The language of the protein universe

Current Opinion in Genetics and Development

Volumn 35, Issue , 2015, Pages 50-56

  Scaiewicz, Andrea ^a   Levitt, Michael ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; GRAMMAR; HUMAN; HUMAN GENOME; LANGUAGE; LINGUISTICS; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NOMENCLATURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; REVIEW; SEMANTICS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; BIOLOGY; GENETICS; GENOME; METABOLISM; PROTEIN TERTIARY STRUCTURE;

PROTEIN;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME; HUMANS; LANGUAGE; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84943575068     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2015.08.010     Document Type: Review

References (75)

1. Searls D.B. The language of genes. Nature 2002, 420:211-217.
2. Gimona M. Protein linguistics-a grammar for modular protein assembly?. Nat Rev Mol Cell Biol 2006, 7:68-73.
3. Eisenhaber F. A decade after the first full human genome sequencing: when will we understand our own genome?. J Bioinf Comput Biol 2012, 10.
4. Chomsky N. Logical-structures in language. Am Doc 1957, 8:284-291.
5. Chomsky N. Fundamentals of language-jakobson,r, halle,m. Int J Am Linguist 1957, 23:234-242.
6. Botstein D., Cherry J.M. Molecular linguistics: extracting information from gene and protein sequences. Proc Natl Acad Sci U S A 1997, 94:5506-5507.
7. Group N.P. Folding as grammar. Nat Struct Biol 2002, 9. 713-713.
8. Chothia C., Gough J. Genomic and structural aspects of protein evolution. Biochem J 2009, 419:15-28.
9. Finn R.D., Mistry J., Tate J., Coggill P., Heger A., Pollington J.E., Gavin O.L., Gunasekaran P., Ceric G., Forslund K., et al. The pfam protein families database. Nucleic Acids Res 2010, 38(Database Issue):D211-D222.
10. Portugaly E., Linial N., Linial M. Everest: a collection of evolutionary conserved protein domains. Nucleic Acids Res 2007, 35(Database Issue):D241-D246.
11. Letunic I., Doerks T., Bork P. Smart 6: recent updates and new developments. Nucleic Acids Res 2009, 37(Database Issue):D229-D232.
12. Mi H.Y., Dong Q., Muruganujan A., Gaudet P., Lewis S., Thomas P.D. Panther version 7: improved phylogenetic trees, orthologs and collaboration with the gene ontology consortium. Nucleic Acids Res 2010, 38(Database Issue):D204-D210.
13. Attwood T.K., Bradley P., Flower D.R., Gaulton A., Maudling N., Mitchell A.L., Moulton G., Nordle A., Paine K., Taylor P., et al. Prints and its automatic supplement, preprints. Nucleic Acids Res 2003, 31:400-402.
14. Sigrist C.J.A., Cerutti L., de Castro E., Langendijk-Genevaux P.S., Bulliard V., Bairoch A., Hulo N. Prosite, a protein domain database for functional characterization and annotation. Nucleic Acids Res 2010, 38(Database Issue):D161-D166.
15. Bru C., Courcelle E., Carrre S., Beausse Y., Dalmar S., Kahn D. The prodom database of protein domain families: more emphasis on 3d. Nucleic Acids Res 2005, 33(Database Issue):D212-D215.
16. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. Scop: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
17. Andreeva A., Howorth D., Chandonia J.M., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. Data growth and its impact on the scop database: new developments. Nucleic Acids Res 2008, 36(Database issue):D419-D425.
18. Andreeva A., Howorth D., Chothia C., Kulesha E., Murzin A.G. Scop2 prototype: a new approach to protein structure mining. Nucleic Acids Res 2014, 42(D1):D310-D314.
19. Orengo C.A., Bray J.E., Buchan D.W., Harrison A., Lee D., Pearl F.M., Sillitoe I., Todd A.E., Thornton J.M. The cath protein family database: a resource for structural and functional annotation of genomes. Proteomics 2002, 2(1):11-21.
20. Cuff A.L., Sillitoe I., Lewis T., Clegg A.B., Rentzsch R., Furnham N., Pellegrini-Calace M., Jones D., Thornton J., Orengo C.A. Extending cath: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res 2011, 39(Database issue):D420-D426.
21. Sillitoe I., Lewis T.E., Cuff A., Das S., Ashford P., Dawson N.L., Furnham N., Laskowski R.A., Lee D., Lees J.G., et al. Cath: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 2015, 43(Database issue):D376-D381.
22. Gough J., Chothia C. Superfamily: hmms representing all proteins of known structure. Scop sequence searches, alignments and genome assignments. Nucleic Acids Res 2002, 30:268-272.
23. Wilson D., Pethica R., Zhou Y., Talbot C., Vogel C., Madera M., Chothia C., Gough J. Superfamily-sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res 2009, 37(Database issue):D380-D386.
24. Yeats C., Lees J., Carter P., Sillitoe I., Orengo C. The gene3d web services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Res 2011, 39(Web Server issue):W546-W550.
25. Lees J.G., Lee D., Studer R.A., Dawson N.L., Sillitoe I., Das S., Yeats C., Dessailly B.H., Rentzsch R., Orengo C.A. Gene3d: multi-domain annotations for protein sequence and comparative genome analysis. Nucleic Acids Res 2014, 42(Database issue):D240-D245.
26. Cheng H., Schaeffer R.D., Liao Y., Kinch L.N., Pei J., Shi S., Kim B.H., Grishin N.V. Ecod: an evolutionary classification of protein domains. PLoS Comput Biol 2014, 10:e1003926.
27. Suhrer S.J., Wiederstein M., Gruber M., Sippl M.J. Cops-a novel workbench for explorations in fold space. Nucleic Acids Res 2009, 37(Web Server issue):W539-W544.
28. Marchler-Bauer A., Anderson J.B., Derbyshire M.K., DeWeese-Scott C., Gonzales N.R., Gwadz M., Hao L.N., He S.Q., Hurwitz D.I., Jackson J.D., et al. Cdd: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 2007, 35(Database issue):D237-D240.
29. Marchler-Bauer A., Zheng C., Chitsaz F., Derbyshire M.K., Geer L.Y., Geer R.C., Gonzales N.R., Gwadz M., Hurwitz D.I., Lanczycki C.J., et al. Cdd: conserved domains and protein three-dimensional structure. Nucleic Acids Res 2013, 41(Database issue):D348-D352.
30. Geer L.Y., Domrachev M., Lipman D.J., Bryant S.H. Cdart: protein homology by domain architecture. Genome Res 2002, 12:1619-1623.
31. Mitchell A., Chang H.Y., Daugherty L., Fraser M., Hunter S., Lopez R., McAnulla C., McMenamin C., Nuka G., Pesseat S., et al. The interpro protein families database: the classification resource after 15 years. Nucleic Acids Res 2015, 43(Database issue):D213-D221.
32. Levitt M. Nature of the protein universe. Proc Natl Acad Sci U S A 2009, 106:11079-11084.
33. Ben-Tal N., Kolodny R. Representation of the protein universe using classifications, maps, and networks. Israel J Chem 2014, 54:1286-1292.
34. Rekapalli B., Wuichet K., Peterson G.D., Zhulin I.B. Dynamics of domain coverage of the protein sequence universe. BMC Genomics 2012, 13:634.
35. Nepomnyachiy S, Ben-Tal N, Kolodny R: Global view of the protein universe. Proc Natl Acad Sci U S A 2014, 111:11691-11696.
36. Kummerfeld S.K., Teichmann S.A. Protein domain organisation: adding order. BMC Bioinform 2009, 10:39.
37. Terrapon N., Weiner J., Grath S., Moore A.D., Bornberg-Bauer E. Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics 2014, 30:274-281.
38. Kemena C., Bitard-Feildel T., Bornberg-Bauer E. Mdat-aligning multiple domain arrangements. BMC Bioinformatics 2015, 16:19.
39. Syamaladevi D.P., Joshi A., Sowdhamini R. An alignment-free domain architecture similarity search (adass) algorithm for inferring homology between multi-domain proteins. Bioinformation 2013, 9:491-499.
40. Lhota J., Hauptman R., Hart T., Ng C., Xie L. A new method to improve network topological similarity search: applied to fold recognition. Bioinformatics 2015, 31:2106-2114.
41. Tamuri A.U., Laskowski R.A. Archschema: a tool for interactive graphing of related pfam domain architectures. Bioinformatics 2010, 26:1260-1261.
42. Moore A.D., Held A., Terrapon N., Weiner J., Bornberg-Bauer E. Domosaics: software for domain arrangement visualization and domain-centric analysis of proteins. Bioinformatics 2014, 30:282-283.
43. Adebali O., Ortega D.R., Zhulin I.B. Cdvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics 2015, 31:1475-1477.
44. Haynie D.T., Xue B. Superdomains in the protein structure hierarchy: the case of ptp-c2. Protein Sci 2015, 24:874-882.
45. Vogel C., Berzuini C., Bashton M., Gough J., Teichmann S.A. Supra-domains: evolutionary units larger than single protein domains. J Mol Biol 2004, 336:809-823.
46. Bornberg-Bauer E. Signals: tinkering with domains. Sci Signal 2010, 3.
47. Weiner J., Moore A.D., Bornberg-Bauer E. Just how versatile are domains?. Bmc Evol Biol 2008, 8.
48. Buljan M., Frankish A., Bateman A. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol 2010, 11.
49. Nasir A., Kim K.M., Caetano-Anolles G. Global patterns of protein domain gain and loss in superkingdoms. PLoS Comput Biol 2014, 10:e1003452.
50. Bjorklund A.K., Ekman D., Light S., Frey-Skott J., Elofsson A. Domain rearrangements in protein evolution. J Mol Biol 2005, 353:911-923.
51. Xie X.Y., Jin J., Mao Y.Y. Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks. Bmc Evol Biol 2011, 11.
52. Basu M.K., Carmel L., Rogozin I.B., Koonin E.V. Evolution of protein domain promiscuity in eukaryotes. Genome Res 2008, 18:449-461.
53. Barrera A., Alastruey-Izquierdo A., Martin M.J., Cuesta I., Vizcaino J.A. Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PLoS Comput Biol 2014, 10:e1003733.
54. Basu M.K., Poliakov E., Rogozin I.B. Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform 2009, 10:205-216.
55. Hsu C.H., Chen C.K., Hwang M.J. The architectural design of networks of protein domain architectures. Biol Lett 2013, 9:20130268.
56. Andreeva A. Classification of proteins: available structural space for molecular modeling. Homology Modeling, Methods and Protocols 857 2012, 1-31. Springer. J.W. Andrew, R.A. Orry (Eds.).
57. Mi H.Y., Muruganujan A., Thomas P.D. Panther in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013, 41:D377-D386.
58. Abhiman S., Sonnhammer E.L.L. Funshift: a database of function shift analysis on protein subfamilies. Nucleic Acids Res 2005, 33(Database issue):D197-D200.
59. Akiva E., Brown S., Almonacid D.E., Barber A.E., Custer A.F., Hicks M.A., Huang C.C., Lauck F., Mashiyama S.T., Meng E.C., et al. The structure-function linkage database. Nucleic Acids Res 2014, 42:D521-D530.
60. Hernandez S., Ferragut G., Amela I., Perez-Pons J., Pinol J., Mozo-Villarias A., Cedano J., Querol E. Multitaskprotdb: a database of multitasking proteins. Nucleic Acids Res 2014, 42:D517-D520.
61. Huberts D.H.E.W., van der Klei I.J. Moonlighting proteins: an intriguing mode of multitasking. Bba-Mol Cell Res 2010, 1803:520-525.
62. Mani M., Chen C., Amblee V., Liu H., Mathur T., Zwicke G., Zabad S., Patel B., Thakkar J., Jeffery C.J. Moonprot: a database for proteins that are known to moonlight. Nucleic Acids Res 2015, 43(Database issue):D277-D282.
63. Fang H., Gough J. Dcgo: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res 2013, 41(Database issue):D536-D544.
64. Radivojac P., Clark W.T., Oron T.R., Schnoes A.M., Wittkop T., Sokolov A., Graim K., Funk C., Verspoor K., Ben-Hur A., et al. A large-scale evaluation of computational protein function prediction. Nat Methods 2013, 10:221-227.
65. Swadesh M. Unaaliq and proto eskimo v: comparative vocabulary. Int J Am Linguist 1952, 18:241-256.
66. Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 2001, 310:311-325.
67. Zmasek C.M., Godzik A. This deja vu feeling-analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol 2012, 8.
68. Moore A.D., Grath S., Schuler A., Huylmans A.K., Bornberg-Bauer E. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. Biochim Biophys Acta 2013, 1834:898-907.
69. Forslund K., Henricson A., Hollich V., Sonnhammer E.L. Domain tree-based analysis of protein architecture evolution. Mol Biol Evol 2008, 25:254-264.
70. Gough J. Convergent evolution of domain architectures (is rare). Bioinformatics 2005, 21:1464-1471.
71. Suen S., Lu H.H., Yeang C.H. Evolution of domain architectures and catalytic functions of enzymes in metabolic systems. Genome Biol Evol 2012, 4:976-993.
72. Linkeviciute V., Rackham O.J., Gough J., Oates M.E., Fang H. Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie 2015, in press. 10.1016/j.biochi.2015.05.003.
73. Vogel C., Teichmann S.A., Pereira-Leal J. The relationship between domain duplication and recombination. J Mol Biol 2005, 346:355-365.
74. Bornberg-Bauer E., Alba M.M. Dynamics and adaptive benefits of modular protein evolution. Curr Opin Struct Biol 2013, 23:459-466.
75. Forslund K., Sonnhammer E.L. Evolution of protein domain architectures. Methods Mol Biol 2012, 856:187-216.