Review: Proteins with repeated sequence - Structural prediction and modeling

Journal of Structural Biology

Volumn 134, Issue 2-3, 2001, Pages 132-144

  Kajava, Andrey V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Classification; Molecular modeling; Prediction; Structural bioinformatics; Tandem repeats

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; LEUCINE; PENTAPEPTIDE;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; CORRELATION ANALYSIS; CYANOBACTERIUM; MOLECULAR BIOLOGY; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; REVIEW; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); SOLENOIDEA;

EID: 0035783062     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2000.4328     Document Type: Review

References (92)

1. Andrade, M. A., Ponting, C. P., Gibson, T. J., and Bork, P. (2000) Homology-based method for identification of protein repeats using statistical significance estimates, J. Mol. Biol. 298, 521-537.
2. Bateman, A., Murzin, A. G., and Teichmann, S. A. (1998) Structure and distribution of pentapeptide repeats in bacteria. Protein Sci. 7, 1477-1480.
3. Baumann, U., Wu, S., Flaherty, K. M., and McKay, D. B. (1993) Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: A two-domain protein with a calcium binding parallel beta roll motif, EMBO J. 12, 3357-3364.
4. Bhowmick, N., Huang, J., Puett, D., Isaacs, N. W., and Lapthorn, A. J. (1996) Determination of residues important in hormone binding to the extracellular domain of the luteinizing hormone/chorionic gonadotropic receptor by site-directed mutagenesis and modeling, Mol. Endocrinol. 10, 1147-1159.
5. Black, K., Buikema, W. J., and Haselkorn, R. (1995) The hglK gene is required for localization of heterocyst-specific glycolipids in the cyanobacterium Anabaena sp. strain PCC 7120, J. Bacteriol. 177, 6440-6448.
6. Bork, P., and Doolittle, R. F. (1994) Drosophila kelch motif is derived from a common enzyme fold, J. Mol. Biol. 236, 1277-1282.
7. Borza, D. B., Tatum, F. M., and Morgan, W. T. (1996) Domain structure and conformation of histidine-proline-rich glycoprotein, Biochemistry 35, 1925-1934.
8. Brazill, D. T., Caprette, D. R., Myler, H. A., Hatton, R. D., Ammann, R. R., Lindsey, D. F., Brock, D. A., and Gomer, R. H. (2000) A protein containing a serine-rich domain with vesicle fusing properties mediates cell cycle-dependent cytosolic pH regulation, J. Biol. Chem. 275, 19231-19240.
9. Britten, R. J., and Kohne, D. E. (1968) Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms, Science 161, 529-540.
10. Buard, J., and Vergnaud, G. (1994) Complex recombination events at the hypermutable minisatellite CEB1 (D2S90), EMBO J. 13, 3203-3210.
11. Buchanan, S. G., and Gay, N. J. (1996) Structural and functional diversity in the leucine-rich repeat family of proteins, Prog. Biophys. Mol. Biol. 65, 1-44.
12. Bucher, P., Karplus, K., Moeri, N., and Hofmann, K. (1996) A flexible motif search technique based on generalized profiles, Comput. Chem. 20, 3-23.
13. Chambers, G. K., and MacAvoy, E. S. (2000) Microsatellites: Consensus and controversy, Comp. Biochem. Physiol. B Biochem. Mol. Biol. 126, 455-476.
14. Claudianos, C., and Campbell, H. D. (1995) The novel flightless-I gene brings together two gene families, actin-binding proteins related to gelsolin and leucine-rich-repeat proteins involved in Ras signal transduction, Mol. Biol. Evol. 12, 405-414.
15. Collinson, S. K., Parker, J. M., Hodges, R. S., and Kay, W. W. (1999) Structural predictions of AgfA, the insoluble fimbrial subunit of Salmonella thin aggregative fimbriae, J. Mol. Biol. 290, 741-756.
16. Conti, E., Uy, M., Leighton, L., Blobel, G., and Kuriyan, J. (1998) Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha. Cell 94, 193-204.
17. Dayring, H. E., Tramonato, A., Sprang, S. R., and Fletterick, R. J. (1986) Interactive program for visualization and modeling of proteins, nucleic acids and small molecules, J. Mol. Graph. 4, 82-87.
18. Di Francesco, V., Garnier, J., and Munson, P. J. (1996) Improving protein secondary structure prediction with aligned homologous sequences, Protein Sci. 5, 106-113.
19. 1H NMR, Biochemistry 29, 7828-7837.
20. Efimov, A. V. (1993) Standard structures in proteins, Prog. Biophys. Mol. Biol. 60, 201-239.
21. 1H-NMR studies of synthetic polypeptide models of Plasmodium falciparum circumsporozoite protein tandemly repeated sequence, Biopolymers 28, 225-246.
22. Fraser, R. D. B., and MacRae, T. P. (1973) Conformation in Fibrous Proteins and Related Synthetic Polypeptides. Academic Press, London/New York.
23. Fulop, V., and Jones, D. T. (1999) Beta propellers: Structural rigidity and functional diversity, Curr. Opin. Struct. Biol. 9, 715-721.
24. Govindarajan, A. G., and Lindow, S. E. (1988) Phospholipid requirement for expression of ice nuclei in Pseudomonas syringae and in vitro, J. Biol. Chem. 263, 9333-9338.
25. Graether, S. P., Kuiper, M. J., Gagne, S. M., Walker, V. K., Jia, Z., Sykes, B. D., and Davies, P. L. (2000) Beta-helix structure and ice-binding properties of a hyperactive antifreeze protein from an insect, Nature 406, 325-328.
26. Green, R. L., and Warren, G. J. (1985) Physical and functional repetition in bacterial ice nucleation gene, Nature 317, 645-648.
27. Groves, M. R., and Barford, D. (1999) Topological characteristics of helical repeat proteins, Curr. Opin. Struct. Biol. 9, 383-389.
28. Groves, M. R., Hanlon, N., Turowski, P., Hemmings, B. A., and Barford, D. (1999) The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs, Cell 96, 99-110.
29. Harbury, P. B., Tidor, B., and Kim, P. S. (1995) Repacking protein cores with backbone freedom: Structure prediction for coiled coils, Proc. Natl. Acad. Sci. USA 92, 8408-8412.
30. Hartman, P. G., Chapman, G. E., Moss, T., and Bradbury, E. M. (1977) Studies on the role and mode of operation of the verylysine-rich histone H1 in eukaryote chromatin. The three structural regions of the histone H1 molecule. Eur. J. Biochem. 77, 45-51.
31. Heringa, J. (1998) Detection of internal repeats: How common are they? Curr. Opin. Struct. Biol. 8, 338-345.
32. Hillig, R. C., Renault, L., Vetter, I. R., Drell, T., IV, Wittinghofer, A., and Becker, J. (1999) The crystal structure of rna1p: A new fold for a GTPase-activating protein, Mol. Cell 3, 781-791.
33. Hinman, M. B., Jones, J. A., and Lewis, R. V. (2000) Synthetic spider silk: A modular fiber, Trends Biotechnol. 18, 374-379.
34. Hodges, R. S. (1996) Boehringer Mannheim Award Lecture 1995. De novo design of alpha-helical proteins: Basic research to medical applications, Biochem. Cell Biol. 74, 133-154.
35. Huber, A. H., Nelson, W. J., and Weis, W. I. (1997) Three-dimensional structure of the armadillo repeat region of beta-catenin. Cell 90, 871-882.
36. Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985) Hypervariable 'minisatellite' regions in human DNA, Nature 314, 67-73.
37. Jiang, X., Dreano, M., Buckler, D. R., Cheng, S., Ythier, A., Wu, H., Hendrickson, W. A., and el Tayar, N. (1995) Structural predictions for the ligand-binding region of glycoprotein hormone receptors and the nature of hormone-receptor interactions, Structure 3, 1341-1353.
38. Kajava, A. V. (1991) Molecular packing in type I collagen fibrils. A model with neighbouring collagen molecules aligned in axial register, J. Mol. Biol. 218, 815-823.
39. Kajava, A. V. (1996) Modeling of a five-stranded coiled coil structure for the assembly domain of the cartilage oligomeric matrix protein, Proteins 24, 218-226.
40. Kajava, A. V. (1998) Structural diversity of leucine-rich repeat proteins, J. Mol. Biol. 277, 519-527.
41. Kajava, A. V. (1999) Dimorphism of polyglycine I: Structural models for crystal modifications, Acta Crystallogr. Sect. D 55, 436-442.
42. Kajava, A. V. (2000) α-Helical solenoid model for the human involucrin. FEBS Lett. 473, 127-131.
43. Kajava, A. V., and Lindow, S. E. (1993) A model of the three-dimensional structure of ice nucleation proteins, J. Mol. Biol. 232, 709-717.
44. Kajava, A. V., Vassart, G., and Wodak, S. J. (1995) Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats, Structure 3, 867-877.
45. Kieselbach, T., Mant, A., Robinson, C., and Schroder, W. P. (1998) Characterisation of an Arabidopsis cDNA encoding a thylakoid lumen protein related to a novel 'pentapeptide repeat' family of proteins, FEBS Lett. 428, 241-244.
46. Kobe, B., and Deisenhofer, J. (1993) Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats, Nature 366, 751-756.
47. Kobe, B., and Deisenhofer, J. (1994) The leucine-rich repeat: A versatile binding motif, Trends Biochem. Sci. 19, 415-421.
48. Kobe, B., and Deisenhofer, J. (1995) Proteins with leucine-rich repeats. Curr. Opin. Struct. Biol. 5, 409-416.
49. Kobe, B., and Kajava, A. V. (2000) When protein folding is simplified to protein coiling: The continuum of solenoid protein structures, Trends Biochem. Sci. 25, 509-515.
50. Korotkov, E. V., Korotkova, M. A., Rudenko, V. M., and Skriabin, K. G. (1999) Regions with latent periodicity in protein amino acid sequences, Mol. Biol. 33, 688-695. [Mosk Russian]
51. Kreil, D. P., and Kreil, G. (2000) Asparagine repeats are rare in mammalian proteins, Trends Biochem. Sci. 25, 270-271.
52. Kruglyak, S., Durrett, R. T., Schug, M. D., and Aquadro, C. F. (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations, Proc. Natl. Acad. Sci. USA 95, 10774-10778.
53. Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., and Wright, P. E. (1989) Three-dimensional solution structure of a single zinc finger DNA-binding domain, Science 245, 635-637.
54. Lim, V. I. (1974) Algorithms for prediction of alpha-helical and beta-structural regions in globular proteins, J. Mol. Biol. 88, 873-894.
55. Liou, Y. C., Tocilj, A., Davies, P. L., and Jia, Z. (2000) Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein, Nature 406, 322-324.
56. Litt, M., and Luty, J. A. (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene, Am. J. Hum. Genet. 44, 397-401.
57. Lucas, F., Barber, M., Wolstenholme, W. A., Geddes, A. J., Graham, G. N., and Morris, H. R. (1969) Mass-spectrometric determination of the amino acid sequences in peptides isolated from the protein silk fibroin of Bombyx mori, Biochem. J. 114, 695-702.
58. Lupas, A. (1996) Prediction and analysis of coiled-coil structures, Methods Enzymol. 266, 513-525.
59. Lupas, A. (1997) Predicting coiled-coil regions in proteins, Curr. Opin. Struct. Biol. 7, 388-393.
60. Lupas, A., Muller, S., Goldie, K., Engel, A. M., Engel, A., Baumeister, W. (1995) Model structure of the Omp alpha rod, a parallel four-stranded coiled coil from hyperthermophilic eubacterium Thermotoga maritima, J. Mol. Biol. 248, 180-189.
61. Malvar, T., Biron, R. W., Kaback, D. B., and Denis, C. L. (1992) The CCR4 protein from Saccharomyces cerevisiae contains a leucine-rich repeat region which is required for its control of ADH2 gene expression, Genetics 132, 951-962.
62. Marcotte, E. M., Pellegrini, M., Yeates, T. O., and Eisenberg, D. A. (1999) Census of protein repeats, J. Mol. Biol. 293, 151-160.
63. Marino, M., Braun, L., Cossart, P., and Ghosh, P. (1999) Structure of the lnlB leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L. monocytogenes, Mol. Cell 4, 1063-1072.
64. Mitas, M. (1997) Trinucleotide repeats associated with human disease, Nucleic Acids Res. 25, 2245-2254.
65. Montgomery, J., Ilg, T., Thompson, J. K., Kobe, B., and Handman, E. (2000) Identification and predicted structure of a leucine-rich repeat motif shared by Leishmania major proteophosphoglycan and parasite surface antigen 2, Mol. Biochem. Parasitol. 107, 289-295.
66. Moult, J., Hubbard, T., Bryant, S. H., Fidelis, K., and Pedersen, J. T. (1997) Critical assessment of methods of protein structure prediction (CASP): Round II, Proteins Suppl. 1: 2-6.
67. Murzin, A. G. (1992) Structural principles for the propeller assembly of beta-sheets: The preference for seven-fold symmetry, Proteins 14, 191-201.
68. Neer, E. J., Schmidt, C. J., Nambudripad, R., and Smith, T. F. (1994) The ancient regulatory-protein family of WD-repeat proteins, Nature 371, 297-300.
69. Nilges, M., and Brunger, A. T. (1993) Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: Comparison to the X-ray structure, Proteins 15, 133-146.
70. Perutz, M. F. (1999) Glutamine repeats and neurodegenerative diseases: Molecular aspects, Trends Biochem. Sci. 24, 58-63.
71. Petersen, T. N., Kauppinen, S., and Larsen, S. (1997) The crystal structure of rhamnogalcturonase A from Aspergillus aculeatus: A right-handed parallel beta helix, Structure 5, 533-544.
72. Price, S. R., Evans, P. R., and Nagai, K. (1998) Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA, Nature 394, 645-650.
73. Raetz, C. R., and Roderick, S. L. (1995) A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase, Science 270, 997-1000.
74. Reddy, P. S., and Housman, D. E. (1997) The complex pathology of trinucleotide repeats, Curr. Opin. Cell Biol. 9, 364-372.
75. Rost, B., Sander, C., and Schneider, R. (1994) PHD - An automatic mail server for protein secondary structure prediction, Comput. Appl. Biosci. 10, 53-60.
76. Sali, A., and Blundell, T. A. (1993) Comparative protein modeling by satisfaction of spatial restrains, J. Mol. Biol. 234, 779-815.
77. Steinert, P. M., Candi, E., Tarcsa, E., Marekov, L. N., Sette, M., Paci, M., Ciani, B., Guerrieri, P., and Melino, G. (1999) Transglutaminase crosslinking and structural studies of the human small proline rich 3 protein, Cell Death Differ. 6, 916-930.
78. Thibodeau, S. N., Bren, G., and Schaid, D. (1993) Microsatellite instability in cancer of the proximal colon, Science 260, 816-819.
79. Tormo, J., Puiggali, J., Vives, J., Fita, I., Lloveras, J., Bella, J., Aymami, J., and Subirana, J. A. (1992) Crystal structure of a helical oligopeptide model of polyglycine II and of other polyamides: Acetyl-(glycyl-β-alanyl)2-NH propyl, Biopolymers 32, 643-648.
80. Traub, W., and Steinmann, B. (1986) Structural study of a mutant type I collagen from a patient with lethal osteogenesis imperfecta containing an intramolecular disulfide bond in the triple-helical domain, FEBS Lett. 198, 213-216.
81. Urry, D. W., Luan, C. H., and Peng, S. Q. (1995) Molecular biophysics of elastin structure, function and pathology, Ciba Found. Symp. 192, 4-22.
82. Van Belkum, A., Scherer, S., van Alphen, L., and Verbrugh, H. (1998) Short-sequence DNA repeats in prokaryotic genomes, Microbiol. Mol. Biol. Rev. 62, 275-293.
83. Van Dijk, A. A., De Boef, E., Bekkers, A., Van Wijk, L. L., Van Swieten, E., Hamer, R. J., and Robillard, G. T. (1997) Structure characterization of the central repetitive domain of high molecular weight gluten proteins. II. Characterization in solution and in the dry state, Protein Sci. 6, 649-656.
84. Van Raaij, M. J., Mitraki, A., Lavigne, G., and Cusack, S. (1999) A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein, Nature 401, 935-938.
85. Venugopal, M. G., Ramshaw, J. A., Braswell, E., Zhu, D., and Brodsky, B. (1994) Electrostatic interactions in collagen-like triple-helical peptides, Biochemistry 33, 7948-7956.
86. Weber, I. T., Harrison, R. W., and Iozzo, R. V. (1996) Model structure of decorin and implications for collagen fibrillogenesis, J. Biol. Chem. 271, 31767-31770.
87. Werner, E. B., Taylor, W. R., and Holder, A. A. (1998) A Plasmodium chabaudi protein contains a repetitive region with a predicted spectrin-like structure, Mol. Biochem. Parasitol. 94, 185-196.
88. Whitby, F. G., and Phillips, G. N., Jr. (2000) Crystal structure of tropomyosin at 7 angstroms resolution, Proteins 38, 49-59.
89. Wolffe, A. P., and Guschin, D. (2000) Review: Chromatin structural features and targets that regulate transcription, J. Struct Biol. 129, 102-122.
90. Wu, H., Maciejewski, M. W., Marintchev, A., Benashski, S. E., Mullen, G. P., and King, S. M. (2000) Solution structure of a dynein motor domain associated light chain, Nat. Struct. Biol. 7, 575-579.
91. Yoder, M. D., Keen, N. T., and Jurnak, F. (1993) New domain motif: The structure of pectate lyase C, a secreted plant virulence factor, Science 260, 1503-1507.
92. Zhang, H., Seabra, M. C., and Deisenhofer, J. (2000) Crystal structure of Rab geranylgeranyltransferase at 2.0 Å resolution, Struct. Fold Des. 8, 241-251.