7, 3745-3755.
15. 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. (1989). Conformations of immunoglobulin hypervariable regions. Nature, 342, 877-883.
16. H segments. J. Mol. Biol. 227, 799-817.
17. Clackson, T. & Wells, J. A. (1995). A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
18. Cohen, F. E., Sternberg, M. J. E. & Taylor, W. R. (1981). Analysis of the tertiary structure of protein β-sheet sandwiches. J. Mol. Biol. 148, 253-272.
19. Cook, G. P., Tomlinson, I. M., Walter, G., Riethman, H., Carter, N. P., Buluwela, L., Winter, G. & Rabbitts, (1994). A map of the human immunoglobulin VH locus completed by analysis of the telomeric region of chromosome 14Q. Nature Genet. 7, 162-168.
20. Cunningham, B. C. & Wells, J. A. (1993). Comparison of a structural and functional epitope. J. Mol. Biol. 234, 554-563.
21. Diamond, R. D. (1992). On the multiple simultaneous superposition of molecular structures by rigid-body transformations. Protein Sci. 1, 1279-1287.
22. Fauchere, J. L. & Pliska, V. (1983). Hydrophobic parameters, π, of amino acid side-chains from the partitioning of N-acetyl amino acid amides. Eur. J. Med. Chem. 18, 369-375.
23. Frisch, C., Kolmar, H., Schmidt, A., Kleemann, G., Reinhardt, A., Pohl, I., Schneider, T. R. & Fritz, H.-J. (1996). Contribution of the intramolecular disulphide bridge to the folding stability of REI, the variable domain of a human immunoglobulin κ light chain. Folding Design, 1, 431-440.
24. Garrett, T. P. J., Wang, J., Yan, Y., Liu, J. & Harrison, S. C. (1993). Refinement and analysis of the structure of the first two domains of human CD4. J. Mol. Biol. 234, 763-778.
25. Gassner, N. C., Baase, W. A. & Matthews, B. W. (1996). A test of the jigsaw puzzle model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc. Natl Acad. Sci. USA, 93, 12155-12158.
26. Gelfand, I. M. & Kister, A. E. (1995). Analysis of the relation between the sequence and secondary and three dimensional structures of immunoglobulin molecules. Proc. Natl Acad. Sci. USA, 92, 10884-10888.
27. H domains. Proc. Natl Acad. Sci. USA, 93, 3675-3678.
28. H domains. J. Comput. Biol. In the press.
29. Gerstein, M. & Altman, R. B. (1995). Average core structures and variability measures for protein families: application to the immunoglobulins. J. Mol. Biol. 251, 161-175.
30. Guillet, V., Lapthorn, A., Hartley, R. W. & Mauguen, Y. (1993). Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar. Structure, 1, 165-177.
31. Hemmingsen, J. M., Gernert, K. M., Richardson, J. S. & Richardson, D. C. (1994). The tyrosine corner: a feature of most Greek key β-barrel proteins. Protein Sci. 3, 1927-1937.
32. Hieter, P. A., Maizel, J. V. & Leder, P. (1982). Evolution of human immunoglobulin κ J region genes. J. Biol. Chem. 257, 536-540.
33. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-128.
34. γ repertoire. J. Mol. Biol. 268, 69-77.
35. Jones, E. Y., Davis, S. J., Williams, A. F., Harlos, K. & Stuart, D. I. (1992). Crystal structure at 2.8 Å resolution of a soluble form of the cell adhesion molecule CD2. Nature, 360, 232-239.
36. Kabat, E., Wu, T., Perry, H., Gottesman, K. & Foeller, C. (1991). Sequences of Proteins of Immunological Interest. National Institutes of Health Publ. No 91-3242, 5th edit., DHHS, PHS, Natl. Inst. of Health, Bethesda, MD.
37. Karpusas, M., Baase, W. A., Matsumura, M. & Matthews, B. W. (1989). Hydrophobic packing in T4 lysozyme probed by cavity filling mutants. Proc. Natl Acad. Sci. USA, 86, 8237-8241.
38. Leahy, D. J., Axel, R. & Hendrickson, W. A. (1992). Crystal structure of a soluble form of the human T cell receptor CDS at 2.6 A. Cell, 68, 1145-1162.
39. Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
40. Lesk, A. M. & Chothia, C. (1980). How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 136, 223-268.
41. Lesk, A. M. & Chothia, C. (1982). The evolution of proteins formed by β-sheets. II. The core of the immunoglobulin domains. J. Mol. Biol. 160, 325-342.
42. Lesk, A. M. & Chothia, C. (1988). Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint. Nature, 335, 188-190.
43. Lieberman, R., Potter, M., Humphrey, W., Jr, Mushinski, E. B. & Vrana, M. (1975). Multiple individual and cross-specific idiotypes of 13 levan-binding myeloma proteins of BALB/c mice. J. Exp. Med. 142, 106-119.
44. Lim, W. A. & Sauer, R. T. (1989). Alternative packing arrangements in the hydrophobic core of λ-repressor. Nature, 339, 31-36.
45. Matsuda, F., Shin, E. K., Nagaoka, H., Matsumura, R., Haino, M., Fukita, Y., Taka-ishi, S., Imai, T., Riley, J. H., Anand, R., Soeda, E. & Honjo, T. (1993). Structure and physical map of 64 variable segments in the 3′ 0. 8-megabase region of the human immunoglobulin heavy-chain locus. Nature Genet. 3, 88-94.
46. Miller, S., Janin, J., Lesk, A. M. & Chothia, C. (1987). Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656.
47. H: consequences for thermodynamic stability and folding. J. Mol. Biol. 265, 161-172.
48. Ravetch, J. V., Siebenlist, U., Korsmeyer, S., Waldmann, T. & Leder, P. (1981). Structure of the human immunoglobulin μ locus: characterisation of embryonic and rearranged J and D genes. Cell, 27, 583-591.
49. Rennell, D., Bouvier, S. E., Hardy, L. W. & Poteete, A. R. (1991). Systematic mutation of bacteriophage T4 lysozyme. J. Mol. Biol. 222, 67-87.
50. Ryu, S. E., Kwong, P. D., Truneh, A., Porter, T. G., Arthos, J., Rosenberg, M., Dai, X. P., Xuong, N. H., Axel, R., Sweet, R. W. & Hendrickson, W. A. (1990). Crystal structure of an HIV-binding recombinant fragment of human CD4. Nature, 348, 419-426.
51. H framework regions of human and murine immunoglobulins. J. Mol. Biol. 230, 15-20.
52. Schäble, K. F. & Zachau, H. G. (1993). The variable genes of the human immunoglobulin κ locus. Biol. Chem. Hoppe-Seyler, 374, 1001-1022.
53. Schreiber, G. & Fersht, A. R. (1993). Interaction of barnase with its polypeptide inhibitor barstat studied by protein engineering. Biochemistry, 32, 5145-5150.
54. Schreiber, G. & Fersht, A. R. (1995). Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. J. Mol. Biol. 248, 478-486.
55. Shapiro, A., Botha, J. D., Pastore, A. & Lesk, A. M. (1992). A method for multiple superposition of structures. Acta Crystallog, sect. A, 48, 11-14.
56. 0: the major structural protein of peripheral nerve myelin. Neuron, 17, 435-449.
57. Shrake, A. & Rupley, J. A. (1973). Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79, 351-371.
58. Smith, D. K. & Xue, H. (1997). Sequence profiles of immunoglobulin and immunoglobulin-like domains. J. Mol. Biol. 274, 530-545.
59. Taylor, W. R. (1986). Identification of protein sequence homology by consensus template alignment. J. Mol. Biol. 188, 233-258.
60. Taylor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
61. H segments with different hypervariable loops. J. Mol. Biol. 227, 776-798.
62. κ domain. EMBO J. 14, 4628-4638.
63. Udey, J. A. & Blomberg, B. (1987). Human λ light chain locus: organisation and DNA sequences of three genomic J regions. Immunogenet. 25, 63-70.
64. Vos, A. M. de. , Ultsch, M. & Kossiakoff, A. A. (1992). Human growth hormone and extracellular domain of its receptor: crystal structure of hr complex. Science, 255, 306-312.
65. Wang, J. H., Yan, Y. W., Garrett, T. P., Liu, J. H., Rodgers, D. W., Garlick, R. L., Tarr, G. E., Husain, Y., Reinherz, E. L. & Harrison, S. C. (1990). Atomic structure of a fragment of human CD4 containing two immunoglobulin-like domains. Nature, 348, 411-418.
66. λ repertoire. J. Mol. Biol. 264, 220-232.
67. Yee, D. P. & Dill, K. A. (1993). Families and the structural relatedness among globular proteins. Protein Sci. 2, 884-899.