Application of genetic semihomology algorithm to theoretical studies on various protein families

Acta Biochimica Polonica

Volumn 48, Issue 1, 2001, Pages 21-33

  Leluk, Jacek ^a   Hanus Lorenz, Beata ^a   Sikorski, Aleksander F ^a  

^a UNIVERSITY OF WROC AW   (Poland)

Author keywords

Cryptic mutations; Genetic semihomology; Multiple alignment; Sequence consensus

Indexed keywords

AMINO ACID; SPECTRIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; CODON; COMPUTER PROGRAM; DATA BASE; ERYTHROCYTE; HUMAN; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; CODON; DATABASES; ERYTHROCYTES; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; SPECTRIN;

EID: 0035224375     PISSN: 0001527X     EISSN: None     Source Type: Journal    
DOI: 10.18388/abp.2001_5109     Document Type: Article

References (51)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Apweiler, R., Gateau, A., Contrino, S., Martin, M.J., Junker, V., O'Donovan, C., Lang, F., Mitaritonna, N., Kappus, S. & Bairoch, A. (1997) Protein sequence annotation in the genome era: The annotation concept of SWISS-PROT+TREMBL. ISMB-97; in Proceedings 5th International Conference on Intelligent Systems for Molecular Biology, pp. 33-43, AAAI Press, Menlo Park.
3. Baek, J.M., Song, J.C., Choi, Y.D. & Kim, S.I. (1994) Nucleotide sequence homology of cDNAs encoding soybean Bowman-Birk type proteinase inhibitor and its isoinhibitors. Biosci. Biotechnol Biochem. 58, 843-846.
4. Bailey, T.M. & Elkan, C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning J. 21, 51-83.
5. Bailey, T.M. & Gribskov, M (1997) Score distributions for simultaneous matching to multiple motifs. J. Comput. Biol. 4, 45-59.
6. Bailey, T.M. & Gribskov, M. (1998a) Methods and statistics for combining motif match scores, J. Comput. Biol. 5, 211-221.
7. Bailey, T.M. & Gribskov, M. (1998b) Combining evidence using p-values: Application to sequence homology searches. Bioinformatics 14, 48-54.
8. Bairoch, A. & Apweiler, R. (1997) The SWISS-PROT protein sequence database: Its relevance to human molecular medical research. J. Mol. Med. 75, 312-316.
9. Bairoch, A. & Apweiler, R. (1999) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 27, 49-54.
10. Bairoch, A. (1997) Proteome databases; in Proteome Research: New Frontiers in Functional Genomics (Wilkins, M.R., Williams, K.L, Appel, R.D., Hochstrasser, D.H., eds.) pp. 93-132, Springer Verlag, Heidelberg.
11. Bucher, P. & Bairoch, A. (1994) A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. ISMB-94; in Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology (Altman, R., Brutlag, D., Karp, P., Lathrop, R. & Searls, D., eds.) pp. 53-61, AAAIPress, Menlo Park.
12. Chen, X., Qian, Y., Chi, C., Gan, K., Zhang, M. & Chang-Qing, C. (1992) Chemical synthesis, molecular cloning, and expression of the gene coding for the Trichosanthes trypsin inhibitor - a squash family inhibitor. J. Biochem. 112, 45-51.
13. Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16, 10881-10890.
14. Dayhoff, M.O. & Eck, R.V. (1968) Atlas of Protein Sequence and Structure (Dayhoff, M.O. & Eck, R.V., eds.) vol. 3, p. 33, Silver Spring, MD.
15. Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. (1979) Atlas of Protein Sequence and Structure (Dayhoff, M.O., ed.) vol. 5, Suppl. 3, p. 345, Washington, DC.
16. George, D.G., Barker, W.C. & Hunt, L.T. (1990) Mutation data matrix and its uses. Methods Enzymol. 183, 333-351.
17. Gish, W. & States, D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet. 3, 266-272.
18. Grundy, W.N., Bailey, T.M. & Elkan, C.P. (1997) ParaMeme: A parallel implementation and a Web interface for a DNA and protein motif discovery tool. CABIOS 12, 303-310.
19. Hakateyama, T., Hiraoka, M. & Funatsu, G. (1991) Amino acid sequence of the two smallest trypsin inhibitors from sponge gourd seeds. Agric. Biol. Chem. 10, 2641-2642.
20. Haldar, U.C., Saha, S.K., Beavis, R.C. & Sinha, N.K. (1996) Trypsin inhibitors from ridged gourd (Luffa acutangula Linn.) seeds: Purification, properties, and amino acid sequences. J. Protein Chem. 15 177-184.
21. Hamato, N., Koshiba, T., Pham, T., Tatsumi, Y., Nakamura, D., Takano, R., Hayashi, K., Hong, Y. & Hara, S. (1995) Trypsin and elastase inhibitors from bitter gourd (Momordica charantia Linn.) seeds: Purification, amino acid sequences, and inhibitory activities of four new inhibitors. J. Biochem. 117, 432-437.
22. Hayashi, K., Takehisa, T., Hamato, N., Takano, R., Hara, S., Miyata, T. & Kato, H. (1994) Inhibition of serine proteinases of the blood coagulation system by squash family protease inhibitors. J. Biochem. 116, 1013-1018.
23. Heitz, A., Chiche, L., Le-Nguyen, D. & Castro, B. (1989) 1H 2D NMR and distance geometry study of the folding of Ecbalium elaterium trypsin inhibitor, a member of the squash inhibitor family. Biochemistry 28, 2392-2398.
24. Hofmann, K., Bucher, P., Falquet, L. & Bairoch, A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res. 27, 215-219.
25. Joubert, F.J. (1984) Trypsin inhibitors from Momordica repens seeds. Phytochemistry 23, 1401-1406.
26. Junier, T. & Pagni, M. (2000) Dotlet: Diagonal plots in a Web browser. Bioinformatics 16, 178-179.
27. Lee, C. & Lin, J. (1995) Amino acid sequences of trypsin inhibitors from the melon Cucumis melo. J. Biochem. 118, 18-22.
28. Leluk, J. (1998) A new algorithm for analysis of the homology in protein primary structure. Computers Chem. 22, 123-131.
29. Leluk, J. (2000a) A non-statistical approach to protein mutational variability. Biosystems 56, 83-93.
30. Leluk, J. (2000b) Regularities in mutational variability in selected protein families and the Markovian model of amino acid replacement. Computers Chem. 24, 659-672.
31. Leluk, J. (2000c) Serine proteinase inhibitor family in squash seeds: Mutational variability mechanism and correlation. Cell. Mol. Biol. Lett. 5, 91-106.
32. Ling, M.-H., Qi, H. & Chi, C. (1993) Protein, cDNA and genomic DNA sequences of the towel gourd trypsin inhibitor. J. Biol. Chem. 268, 810-814.
33. Matsuo, M., Hamato, N., Takano, R., Kamei-Hayashi, K., Yasuda-Kamatani, Y., Nomoto, K. & Hara, S. (1992) Trypsin inhibitors from bottle gourd (Lagenaria leucantha Rusby var. Depressa Makino) seeds. Purification and amino acid sequences. Biochim. Biophys. Acta 1120, 187-192.
34. McGurl, B., Mukherjee, S., Kahn, M. & Ryan, C.A. (1995) Characterization of two proteinase inhibitor (ATI) cDNAs from alfalfa leaves (Medicago sativa var. Vernema): The expression of ATI genes in response to wounding and soil microorganisms. Plant Mol. Biol. 27, 995-1001.
35. Morgenstern, B., Dress, A. & Werner, T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. U.S.A. 93, 12098-12103.
36. Morgenstern, B. (1999) DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211-218.
37. Nishino, J., Takano, R., Kamei-Hayashi, K., Minakata, H., Nomoto, K. & Hara, S. (1992) Amino-acid sequencers of trypsin inhibitors from oriental pickling melon (Cucumis melo L. var. Conomon Makino) seeds. Biosci. Biotech. Biochem. 56, 1241-1246.
38. Odani, S. & Ikenaka, T. (1978) Studies on soybean trypsin inhibitors, XII. Linear sequences of two soybean double-headed trypsin inhibitors, D-II and E-I. J. Biochem. 83, 737-745.
39. Otlewski, J., Whatley, H., Polanowski, A. & Wilusz, T. (1987) Amino-acid sequences of trypsin inhibitors from watermelon (Citrullus vulgaris) and red bryony (Bryonia dioica). Biol. Chem. Hoppe-Seyler 368, 1505-1507.
40. Pearson, W.R. & Lipman, D.J. (1988) Improved tools for biological sequence analysis, Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448.
41. Pearson, W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183, 63-98.
42. Sahr, K.E., Laurila, P., Kotula, L., Scarpa, A.L., Coupal, L., Leto, T.L., Linnenbach, A.J., Winkelmann, J.C., Speicher, D.W., Marchesi, V.T., Curtis, P.J. & Forget, B.G. (1990) The complete cDNA and polypeptide sequences of human erythroid alpha-spectrin. J. Biol. Chem. 265, 4434-4443.
43. Scott, M.J., Huckaby, C.S., Kato, I., Kohr, W., Laskowski, M., Jr., Tsai, M.-J. & O'Malley, B.W. (1987) Ovoinhibitor introns specify functional domains as in the related and linked ovomucoid gene. J. Biol. Chem. 262, 5899-5907.
44. Speicher, D.W. & Marchesi, V.T. (1984) Erythrocyte spectrin is comprised of many homologous triple helical segments. Nature 311, 177-180.
45. Stachowiak, D., Polanowski, A., Bieniarz, G. & Wilusz, T. (1996) Isolation and amino-acid sequence of two inhibitors of serine proteinases, members of the squash inhibitor family, from Echinocystis lobata seeds. Acta Biochim. Polon. 43, 507-514.
46. Tatusova, T.A. & Madden, T.A (1999) BLAST 2 SEQUENCES - a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174, 247-250.
47. Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
48. Tomii, K. & Kanehisa, M. (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Engng 9, 27-36.
49. Wasenius, V-M., Saraste, M., Salven, P., Eramaa, M., Holm, L. & Lehto, V.-P. (1989) Primary structure of the brain α-spectrin, J. Cell Biol. 108, 79-93.
50. Wieczorek, M., Otlewski, J., Cook, J., Parks, K., Leluk, J., Wilimowska-Pelc, A., Polanowski, A., Wilusz, T. & Laskowski, M., Jr. (1985) The squash inhibitor family of serine proteinase inhibitors. Amino acid sequences and association equilibrium constants of inhibitors from squash, summer squash, zucchini, and cucumber seeds. Biochem. Biophys. Res. Commun. 126, 646-652.
51. Yan, Y., Winograd, E., Viel, A., Cronin, T., Harrison, S.C. & Branton, D. (1993) Crystal structure of the repetitive segments of spectrin. Science, 262, 2027-2030.