Functional Differentiation of Proteins: Implications for Structural Genomics

Structure

Volumn 15, Issue 4, 2007, Pages 405-415

  Friedberg, Iddo ^a   Godzik, Adam ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

PROTEINS

Indexed keywords

FLAVODOXIN; IMMUNOGLOBULIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CLASSIFICATION; DECISION TREE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; ROC CURVE; SEQUENCE ALIGNMENT; STRUCTURAL GENOMICS;

GENOMICS; HUMANS; MULTIGENE FAMILY; NUCLEAR PROTEINS;

EID: 34047273007     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.02.005     Document Type: Article

References (53)

1. Abergel C., Coutard B., Byrne D., Chenivesse S., Claude J.B., Deregnaucourt C., Fricaux T., Gianesini-Boutreux C., Jeudy S., Lebrun R., et al. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J. Struct. Funct. Genomics 4 (2003) 141-157
2. Aloy P., Oliva B., Querol E., Aviles F.X., and Russell R.B. Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. Protein Sci. 11 (2002) 1101-1116
3. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 (2000) 25-29
4. Bartlett G.J., Todd A.E., and Thornton J.M. Inferring protein function from structure. Methods Biochem. Anal. 44 (2003) 387-407
5. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., and Sonnhammer E.L. The Pfam protein families database. Nucleic Acids Res. 30 (2002) 276-280
6. Brenner S.E. Target selection for structural genomics. Nat. Struct. Biol. 7 Suppl (2000) 967-969
7. Camon E., Barrell D., Lee V., Dimmer E., and Apweiler R. The Gene Ontology Annotation (GOA) Database-an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol. 4 (2004) 5-6
8. Chandonia J.M., and Brenner S.E. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 58 (2005) 166-179
9. Claverie J.M., Monchois V., Audic S., Poirot O., and Abergel C. In search of new anti-bacterial target genes: a comparative/structural genomics approach. Comb. Chem. High Throughput Screen. 5 (2002) 511-522
10. Cort J., Koonin E., Bash P., and Kennedy M. A phylogenetic approach to target selection for structural genomics: solution structure of YciH. Nucleic Acids Res. 27 (1999) 4018-4027
11. Coulson A.F., and Moult J. A unifold, mesofold, and superfold model of protein fold use. Proteins 46 (2002) 61-71
12. Devos D., and Valencia A. Practical limits of function prediction. Proteins 41 (2000) 98-107
13. Feder M., and Bujnicki J.M. Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics 6 (2005) 21
14. Friedberg I. Automated protein function prediction-the genomic challenge. Brief. Bioinform. 7 (2006) 225-242
15. Friedberg I., Jaroszewski L., Ye Y., and Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics. Curr. Opin. Struct. Biol. 14 (2004) 307-312
16. Galperin M.Y., Walker D.R., and Koonin E.V. Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 8 (1998) 779-790
17. Gerlt J.A., and Babbitt P.C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu. Rev. Biochem. 70 (2001) 209-246
18. Gough J., and Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 30 (2002) 268-272
19. Goulding C.W., Perry L.J., Anderson D., Sawaya M.R., Cascio D., Apostol M.I., Chan S., Parseghian A., Wang S.S., Wu Y., et al. Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA. Biophys. Chem. 105 (2003) 361-370
20. Hegyi H., and Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288 (1999) 147-164
21. Hegyi H., and Gerstein M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 11 (2001) 1632-1640
22. Jaroszewski L., Rychlewski L., Li Z., Li W., and Godzik A. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res. 33 (2005) W284-W288
23. Joslyn C.A., Mniszewski S.M., Fulmer A., and Heaton G. The gene ontology categorizer. Bioinformatics 20 Suppl 1 (2004) I169-I177
24. Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
25. Li W., Jaroszewski L., and Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17 (2001) 282-283
26. Linial M., and Yona G. Methodologies for target selection in structural genomics. Prog. Biophys. Mol. Biol. 73 (2000) 297-320
27. Liu J., and Rost B. Target space for structural genomics revisited. Bioinformatics 18 (2002) 922-933
28. Liu J., Hegyi H., Acton T.B., Montelione G.T., and Rost B. Automatic target selection for structural genomics on eukaryotes. Proteins 56 (2004) 188-200
29. Lord P.W., Stevens R.D., Brass A., and Goble C.A. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19 (2003) 1275-1283
30. Lord P.W., Stevens R.D., Brass A., and Goble C.A. Semantic similarity measures as tools for exploring the gene ontology. Pac. Symp. Biocomput. 8 (2003) 601-612
31. Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., He S., Hurwitz D.I., Jackson J.D., Ke Z., et al. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33 (2005) D192-D196
32. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
33. Nagano N., Orengo C.A., and Thornton J.M. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J. Mol. Biol. 321 (2002) 741-765
34. Norvell J.C., and Machalek A.Z. Structural genomics programs at the US National Institute of General Medical Sciences. Nat. Struct. Biol. 7 Suppl (2000) 931
35. Pandit S.B., Bhadra R., Gowri V.S., Balaji S., Anand B., and Srinivasan N. SUPFAM: a database of sequence superfamilies of protein domains. BMC Bioinformatics 5 (2004) 28
36. Pawlowski K., Jaroszewski L., Rychlewski L., and Godzik A. Sensitive sequence comparison as protein function predictor. Pac. Symp. Biocomput. 5 (2000) 42-53
37. Quinlan J.R. C4.5: Programs for Machine Learning (1993), Morgan Kaufmann, San Diego
38. Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318 (2002) 595-608
39. Schwarzenbacher R., Godzik A., Grzechnik S.K., and Jaroszewski L. The importance of alignment accuracy for molecular replacement. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1229-1236
40. Shah I., and Hunter L. Predicting enzyme function from sequence: a systematic appraisal. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5 (1997) 276-283
41. Shah I., and Hunter L. Identification of divergent functions in homologous proteins by induction over conserved modules. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6 (1998) 157-164
42. Shakhnovich B.E. Improving the precision of the structure-function relationship by considering phylogenetic context. PLoS Comput. Biol. 1 (2005) e9
43. Stevens R.C., Yokoyama S., and Wilson I.A. Global efforts in structural genomics. Science 294 (2001) 89-92
44. Thornton J.M., Orengo C.A., Todd A.E., and Pearl F.M. Protein folds, functions and evolution. J. Mol. Biol. 293 (1999) 333-342
45. Tian W., and Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity?. J. Mol. Biol. 333 (2003) 863-882
46. Todd A.E., Orengo C.A., and Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307 (2001) 1113-1143
47. Todd A.E., Orengo C.A., and Thornton J.M. Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10 (2002) 1435-1451
48. Wang K., and Samudrala R. FSSA: a novel method for identifying functional signatures from structural alignments. Bioinformatics 21 (2005) 2969-2977
49. Whisstock J.C., and Lesk A.M. Prediction of protein function from protein sequence and structure. Q. Rev. Biophys. 36 (2003) 307-340
50. Witten I., and Eibe F. Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations. First Edition (2000), Morgan Kaufmann, San Diego
51. Wong P., and Frishman D. Fold designability, distribution, and disease. PLoS Comput. Biol. 2 (2006) e40
52. Xie L., and Bourne P.E. Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput. Biol. 1 (2005) e31
53. Zhu J., Burgner J.W., Harms E., Belitsky B.R., and Smith J.L. A new arrangement of (β/α)8 barrels in the synthase subunit of PLP synthase. J. Biol. Chem. 280 (2005) 27914-27923