Amino acid repeat patterns in protein sequences: Their diversity and structural-functional implications

Protein Science

Volumn 9, Issue 6, 2000, Pages 1203-1209

  Katti, Mukund V ^a   Sami Subbu, R ^a   Ranjekar, Prabhakar K ^a   Gupta, Vidya S ^a  

^a NATIONAL CHEMICAL LABORATORY   (India)

Author keywords

Amino acid repeats; Database; Periodic patterns; Protein structure and function

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; TANDEM REPEAT; UNINDEXED SEQUENCE;

EID: 0033919542     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.6.1203     Document Type: Article

References (27)

1. Bairoch A, Apweiler R. 1999. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res 27:49-54.
2. Bateman A, Murzin AG, Teichmann SA. 1998. Structure and distribution of pentapeptide repeats in bacteria. Protein Sci 7:1477-1480.
3. Brodsky B. 1990. Fibrous proteins: Folding and higher order structure. In: Gierasch LM, King J. eds. Protein folding. Washington. DC: American Association for the Advancement of Science, pp 55-62.
4. Buscaglia CA, Alfonso J, Campetella O, Frasch AC. 1999. Tandem amino acid repeats from Trypanosoma crazi shed antigens increase the half-life of proteins in blood. Blood 15:2025-2032.
5. Corden JL, Patturajan M. 1997. A CTD function linking transcription to splicing. Trends Biochem Sci 22:413-416.
6. Coward E, Drablos F. 1998. Detecting periodic patterns in biological sequences. Bioinformatics 14:498-507.
7. Doolittle RF. 1989. Redundancies in protein sequences. In: Fasman GD, ed. Prediction of protein structure and the principles of protein conformation. New York: Plenum Press, pp 599-623.
8. Gerber HP, Seipel K, Georgiev O, Hofferer M, Hug M, Rusconi S, Schaffner W. 1994. Transcription activation modulated by homopolymeric glutamine and proline stretches. Science 263:808-811.
9. Goldinq GB. 1999. Simple sequence is abundant in eukaryotic proteins. Protein Sci 8:1358-1361.
10. Green H, Wang N. 1994. Codon reiteration and the evolution of proteins. Proc Natl Acad Sci USA 91:4298-4302.
11. Groves MR, Barford D. 1999. Topological characteristics of helical repeat proteins. Curr Opin Struct Biol 9:383-389.
12. Heringa J. 1998. Detection of internal repeats: How common are they? Curr Opin Struct Biol 8:338-345.
13. Heringa J, Argos P. 1993. A method to recognize distant repeats in protein sequences. Proteins 17:391-411.
14. Heringa J, Taylor WR. 1997. Three-dimensional domain duplication, swapping and stealing. Curr Opin Struct Biol 7:416-421.
15. Julien JP, Mushynski WE. 1998. Neurofilaments in health and disease. Prog Nucleic Acid Res Mol Biol 61:1-23.
16. Kajava AV, Lindow SE. 1993. A model of the three-dimensional structure of ice nucleation proteins. J Mol Biol 232:709-717.
17. Kashi Y, King D, Soller M. 1997. Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13:74-78.
18. Landschulz WH, Johnson PF, McKnight SL. 1988. The leucine zipper: A hypothetical structure common to a new class of DNA binding proteins. Science 240:1759-1764.
19. Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D. 1999. A census of protein repeats. J Mol Biol 293:151-160.
20. McLachlan AD, 1993. Multichannel Fourier analysis of patterns in protein sequences. J Phys Chem 97:3000-3006.
21. Muragaki Y, Mundlos S, Upton J, Olsen BR. 1996. Altered growth and branching patterns in synpolydactyly caused by mutations in HOXD13. Science 272:548-551.
22. Pearson CE, Sinden RR. 1998. Trinucleotide repeat DNA structures: Dynamic mutations from dynamic DNA. Curr Opin Struct Biol 8:321-330.
23. Pellegrini M, Marcotte EM, Yeates TO. 1999. A fast algorithm for genome-wide analysis of proteins with repeated sequences. Proteins 35:440-446.
24. Perutz MF. 1999. Glutamine repeats and neurodegenerative diseases: Molecular aspects. Trends Biochem Sci 24:58-63.
25. Perutz MF, Johnson T. Suzuki M, Finch JT, 1994. Glutamine repeats as polar zippers: Their possible role in inherited neurodegenerative diseases. Proc Natl Acad Sci USA 91:5355-5358.
26. Raetz CRH, Roderick SL. 1995. A left-handed parallel β helix in the structure of UDP-N-acetylglucosamine acetyltransferase. Science 270:997-1000.
27. Sicheri F, Yang DS. 1995. Ice-bindinq structure and mechanism of an antifreeze protein from winter flounder. Nature 375:427-431.