A non-statistical approach to protein mutational variability

BioSystems

Volumn 56, Issue 2-3, 2000, Pages 83-93

  Leluk, Jacek ^a  

^a UNIVERSITY OF WROC AW   (Poland)

Author keywords

Genetic semihomology; Mutations; Protein homology; Variability

Indexed keywords

OVOMUCOID; PROTEIN; PROTEINASE INHIBITOR;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHICKEN; GENETIC VARIABILITY; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT SEED; SEQUENCE HOMOLOGY;

EID: 0034086637     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(00)00074-5     Document Type: Article

References (35)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Baek J.M., Song J.C., Choi Y.D., Kim S.I. Nucleotide sequence homology of cDNAs encoding soybean Bowman-Birk type proteinase inhibitor and its isoinhibitors. Biosci. Biotechnol. Biochem. 58:1994;843-846.
3. Catterall J.F., Stein J.P., Kristo P., Means A.R., O'Malley B.W. Primary sequence of ovomucoid messenger RNA as determined from cloned complementary DNA. J. Cell Biol. 87:1980;480-487.
4. Chen X., Qian Y., Chi C., Gan K., Zhang M., Chang-Qing C. Chemical synthesis, molecular cloning, and expression of the gene coding for the Trichosanthes trypsin inhibitor - a squash family inhibitor. J. Biochem. 112:1992;45-51.
5. Chen P., Rose J., Love R., Wei C.H., Wang B.C. Reactive sites of an anticarcinogenic Bowman-Birk proteinase inhibitor are similar to other trypsin inhibitors. J. Biol. Chem. 267:1992;1990-1994.
6. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16:1988;10881-10890.
7. Dayhoff M.O., Eck R.V. Dayhoff M.O., Eck R.V. Atlas of Protein Sequence and Structure. 3:1968;33 National Biomedical Research Foundation, Silver Spring, MD.
8. Dayhoff M.O., Schwartz R.M., Orcutt B.C. Dayhoff M.O. Atlas of Protein Sequence and Structure. 5:1979;345 National Biomedical Research Foundation, Washington, DC.
9. George D.G., Barker W.C., Hunt L.T. Mutation data matrix and its uses. Doolittle R.F. Methods in Enzymology. 183:1990;337 Academic Press, San Diego, CA.
10. Gerlinger P., Krust A., Lemeur M., Perrin F., Cochet M., Gannon F., Dupret D., Chambon P. Multiple initiation and polyadenylation sites for the chicken ovomucoid transcription unit. J. Mol. Biol. 162:1982;345-364.
11. Gish W., States D.J. Identification of protein coding regions by database similarity search. Nat. Genet. 3:1993;266-272.
12. Hakateyama T., Hiraoka M., Funatsu G. Amino acid sequence of the two smallest trypsin inhibitors from sponge gourd seeds. Agric. Biol. Chem. 10:1991;2641-2642.
13. Haldar U.C., Saha S.K., Beavis R.C., Sinha N.K. Trypsin inhibitors from ridged gourd (Luffa acutangula Linn.) seeds: purification, properties, and amino acid sequences. J. Protein Chem. 15:1996;177-184.
14. Hamato N., Koshiba T., Pham T., Tatsumi Y., Nakamura D., Takano R., Hayashi K., Hong Y., Hara S. Trypsin and elastase inhibitors from bitter gourd (Momordica charantia Linn.) seeds: purification, amino acid sequences, and inhibitory activities of four new inhibitors. J. Biochem. 117:1995;432-437.
15. Hayashi K., Takehisa T., Hamato N., Takano R., Hara S., Miyata T., Kato H. Inhibition of serine proteinases of the blood coagulation system by squash family protease inhibitors. J. Biochem. 116:1994;1013-1018.
16. Heitz A., Chiche L., Le-Nguyen D., Castro B. 1H 2D NMR and distance geometry study of the folding of Ecbalium elaterium trypsin inhibitor, a member of the squash inhibitor family. Biochemistry. 28:1989;2392-2398.
17. Joubert F.J. Trypsin inhibitors from Momordica repens seeds. Phytochemistry. 23:1984;1401-1406.
18. Lai E.C., Roop D.R., Tsai M.-J., Woo S.L.C., O'Malley B.W. Heterogeneous initiation regions for transcription of the chicken ovomucoid gene. Nucleic Acids Res. 10:1982;5553-5567.
19. Lee C., Lin J. Amino acid sequences of trypsin inhibitors from the melon Cucumis melo. J. Biochem. 118:1995;18-22.
20. Leluk J. A new algorithm for analysis of the homology in protein primary structure. Comput. Chem. 22:1998;123-131.
21. Ling M.-H., Qi H., Chi C. Protein, cDNA and genomic DNA sequences of the towel gourd trypsin inhibitor. J. Biol. Chem. 268:1993;810-814.
22. Matsuo M., Hamato N., Takano R., Kamei-Hayashi K., Yasuda-Kamatani Y., Nomoto K., Hara S. Trypsin inhibitors from bottle gourd (Lagenaria leucantha Rusby var. Depressa makino) seeds. Purification and amino acid sequences. Biochim. Biophys. Acta. 1120:1992;187-192.
23. McGurl B., Mukherjee S., Kahn M., Ryan C.A. 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. 27:1995;995-1001.
24. Nishino J., Takano R., Kamei-Hayashi K., Minakata H., Nomoto K., Hara S. Amino-acid sequencers of trypsin inhibitors from oriental pickling melon (Cucumis melo L. var. Conomon makino) seeds. Biosci. Biotechnol. Biochem. 56:1992;1241-1246.
25. Odani S., Ikenaka T. Studies on soybean trypsin inhibitors, XII. Linear sequences of two soybean double-headed trypsin inhibitors, D-II and E-I. J. Biochem. 83:1978;737-745.
26. Otlewski J., Whatley H., Polanowski A., Wilusz T. Amino-acid sequences of trypsin inhibitors from watermelon (Citrullus vulgaris) and red bryony (Bryonia dioica). Biol. Chem. Hoppe-Seyler. 368:1987;1505-1507.
27. Scott M.J., Huckaby C.S., Kato I., Kohr W., Laskowski M. Jr., Tsai M.-J., O'Malley B.W. Ovoinhibitor introns specify functional domains as in the related and linked ovomucoid gene. J. Biol. Chem. 262:1987;5899-5907.
28. Siemion I.Z. Compositional frequencies of amino acids in the proteins and the genetic code. Biosystems. 32:1994;163-170.
29. Siemion I.Z. The regularities of the changes of amino acid physico-chemical properties within the genetic code. Amino Acids. 8:1995;1-13.
30. Siemion I.Z., Stefanowicz P. Periodical changes of amino acid reactivity within genetic code. Biosystems. 27:1992;77-84.
31. Stachowiak D., Polanowski A., Bieniarz G., Wilusz T. Isolation and amino-acid sequence of two inhibitors of serine proteinases, members of the squash inhibitor family, from Echinocystis lobata seeds. Acta Biochim. Polon. 43:1996;507-514.
32. Tatusova T.A., Madden T.A. BLAST 2 SEQUENCES - a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174:1999;247-250.
33. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
34. Tomii K., Kanehisa M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9:1996;27-36.
35. Wieczorek M., Otlewski J., Cook J., Parks K., Leluk J., Wilimowska-Pelc A., Polanowski A., Wilusz T., Laskowski M. Jr. 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. 126:1985;646-652.