Average core structures and variability measures for protein families: Application to the immunoglobulins

Journal of Molecular Biology

Volumn 251, Issue 1, 1995, Pages 161-175

  Gerstein, Mark ^a   Altman, Russ B ^b  

^a Fairchild ^*  (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Alignment; Classification; Statistical analysis; Structural; Structure motif; Substructures

Indexed keywords

IMMUNOGLOBULIN;

AMINO ACID SEQUENCE; ARTICLE; LIBRARY; METHODOLOGY; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN STRUCTURE; ROTATION; STATISTICAL ANALYSIS; VARIANCE;

EID: 0029091249     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1995.0423     Document Type: Article

References (78)

1. Altman, R. & Gerstein, M. (1994). Finding an average core structure: application to the globins. Proc. Second Int. Conf. Intel! Sys. Mol. Biol., pp. 19-27, AAAI Press, Menlo Park, CA.
2. Altmann, S. L. (1986). Rotations, Quaternions and Double Groups, Oxford University Press, New York.
3. Amit, A. G., Mariuzza, R. A., Phillips, S. E. V. & Poljak, R. J. (1986). Three dimensional structure of an antigen-antibody complex at 2.8 A resolution. Science, 233, 747-753.
4. Arevalo, J. H., Stura, E. A., Taussig, M. J. & Wilson, I. A. (1993). Three-dimensional structure of an anti-steroid Fab and progesterone-Fab complex. J. Mol. Biol. 231, 103-118.
5. Baldwin, E. P., Hajiseyedjavadi, O., Baase, W. A. & Matthews, B. W. (1993). The role of backbone flexibility in accomodation of variants that repack the core of T4 lysozyme. Science, 262, 1715-1718.
6. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer EF., Jr, 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.
7. Bork, P., Holm, L. & Sander, C. (1994). The immunoglobulin fold: structural classification, sequence patterns and common core. J. Mol. Biol. 242, 309-320.
8. Bowie, J. U., Luthy R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
9. Bryant, S. H. & Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16, 92-112.
10. Chothia, C. (1992). Proteins, 1000 families for the molecular biologist. Nature, 357, 543-544.
11. Chothia, C. & Finkelstein, AV. (1990). The classification and origins of protein folding patterns. Annu. Rev. Biochem. 59, 1007-1039.
12. Chothia, C. & Lesk, A. M. (1986). The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
13. Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of the immunoglobulins. J. Mol. Biol. 196, 901-917.
14. Chothia, C., Novotny J., Bruccoleri, R. & Karplus, M. (1985). Domain association in immunoglobulin molecules: the packing of variable domains. J. Mol. Biol. 186, 651-663.
15. Chothia, C., Boswell, D. R. & Lesk, A. M. (1988). The outline structure of the T-cell aP-receptor. EMBO J. 7, 3745-3755.
16. 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 the immunoglobulin hypervariable regions.Nature, 342, 877-883.
17. Colman, P. M., Tulip, W. R., Varghese, J. N., Baker, A. T. & Tuloch, P. A. (1987). NC41 Complex structure determination. Nature, 326, 358-363.
18. Diamond, R. D. (1992). On the multiple simultaneous superposition of molecular structures by rigid-body transformations. Protein Sci. 1, 1279-1287.
19. Epp, O., Latham, E., Schiffer, M., Huber, R. & Palm, W. (1975). The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0 A resolution. Biochemistry, 14, 4943-4952.
20. Eriksson, A. E., Baase, W. A., Zhang, X. J., Heinz, D. W., Blaber, M., Baldwin, E. P. & Matthews, B. W. (1992). Response of a protein structure to cavity creating mutations and its relation to the hydrophobic effect. Science, 255, 178-183.
21. Felsenstein, J. (1989). PHYLIP (phylogeny inference package version 3.2). Cladistics, 5, 164-166.
22. Felsenstein, J. (1993). PHYLIP (phylogeny inference package) version 3.5c. Department of Genetics, University of Washington, Seattle.
23. Finkelstein, A. V. & Reva, B. A. (1993). A search for the most stable folds of protein chains. Nature, 351, 497-500.
24. Gerber, P. R. & Muller, K. (1987). Superimposing several sets of atomic coordinates. Acta Crystallog. sect. A, 43, 426-428.
25. Gerstein, M. & Chothia, C. H. (1991). Analysis of protein loop closure: two types of hinges produce one motion in lactate dehydrogenase. J. Mol. Biol. 220, 133-149.
26. Gerstein, M., Lesk, A. M., Baker, E. N., Anderson, B., Norris, G. & Chothia, C. (1993). Domain closure in lactoferrin: two hinges produce a see-saw motion between alternative close-packed interfaces. J. Mol. Biol. 234, 357-372.
27. Gerstein, M., Lesk, A. M. & Chothia, C. (1994). Structural mechanisms for domain movements. Biochemistry, 33, 6739-6749.
28. Goldstein, H. (1980). Classical Mechanics, Addison-Wesley New York.
29. Gribskov, M., Luthy R. & Eisenberg, D. (1990). Profile analysis. Methods Enzymol. 183, 146-159.
30. Harpaz, Y. & Chothia, C. (1994). Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains. J. Mol. Biol. 238, 528-539.
31. Herron, J. N., He, X., Mason, M. L., Voss, E. W. & Edmundson, A. B. (1989). Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2.4-pentandiol. Proteins: Struct. Funct. Genet. 5, 271-280.
32. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-128.
33. Holm, L., Ouzounis, C., Sander, C., Tuparev, G. & Vriend, G. (1993). A database of protein structure families with common folding motifs. Protein Sci. 1, 1691-1698.
34. Johnson, M. S., Sali, A. & Blundell, T. L. (1990). Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol. 183, 670-691.
35. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-89.
36. Kabat, E. A., Wu, T. T., Bilofsky H., Reid-Milner. M. & PerryH. (1983). Sequences of Proteins of Immunological Interest. National Institutes of Health, Washington, DC.
37. Kearsley S. K. (1990). An algorithm for the simultaneous superposition of a structural series. J. Comp. Chem. 11, 1187-1192.
38. Krogh, A., Brown, M., Mian, I. S., Sjolander, K. & Haussler D. (1994). Hidden Markov models in computational biology: applications to protein modelling. J. Mol. Biol. 235, 1501-1531.
39. Lesk, A. M. (1991). Protein Architecture: A Practical Approach. IRL Press, Oxford.
40. Lesk, A. M. & Chothia, C. H. (1980). How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 136, 225-270.
41. Lesk, A. M. and Chothia, C. (1982). Evolution of proteins formed by P-sheets, II. The core of the immunoglobulin domains. J. Mol. Biol. 160, 325-342.
42. Lesk, A. M. & Chothia, C. (1984). Mechanisms of domain closure in proteins. J. Mol. Biol. 174, 175-191.
43. Levitt, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107.
44. Levitt, M. & Chothia, C. (1976). Structural patterns in globular proteins. Nature, 261, 552-558.
45. Madej, T. & Mossing, M. C. (1994). Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principles. J. Mol. Biol. 233, 480-487.
46. Marquart, M., Deisenhofer, J., Huber, R. & Palm, W. (1980). Crystallographic refinement and atomic models of the intact immunoglobulin molecule KOL and its antigen-binding fragment at 3.0 A and 1.9 A resolution. J. Mol. Biol. 141, 369-391.
47. McLachlan, A. D. (1984). How alike are the shapes of two random chains? Biopolymers, 23, 1325-1331.
48. Murzin, A., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
49. Orengo, C. A. (1994). Classification of protein folds. Curr. Opin. Struct. Biol. 4, 429-440.
50. Orengo, C. A., Flores, T. P., Taylor, W. R. & Thornton, J. M. (1993). Identifying and classifying protein fold families. Protein Eng. 6, 485-500.
51. Orengo, C. A., Jones, D. T. & Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature, 372, 631-634.
52. Overington, J., Donnelly, D., Johnson, M. S., Sali, A. & Blundell, T. L. (1992). Environment-specific amino acid substitution tables: tertiary templates and pre-dition of protein folds. Protein Sci. 1, 216-226.
53. Padlan, E. A., Silverton, E. W., Sheriff, S., Cohen, G. H., Smith-Gill, G. S. & Davies, D. R. (1989). Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. Proc. Natl Acad. Sci. USA, 86, 5938-5942.
54. Pascarella, S. & Argos, P. (1992). A databank merging related protein structures and sequences. Protein Eng. 5, 121-137.
55. Ponder, J. W. & Richards, F. M. (1987). Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.
56. Remington, S. J. & Matthews, B. W. (1980). A systematic approach to the comparison of protein structures. J. Mol. Biol. 140, 77-99.
57. Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34, 167-334.
58. Sali, A. & Blundell, T. L. (1990). The definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212, 403-428.
59. Sander, C. & Schneider, R. (1991). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet. 9, 56-68.
60. Satow, Y., Cohen, G. H., Padlan, E. A. & Davies, D. R. (1987). Phosphocholine binding immunoglobulin Fab McPC603: an X-ray diffraction study at 2.7 A. J. Mol. Biol. 190, 593-604.
61. Schneider, T. D. & Stephens, R. M. (1991). Sequence logos: a new way to display consensus sequences. Nucl. Acids Res. 18, 6097-6100.
62. Schneider, T. D., Stormo, G. D., Gold, L. & Ehrenfeucht, A. (1986). Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188, 415-431.
63. Schulze-Gahmen, U., Rini, J. M., Arevalo, J., Stura, E. A., Kenten, J. H. & Wilson, I. A. (1988). Preliminary crystallographic data, primary sequence, and binding data for an anti-peptide Fab and its complex with a synthetic peptide from influenza virus hemagglutinin. J. Biol. Chem. 263, 17100-17105.
64. Shapiro, A., Botha, J. D., Pastore, A. & Lesk, A. M. (1992). A method for the multiple superposition of structures. Acta Crystallog. sect. A, 48, 11-14.
65. Shenkin, P. S., Erman, B. & Mastrandrea, L. D. (1991). Information-theoretical entropy as a measure of sequence variability. Proteins: Struct. Funct. Genet. 11, 297-313.
66. 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.
67. Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force: an approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-884.
68. Stanfield, R. L., Fieser, T. M., Lerner, R. A. & Wilson, I. A. (1990). Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A. Science, 248, 712-719.
69. Strong, R. K., Campbell, R., Rose, D. R., Petsko, G. A., Sharon, J. & Margolies, M. N. (1991). Threedimensional structure of murine anti-p-azophenyl-arsonate Fab 36-71: 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten. Biochemistry, 30, 3739-3748.
70. Subbiah, S. & Harrison, S. C. (1989). A method for multiple sequence alignment with gaps. J. Mol. Biol. 209, 539-548.
71. Subbiah, S., Laurents, D. V. & Levitt, M. (1993). Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr. Biol. 3, 141-148.
72. Suh, S. W., Bhat, T. N., Navia, M. A., Cohen, G. H., Rao, D. N., Rudikoff, S. & Davies, D. R. (1986). The galactan-binding immunoglobulin Fab J539. An X-ray diffraction study at 2.6 A resolution. Proteins: Struct. Funct. Genet. 1, 74-80.
73. Suzuki, M., Gerstein, M. & Yagi, N. (1994). The stereochemical basis for DNA recognition by Zn fingers. Nucl. Acid. Res. 22, 3397-3405.
74. Suzuki, M., Yagi, N. & Gerstein, M. (1995). DNA-recognition and superstructure-formation by helix-turn-helix proteins. Protein Eng. 4, In the press.
75. Swindells, M. B. (1995). A procedure for the automatic determination of hydrophobic cores in protein structures. Protein Sci. 4, 93-102.
76. Taylor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
77. Williams, A. F. & Barclay A. N. (1988). The immunoglobulin superfamily domains for surface recognition. Annu. Rev. Immunol. 6, 381-405.
78. Yee, D. P. & Dill, K. A. (1993). Families and the structural relatedness among globular proteins. Protein Sci. 2, 884-899.