Unexpected features of the dark proteome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 52, 2015, Pages 15898-15903

  Perdigão, Nelson ^a,b   Heinrich, Julian ^c   Stolte, Christian ^c   Sabir, Kenneth S ^d,e   Buckley, Michael J ^c   Tabor, Bruce ^c   Signal, Beth ^d   Gloss, Brian S ^d   Hammang, Christopher J ^d   Rost, Burkhard ^f   Schafferhans, Andrea ^f   O'donoghue, Seán I ^c,d,e  

^a INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^b INSTITUTE FOR SYSTEMS AND ROBOTICS   (Portugal)

^c CSIRO   (Australia)

^d GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^e UNIVERSITY OF SYDNEY   (Australia)

^f TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Protein disorder; Secreted proteins; Structure prediction; Transmembrane proteins; Unknown unknowns

Indexed keywords

MEMBRANE PROTEIN; PROTEOME; PROTEIN;

ARTICLE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; ALGORITHM; ANIMAL; ARCHAEON; BACTERIUM; BIOLOGY; CHEMISTRY; EUKARYOTE; GENETICS; HUMAN; METABOLISM; MOLECULAR MODEL; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; VIRUS;

ALGORITHMS; ANIMALS; ARCHAEA; BACTERIA; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EUKARYOTA; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; PROTEOME; VIRUSES;

EID: 84952837993     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1508380112     Document Type: Article

References (47)

1. Berman HM, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235-242.
2. Haas J, et al. (2013) The Protein Model Portal-A comprehensive resource for protein structure and model information. Database (Oxford) 2013:bat031.
3. Petrey D, et al. (2015) Template-based prediction of protein function. CurrOpin Struct Biol 32:33-38.
4. Chothia C (1992) Proteins. One thousand families for the molecular biologist. Nature 357(6379):543-544.
5. Holm L, Sander C (1996) Mapping the protein universe. Science 273(5275):595-603.
6. Levitt M (2009) Nature of the protein universe. Proc Natl Acad Sci USA 106(27):11079-11084.
7. Nepomnyachiy S, Ben-Tal N, Kolodny R (2014) Global view of the protein universe. Proc Natl Acad Sci USA 111(32):11691-11696.
8. Khafizov K, Madrid-Aliste C, Almo SC, Fiser A (2014) Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative. Proc Natl Acad Sci USA 111(10):3733-3738.
9. Burley SK, et al. (1999) Structural genomics: Beyond the human genome project. Nat Genet 23(2):151-157.
10. Marsden RL, Lewis TA Orengo CA (2007) Towards a comprehensive structural coverage of completed genomes: A structural genomics viewpoint. BMC Bioinformatics 8:86.
11. Bertone G, Hooper D, Silk J (2005) Particle dark matter: Evidence, candidates and constraints. Phys Rep 405(5-6):279-390.
12. Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I (2009) Probing the "dark matter" of protein fold space. Structure 17(9):1244-1252.
13. Travis J (2002) Biological Dark Matter: Newfound RNA suggests a hidden complexity inside cells. Sci News 161(2):24-25.
14. Mattick JS (2003) Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25(10):930-939.
15. Oldfield CJ, et al. (2013) Utilization of protein intrinsic disorder knowledge in structural proteomics. Biochim Biophys Acta 1834(2):487-498.
16. Dunker AK, et al. (2001) Intrinsically disordered protein. J Mol Graph Model 19(1):26-59.
17. Oldfield CJ, Dunker AK (2014) Intrinsically disordered proteins and intrinsically disordered protein regions. Annu Rev Biochem 83:553-584.
18. Carpenter EP, Beis K, Cameron AD, Iwata S (2008) Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 18(5):581-586.
19. O'Donoghue SI, et al. (2015) Aquaria: Simplifying discovery and insight from protein structures. Nat Methods 12(2):98-99.
20. UniProt Consortium (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42(Database issue):D191-D198.
21. Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28(1):45-48.
22. Remmert M, Biegert A, Hauser A, Söding J (2012) HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9(2):173-175.
23. Dosztányi Z, Csizmok V, Tompa P, Simon I (2005) IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21(16):3433-3434.
24. Ota M, et al. (2013) An assignment of intrinsically disordered regions of proteins based on NMR structures. J Struct Biol 181(1):29-36.
25. Huntley MA, Golding GB (2002) Simple sequences are rare in the Protein Data Bank. Proteins 48(1):134-140.
26. Punta M, et al. (2009) Structural genomics target selection for the New York consortium on membrane protein structure. J Struct Funct Genomics 10(4):255-268.
27. Rost B, Casadio R, Fariselli P, Sander C (1995) Transmembrane helices predicted at 95% accuracy. Protein Sci 4(3):521-533.
28. Bigelow H, Rost B (2006) PROFtmb: A web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res 34(Web Server issue):W186-W188.
29. Drake JW, Charlesworth B, Charlesworth D, Crow JF (1998) Rates of spontaneous mutation. Genetics 148(4):1667-1686.
30. Cedano J, Aloy P, Pérez-Pons JA, Querol E (1997) Relation between amino acid composition and cellular location of proteins. J Mol Biol 266(3):594-600.
31. Andrade MA, O'Donoghue SI, Rost B (1998) Adaptation of protein surfaces to subcellular location. J Mol Biol 276(2):517-525.
32. Slabinski L, et al. (2007) The challenge of protein structure determination-lessons from structural genomics. Protein Sci 16(11):2472-2482.
33. Franceschini A, et al. (2013) STRING v9.1: Protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41(Database issue):D808-D815.
34. Kong L, et al. (2007) CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35(Web Server issue):W345-W349.
35. Edwards H, Abeln S, Deane CM (2013) Exploring fold space preferences of new-born and ancient protein superfamilies. PLOS Comput Biol 9(11):e1003325.
36. Koonin EV, Wolf YI, Karev GP (2002) The structure of the protein universe and genome evolution. Nature 420(6912):218-223.
37. Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6(11):805-814.
38. Chapman P, Stapleton G, Rodgers P, Micallef L, Blake A (2014) Visualizing Sets: An Empirical Comparison of Diagram Types. Visualizing Sets: An Empirical Comparison of Diagram Types, eds Dwyer T, Purchace H, Delaney A (Springer, Berlin), pp 146-160.
39. Davey NE, Travé G, Gibson TJ (2011) How viruses hijack cell regulation. Trends Biochem Sci 36(3):159-169.
40. Silverman BW (1986) Density Estimation for Statistics and Data Analysis (Chapman and Hall, London).
41. Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337(3):635-645.
42. Schlessinger A, Punta M, Yachdav G, Kajan L, Rost B (2009) Improved disorder prediction by combination of orthogonal approaches. PLoS One 4(2):e4433.
43. Hauser M, Mayer CE, Söding J (2013) kClust: Fast and sensitive clustering of large protein sequence databases. BMC Bioinformatics 14:248.
44. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol 57(1):289-300.
45. Shneiderman B (1992) Tree visualization with Tree-Maps: 2-D space-filling approach. ACM T Graphic 11(1):92-99.
46. Binder JX, et al. (2014) COMPARTMENTS: Unification and visualization of protein subcellular localization evidence. Database (Oxford) 2014:bau012.
47. Durinck S, Spellman PT, Birney E, Huber W (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc 4(8):1184-1191.