Tendency for local repetitiveness in amino acid usages in modern proteins

Journal of Molecular Biology

Volumn 294, Issue 4, 1999, Pages 937-953

  Nishizawa, Kazuhisa ^a   Nishizawa, Manami ^a   Kim, Ki Seok ^b  

^a TEIKYO UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^b DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

Coding regions; Microsatellite; Peptide motif; Triplet repeat

Indexed keywords

BACTERIAL PROTEIN; COMPLEMENTARY DNA; ZINC FINGER PROTEIN;

ALGORITHM; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CODON; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; HUMAN; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0033544693     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3275     Document Type: Article

References (41)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment tool. J. Mol. Biol. 215:1990;403-410.
2. Bairoch A. P., Bucher P., Hofmann K. The PROSITE database, its status in 1997. Nucl. Acids Res. 25:1997;217-221.
3. Bajaj N. P., Miller C. C. Phosphorylation of neurofilament heavy-chain side-arm fragments by cyclin-dependent kinase-5 and glycogen synthase kinase-3alpha in transfected cells. J. Neurochem. 69:1997;737-743.
4. Bernardi G. D. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29:1995;445-476.
5. Bjellqvist B., Basse B., Olsen E., Celis J. E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis. 15:1994;529-539.
6. Dayhoff M. O., Schwarz R. M., Orcutt B. C. A model of evolutionary change in proteins. Atlas Protein Sequence Struct. 5:1978;345-352.
7. D'Onofrio G., Mouchirroud D., Aissani B., Gautier C., Bernardi G. Correlation between the compositional properties of human genes. Codon usage and amino acid composition of proteins. J. Mol. Evol. 32:1991;504-510.
8. Doolittle R. F. Redundancies in protein sequences. Fasman G. D. Prediction of Protein Structure and the Principles of Protein Conformation. 1989;599-623 Plenum, New York.
9. Doolittle R. F., Feng D. F., Johnsom M. S., McClure M. A. Relationships of human protein sequences to these of other organisms. Cold Spring Harbor Symp. Quant. Biol. 51:1986;447-455.
10. Fowlkes J. L., Thrailkill K. M., George-Nascimento C., Rosenberg C. K., Serra D. M. Heparin-binding, highly basic regions within the thyroglobulin type-1 repeat of insulin-like growth factor (IGF)-binding proteins (IGFBPs) -3, -5, and -6 inhibit IGFBP-4 degradation. Endocrinology. 138:1997;2280-2285.
11. Goldstein D. B., Linares A. R., Cavalli-Sforza L. L., Feldman M. W. An evaluation of genetic distances for use with microsatellite loci. Genetics. 139:1995;463-471.
12. Gu X., Li W. H. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J. Mol. Evol. 40:1995;464-473.
13. Guerin B., Bukusoglu C., Rakotomanana F., Wohlrab H. Mitochondrial phosphate transport. N-ethylmaleimide insensitivity correlates with absence of beef heart-like Cys42 from the Saccharomyces cerevisiae phosphate transport protein. J. Biol. Chem. 265:1990;19736-19741.
14. Higashi H., Suzuki-Takahashi I., Taya Y., Segawa K., Nishimura S., Kitagawa M. Differences in substrate specificity between Cdk2-cyclin A and Cdk2-cyclin E in vitro. Biochem. Biophys. Res. Commun. 216:1995;520-525.
15. Hill C. S., Packman L. C., Thomas J. O. Phosphorylation at clustered-Ser-Pro-X-Lys/Arg- motifs in sperm-specific histones H1 and H2B. EMBO J. 9:1990;805-813.
16. Ikemura T., Aota S. Global variation in G+C content along vertebrate genbome DNA. Possible correlation with chromosome band structures. J. Mol. Biol. 203:1988;1-3.
17. Iwabe N., Kuma K.-I., Miyata T. Evolution of gene families and relationship with organismal evolution: rapid divergence of tissue-specific genes in the early evolution of chordates. Mol. Biol. Evol. 13:1996;483-493.
18. Karlin S., Altschul S. F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA. 87:1990;2264-2268.
19. Kimmel M., Chakraborty R., Stivers D. N., Deka R. Dynamics of repeat polymorphisms under a forward-backward mutation model: within- and between-population variability at microsatellite loci. Genetics. 143:1996;549-555.
20. Li W.-H., Wu C.-I., Luo C.-C. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21:1984;58-71.
21. Manabe T. Electrical properties of proteins. Proteins: Separation, Purification and Characterization. 1990;Tokyo-Kagaku Dojin, Tokyo. p. 336-339.
22. Molloy S. S., Bresnahan P. A., Leppla S. H., Klimpel K. R., Thomas G. Human furin is a calcium-dependent serine endoprotease that recognizes the sequence Arg-X-X-Arg and efficiently cleaves anthrax toxin protective antigen. J. Biol. Chem. 267:1992;16396-16402.
23. Müller B., Reinhardt J., Strickland M. T. Neural Networks. 1995;Springer-Verlag, Berlin. p. 286-288.
24. Nagahama M., Ikemizu J., Misumi Y., Ikehara Y., Murakami K., Nakayama K. Evidence that differentiates between precursor cleavages at dibasic and Arg-X-Lys/Arg-Arg sites. J. Biochem. 110:1991;806-811.
25. Nei M. Molecular Evolutionary Genetics. 1987;Columbia University Press, New York. p. 19-110.
26. Nishizawa M., Nishizawa K. Biased usages of arginines and lysines in proteins are correlated with local-scale fluctuations of G+C content of DNA sequences. J. Mol. Evol. 47:1998;385-393.
27. Ohno S. Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes. J. Mol. Evol. 20:1984;313-321.
28. Ohno S. Evolution from primordial oligomeric repeats to modern coding sequences. J. Mol. Evol. 25:1987;325-329.
29. Okamoto T., Nishimoto I. Detection of G protein-activator regions in M4 subtype muscarinic, cholinergic, and alpha 2-adrenergic receptors based upon characteristics in primary structure. J. Biol. Chem. 267:1992;8342-8346.
30. Ophir R., Graur D. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene. 205:1997;191-202.
31. Patthy L. Modular exchange principles in proteins. Curr. Opin. Struct. Biol. 1:1991;351-361.
32. Piiper A., Stryjek-Kaminska D., Illenberger D., Klengel R., Schmidt J. M., Gierschik P., Zeuzem S. Synthetic peptides containing a BXBXXXB(B) motif activate phospholipase C-beta1. Biochem. J. 326:1997;669-674.
33. Poolman B., Knol J., Lolkema J. S. Kinetic analysis of lactose and proton coupling in Glu379 mutants of the lactose transport protein of Streptococcus thermophilus. J. Biol. Chem. 270:1995;12995-13003.
34. Rubenstein D. C., Amos W., Leggo J., Goodburn S., Jain S., Li S. H., Margolis R. L., Ross C. A., Ferguson-Smith M. A. Microsatellite evolution-evidence for directionality and variation in rate between species. Nature Genet. 10:1995;337-343.
35. Sueoka N. Correlation between base composition of deoxyribonucleic acid and amino acid composition of proteins. Proc. Natl Acad. Sci. USA. 47:1961;1141-1149.
36. Tautz D., Trick M., Dover G. A. Cryptic simplicity in DNA is a major source of genetic variation. Nature. 322:1986;652-656.
37. Tsonis A. A., Elsner J. B., Tsonis P. A. Periodicity in DNA coding sequences: implications in gene evolution. J. Theor. Biol. 151:1991;323-331.
38. Weber J. L., Wong C. Mutation of human short tandem repeats. Human Mol. Genet. 2:1993;1123-1128.
39. Weekes J., Ball K. L., Caudwell F. B., Hardie D. G. Specificity determinants for the AMP- activated protein kinase and its plant homologue analysed using synthetic peptides. FEBS Letters. 334:1993;335-339.
40. White S. H. Global statistics of protein sequences: Implications of the origin, evolution and prediction of structure. Annu. Rev. Biophys. Biomol. Struct. 23:1994;407-439.
41. Zhong J. M., Chen-Hwang M. C., Hwang Y. W. Switching nucleotide specificity of Ha-Ras p21 by a single amino acid substitution at aspartate 119. J. Biol. Chem. 270:1995;10002-10007.