Structural conservation of a short, functional, peptide-sequence motif

Frontiers in Bioscience

Volumn 14, Issue 3, 2009, Pages 1143-1151

  Fox Erlich, Susan ^a   Schiller, Martin R ^a   Gryk, Michael R ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

Bioinformatics; Protein domains; Protein structure; Review

Indexed keywords

EUKARYOTA;

PEPTIDE;

AMINO ACID SEQUENCE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; REVIEW;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION;

EID: 63849128410     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3299     Document Type: Article

References (45)

1. C. Kosiol, L. Bofkin S. Whelan: Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome. J Biomed Inform 39, 51-61 (2006). (Pubitemid 43140719)
2. D. D. Pollock: Genomic biodiversity, phylogenetics and coevolution in proteins. Appl Bioinformatics 1, 81-92 (2002).
3. S. Whelan, P. Lio N. Goldman: Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 17, 262-272 (2001). (Pubitemid 32378749)
4. D. F. Conrad M. E. Hurles: The population genetics of structural variation. Nat Genet 39, S30-36 (2007).
5. R. Nielsen, I. Hellmann, M. Hubisz, C. Bustamante A. G. Clark: Recent and ongoing selection in the human genome. Nat Rev Genet 8, 857-868 (2007). (Pubitemid 47609088)
6. K. Kiryluk, J. Martino, A. G. Gharavi: Genetic susceptibility, HIV infection, and the kidney. Clin J Am Soc Nephrol 2 Suppl 1, S25-35 (2007).
7. I. J. Kullo, K. Ding: Mechanisms of disease: The genetic basis of coronary heart disease. Nat Clin Pract Cardiovasc Med 4, 558-569 (2007). (Pubitemid 47490763)
8. S. Agrawal, F. Khan: Human genetic variation and personalized medicine. Indian J Physiol Pharmacol 51, 7- 28 (2007). (Pubitemid 46424112)
9. R. C. Edgar, S. Batzoglou: Multiple sequence alignment. Curr Opin Struct Biol 16, 368-373 (2006). (Pubitemid 43831644)
10. M. Sela, F. H. White, Jr. C. B. Anfinsen: Reductive cleavage of disulfide bridges in ribonuclease. Science 125, 691-692 (1957).
11. J. C. Kendrew, G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff, D. C. Phillips: A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181, 662-666 (1958).
12. N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, E. De Castro, P. S. Langendijk-Genevaux, M. Pagni, C. J. Sigrist: The PROSITE database. Nucleic Acids Res 34, D227-230 (2006).
13. C. J. Sigrist, L. Cerutti, N. Hulo, A. Gattiker, L. Falquet, M. Pagni, A. Bairoch, P. Bucher: PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3, 265-274 (2002).
14. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman: Basic local alignment search tool. J Mol Biol 215, 403-410 (1990).
15. H. Matsuoka, N. Iwata, M. Ito, M. Shimoyama, A. Nagata, K. Chihara, S. Takai, T. Matsui: Expression of a kinase-defective Eph-like receptor in the normal human brain. Biochem Biophys Res Commun 235, 487-492 (1997). (Pubitemid 27326506)
16. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne: The Protein Data Bank. Nucleic Acids Res 28, 235-242 (2000). (Pubitemid 30047768)
17. A. Kasuya, J. M. Thornton: Three-dimensional structure analysis of PROSITE patterns. J Mol Biol 286, 1673-1691 (1999). (Pubitemid 29121743)
18. I. Jonassen, I. Eidhammer, S. H. Grindhaug, W. R. Taylor: Searching the protein structure databank with weak sequence patterns and structural constraints. J Mol Biol 304, 599-619 (2000). (Pubitemid 32006193)
19. A. Bateman, L. Coin, R. Durbin, R. D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E. L. Sonnhammer, D. J. Studholme, C. Yeats, S. R. Eddy: The Pfam protein families database. Nucleic Acids Res 32, D138-141 (2004). (Pubitemid 38081623)
20. A. Bateman, E. Birney, R. Durbin, S. R. Eddy, R. D. Finn, E. L. Sonnhammer: Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res 27, 260-262 (1999). (Pubitemid 29209455)
21. J. Schultz, F. Milpetz, P. Bork, C. P. Ponting: SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 95, 5857- 5864 (1998). (Pubitemid 28248931)
22. I. Letunic, L. Goodstadt, N. J. Dickens, T. Doerks, J. Schultz, R. Mott, F. Ciccarelli, R. R. Copley, C. P. Ponting, P. Bork: Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res 30, 242-244 (2002). (Pubitemid 34679554)
23. T. K. Attwood, M. E. Beck: PRINTS-a protein motif fingerprint database. Protein Eng 7, 841-848 (1994). (Pubitemid 24219954)
24. F. Corpet, J. Gouzy, D. Kahn: The ProDom database of protein domain families. Nucleic Acids Res 26, 323-326 (1998). (Pubitemid 28291551)
25. J. Gracy, P. Argos: DOMO: a new database of aligned protein domains. Trends Biochem Sci 23, 495-497 (1998). (Pubitemid 29002916)
26. S. Henikoff, J. G. Henikoff: Automated assembly of protein blocks for database searching. Nucleic Acids Res 19, 6565- 6572 (1991). (Pubitemid 21913091)
27. J. G. Henikoff, E. A. Greene, S. Pietrokovski, S. Henikoff: Increased coverage of protein families with the blocks database servers. Nucleic Acids Res 28, 228-230 (2000). (Pubitemid 30047766)
28. R. Linding, R. B. Russell, V. Neduva, T. J. Gibson: GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 31, 3701-3708 (2003). (Pubitemid 37442227)
29. A. G. Murzin, S. E. Brenner, T. Hubbard, C. Chothia: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247, 536- 540 (1995).
30. P. Ananthalakshmi, K. Kumar Ch, M. Jeyasimhan, K. Sumathi, K. Sekar: Fragment Finder: a web-based software to identify similar three-dimensional structural motif. Nucleic Acids Res 33, W85-88 (2005). (Pubitemid 44529885)
31. B. Balamurugan, M. N. Roshan, D. Michael, M. Ambaree, S. Divya, H. Keerthana, M. Seemanthini, K. Sekar: SMS: sequence, motif and structure-a database on the structural rigidity of peptide fragments in non-redundant proteins. In Silico Biol 6, 229-235 (2006). (Pubitemid 44508932)
32. U. Hobohm, C. Sander: Enlarged representative set of protein structures. Protein Sci 3, 522-524 (1994). (Pubitemid 24103723)
33. R. B. Russell, G. J. Barton: Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14, 309- 323 (1992).
34. S. Balla, V. Thapar, S. Verma, T. Luong, T. Faghri, C. H. Huang, S. Rajasekaran, J. J. del Campo, J. H. Shinn, W. A. Mohler, M. W. Maciejewski, M. R. Gryk, B. Piccirillo, S. R. Schiller, M. R. Schiller: Minimotif Miner: a tool for investigating protein function. Nat Methods 3, 175-177 (2006).
35. P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D. M. Martin, G. Ausiello, B. Brannetti, A. Costantini, F. Ferre, V. Maselli, A. Via, G. Cesareni, F. Diella, G. Superti-Furga, L. Wyrwicz, C. Ramu, C. McGuigan, R. Gudavalli, I. Letunic, P. Bork, L. Rychlewski, B. Kuster, M. Helmer-Citterich, W. N. Hunter, R. Aasland, T. J. Gibson: ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31, 3625- 3630 (2003). (Pubitemid 37448491)
36. J. C. Obenauer, L. C. Cantley, M. B. Yaffe: Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31, 3635- 3641 (2003). (Pubitemid 37442212)
37. M. Fuxreiter, P. Tompa, I. Simon: Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23, 950-956 (2007). (Pubitemid 47050581)
38. A. C. Roque, C. R. Lowe: Lessons from nature: On the molecular recognition elements of the phosphoprotein bindingdomains. Biotechnol Bioeng 91, 546-555 (2005). (Pubitemid 41335492)
39. P. Ettmayer, D. France, J. Gounarides, M. Jarosinski, M. S. Martin, J. M. Rondeau, M. Sabio, S. Topiol, B. Weidmann, M. Zurini, K. W. Bair: Structural and conformational requirements for high-affinity binding to the SH2 domain of Grb2(1). J Med Chem 42, 971-980 (1999). (Pubitemid 29153426)
40. S. Cho, C. A. Velikovsky, C. P. Swaminathan, J. C. Houtman, L. E. Samelson, R. A. Mariuzza: Structural basis for differential recognition of tyrosine-phosphorylated sites in the linker for activation of T cells (LAT) by the adaptor Gads. Embo J 23, 1441-1451 (2004). (Pubitemid 38579505)
41. M. S. Kimber, J. Nachman, A. M. Cunningham, G. D. Gish, T. Pawson, E. F. Pai: Structural basis for specificity switching of the Src SH2 domain. Mol Cell 5, 1043-1049 (2000).
42. K. Ogura, S. Tsuchiya, H. Terasawa, S. Yuzawa, H. Hatanaka, V. Mandiyan, J. Schlessinger, F. Inagaki: Solution structure of the SH2 domain of Grb2 complexed with the Shc-derived phosphotyrosine-containing peptide. J Mol Biol 289, 439-445 (1999). (Pubitemid 29295115)
43. R. Koradi, M. Billeter, K. Wuthrich: MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14, 51-55, 29-32 (1996). (Pubitemid 26152976)
44. C. M. Venkatachalam: Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6, 1425-1436 (1968).
45. Z. Newby, T. T. Lee, R. J. Morse, Y. Liu, L. Liu, P. Venkatraman, D. V. Santi, J. S. Finer-Moore, R. M. Stroud: The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2′-deoxyuridine 5′- monophosphate (dUMP)-binding Tyr-261. Biochemistry 45, 7415-7428 (2006). (Pubitemid 43894935)