Exploration of uncharted regions of the protein universe

PLoS Biology

Volumn 7, Issue 9, 2009, Pages

  Jaroszewski, Lukasz ^a   Li, Zhanwen ^a   Krishna, S Sri ^a   Bakolitsa, Constantina ^a   Wooley, John ^b   Deacon, Ashley M ^c   Wilson, Ian A ^d   Godzik, Adam ^a,b  

^a BURNHAM INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DUF FAMILIES; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; MULTIGENE FAMILY; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY; TIME;

PROTEIN;

ANIMALS; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; MULTIGENE FAMILY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN; TIME FACTORS;

EID: 70349775678     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1000205     Document Type: Article

References (55)

1. Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, et al. (2006) Essential genes on metabolic maps. Curr Opin Biotechnol 17: 448-456.
2. Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, et al. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55: 137-149. (Pubitemid 40127891)
3. Fan JB, Chee MS, Gunderson KL (2006) Highly parallel genomic assays. Nat Rev Genet 7: 632-644.
4. Amos CI (2007) Successful design and conduct of genome-wide association studies. Hum Mol Genet 16 Spec No. 2: R220-R225.
5. Seng KC, Seng CK (2008) The success of the genome-wide association approach: a brief story of a long struggle. Eur J Hum Genet 16: 554-564.
6. Schena M (1996) Genome analysis with gene expression microarrays. Bioessays 18: 427-431. (Pubitemid 126599968)
7. Fan JB, Gunderson KL, Bibikova M, Yeakley JM, Chen J, et al. (2006) Illumina universal bead arrays. Methods Enzymol 410: 57-73.
8. Bier FF, von Nickisch-Rosenegk M, Ehrentreich-Forster E, Reiss E, Henkel J, et al. (2008) DNA microarrays. Adv Biochem Eng Biotechnol 109: 433-453.
9. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669-685.
10. Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92-97. (Pubitemid 43190739)
11. Maron PA, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53: 486-493. (Pubitemid 46716634)
12. Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, et al. (2009) Shotgun metaproteomics of the human distal gut microbiota. Isme J 3: 179-189.
13. Galperin MY (2001) Conserved 'hypothetical' proteins: new hints and new puzzles. Comp Funct Genomics 2: 14-18.
14. Galperin MY, Koonin EV (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 5452-5463.
15. Pawlowski K (2008) Uncharacterized/hypothetical proteins in biomedical 'omics' experiments: is novelty being swept under the carpet? Brief Funct Genomic Proteomic 7: 283-290.
16. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637.
17. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41. (Pubitemid 38751229)
18. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2007) New developments in the InterPro database. Nucleic Acids Res 35: D224-D228.
19. Meinel T, Krause A, Luz H, Vingron M, Staub E (2005) The SYSTERS Protein Family Database in 2005. Nucleic Acids Res 33: D226-D229. (Pubitemid 40207866)
20. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-D288.
21. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16. doi:10.1371/journal.pbio.0050016. (Pubitemid 46422965)
22. Dayhoff MO, Schwartz R, Orcutt BC (1978) A model of evolutionary change in proteins. atlas of protein sequence and structure. Nat Biomed Res Found. pp 345-358.
23. Gribskov M, McLachlan AD, Eisenberg D (1987) Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A 84: 4355-4358.
24. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
25. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D (1994) Hidden Markov models in computational biology. applications to protein modeling. J Mol Biol 235: 1501-1531. (Pubitemid 2022516)
26. Eddy SR (1996) Hidden Markov models. Curr Opin Struct Biol 6: 361-365.
27. Rychlewski L, Jaroszewski L, Weizhong L, Godzik A (2000) Comparison of sequence profiles. structural predictions with no structure information. Protein Science 8: 232-241. (Pubitemid 30126996)
28. Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
29. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res 34: D247-D251.
30. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 33: W284-W288. (Pubitemid 44529927)
31. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36: D419-D425. (Pubitemid 351149760)
32. Walker JE, Fearnley IM, Gay NJ, Gibson BW, Northrop FD, et al. (1985) Primary structure and subunit stoichiometry of F1-ATPase from bovine mitochondria. J Mol Biol 184: 677-701. (Pubitemid 15024774)
33. Stone RL, Dixon JE (1994) Protein-tyrosine phosphatases. J Biol Chem 269: 31323-31326.
34. Doolittle RF (1981) Similar amino acid sequences: chance or common ancestry? Science 214: 149-159.
35. Lupas AN, Ponting CP, Russell RB (2001) On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 134: 191-203.
36. Cheng H, Kim BH, Grishin NV (2008) Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J Mol Biol 377: 1265-1278.
37. Govindarajan S, Recabarren R, Goldstein RA (1999) Estimating the total number of protein folds. Proteins 35: 408-414. (Pubitemid 29264837)
38. Zhang C, DeLisi C (1998) Estimating the number of protein folds. J Mol Biol 284: 1301-1305.
39. Wolf YI, Grishin NV, Koonin EV (2000) Estimating the number of protein folds and families from complete genome data. J Mol Biol 299: 897-905.
40. Grant A, Lee D, Orengo C (2004) Progress towards mapping the universe of protein folds. Genome Biol 5: 107. (Pubitemid 38735655)
41. Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19 Suppl 2: ii246-ii255. (Pubitemid 41296662)
42. Grishin NV (2001) Fold change in evolution of protein structures. J Struct Biol 134: 167-185. (Pubitemid 33733488)
43. Harrison A, Pearl F, Mott R, Thornton J, Orengo C (2002) Quantifying the similarities within fold space. J Mol Biol 323: 909-926. (Pubitemid 35341064)
44. Krishna SS, Grishin NV (2005) Structural drift: a possible path to protein fold change. Bioinformatics 21: 1308-1310.
45. Kolodny R, Petrey D, Honig B (2006) Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 16: 393-398. (Pubitemid 43831645)
46. Honig B (2007) Protein structure space is much more than the sum of its folds. Nat Struct Mol Biol 14: 458.
47. Friedberg I, Godzik A (2005) Connecting the protein structure universe by using sparse recurring fragments. Structure 13: 1213-1224. (Pubitemid 41111488)
48. Rodrigues AP, Grant BJ, Godzik A, Friedberg I (2007) The 2006 automated function prediction meeting. BMC Bioinformatics 8 Suppl 4: S1-S4. (Pubitemid 351833826)
49. Godzik A, Jambon M, Friedberg I (2007) Computational protein function prediction: are we making progress? Cell Mol Life Sci 64: 2505-2511.
50. Redfern OC, Dessailly B, Orengo CA (2008) Exploring the structure and function paradigm. Curr Opin Struct Biol 18: 394-402.
51. Chothia C (1992) Proteins. one thousand families for the molecular biologist. Nature 357: 543-544.
52. Finkelstein AV, Ptitsyn OB (1987) Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol 50: 171-190.
53. Krishna SS, Grishin NV (2004) Structurally analogous proteins do exist! Structure 12: 1125-1127.
54. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659. (Pubitemid 43985301)
55. Holm L, Sander C (1996) Mapping the protein universe. Science 273: 595-603.