Structural Bridges through Fold Space

PLoS Computational Biology

Volumn 11, Issue 9, 2015, Pages

  Edwards, Hannah ^a   Deane, Charlotte M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT METHODS; CLASSIFICATION SCHEME; GLOBAL STRUCTURE; PROBABILITY THRESHOLD; PROTEIN STRUCTURE CLASSIFICATIONS; SIMILAR DISTANCE; STRUCTURAL ALIGNMENTS; STRUCTURAL BRIDGE; STRUCTURAL SUPERPOSITIONS; STRUCTURAL UNIT;

PROTEINS;

ALGORITHM; ARTICLE; CONSENSUS; DATA ANALYSIS; MOLECULAR EVOLUTION; PROBABILITY; PROTEIN DOMAIN; PROTEIN FOLDING; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL MODEL; STRUCTURE ANALYSIS; BIOLOGY; CHEMISTRY; METABOLISM; PROCEDURES; PROTEIN CONFORMATION;

PROTEIN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 84943516185     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004466     Document Type: Article

References (61)

1. Koonin EV, Wolf YI, Karev GP, (2002) The structure of the protein universe and genome evolution. Nature 420: 218–223. doi: 10.1038/nature01256 12432406
2. Ponting CP, Russell RR, (2002) The natural history of protein domains. Annu Rev Biophys Biomol Struct 31: 45–71. doi: 10.1146/annurev.biophys.31.082901.134314 11988462
3. Goldstein RA, (2008) The structure of protein evolution and the evolution of protein structure. Curr Opin Struct Biol 18: 170–127. doi: 10.1016/j.sbi.2008.01.006 18328690
4. Sadowski MI, Taylor WR, (2010) Protein structures, folds and fold spaces. J Phys Condens Matter 22: 033103. doi: 10.1088/0953-8984/22/3/033103 21386276
5. Murzin AG, Brenner SE, Hubbard T, Chothia C, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536–540. doi: 10.1016/S0022-2836(05)80134-2 7723011
6. Orengo C, Michie A, Jones S, Jones D, Swindells M, et al. (1997) CATH– a hierarchic classification of protein domain structures. Structure 5: 1093–1108. doi: 10.1016/S0969-2126(97)00260-8 9309224
7. Davidson A, (2008) A folding space odyssey. PNAS 105: 2759–2760. doi: 10.1073/pnas.0800030105 18287054
8. Farías-Rico JA, Schmidt S, Höcker B, (2014) Evolutionary relationship of two ancient protein superfolds. Nat Chem Biol 10: 710–715. doi: 10.1038/nchembio.1579 25038785
9. Jäckel C, Kast P, Hilvert D, (2008) Protein design by directed evolution. Annu Rev Biophys 37: 153–73. doi: 10.1146/annurev.biophys.37.032807.125832 18573077
10. Höcker B, (2012) A toolbox for protein design. Nature 491: 204–205. doi: 10.1038/491204a 23135466
11. Ben-Tal N, Kolodny R, (2014) Representation of the Protein Universe using Classifications, Maps, and Networks. Isr J Chem 31905: 1286–1292. doi: 10.1002/ijch.201400001
12. Orengo CA, Flores TP, Taylor WR, (1993) Identification and classification of protein fold families. Protein Eng 6: 485–500. doi: 10.1093/protein/6.5.485 8415576
13. Holm L, Sander C, (1996) Mapping the protein universe. Science 273: 595–603. doi: 10.1126/science.273.5275.595 8662544
14. Yona G, Levitt M, (2000) Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins. Proc Int Conf Intell Syst Mol Biol: 395–406. 10977100
15. Grishin V, Grishin N, (2002) Euclidian space and grouping of biological objects. Bioinformatics 18: 1523–1533. doi: 10.1093/bioinformatics/18.11.1523 12424125
16. Røgen P, Fain B, (2003) Automatic classification of protein structure by using Gauss integrals. PNAS 100: 119–124. doi: 10.1073/pnas.2636460100 12506205
17. Hou J, Sims GE, Zhang C, Kim SH, (2003) A global representation of the protein fold space. PNAS 100: 2386–2390. doi: 10.1073/pnas.2628030100 12606708
18. Hou J, Jun SR, Zhang C, Kim SH, (2005) Global mapping of the protein structure space and application in structure-based inference of protein function. PNAS 102: 3651–6. doi: 10.1073/pnas.0409772102 15705717
19. Choi IG, Kim SH, (2006) Evolution of protein structural classes and protein sequence families. PNAS 103: 14056–14061. doi: 10.1073/pnas.0606239103 16959887
20. Budowski-Tal I, Nov Y, Kolodny R, (2010) FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. PNAS 107: 3481–6. doi: 10.1073/pnas.0914097107 20133727
21. Asarnow D, Singh R, (2014) Automatic classification of protein structures using low-dimensional structure space mappings. BMC Bioinform 15 Suppl 2: S1. doi: 10.1186/1471-2105-15-S2-S1
22. Yona G, Linial N, Linial M, (1999) ProtoMap: Automatic Classification of Protein Sequences, a Hierarchy of Protein Families, and Local Maps. Proteins 37: 360–378. doi: 10.1002/(SICI)1097-0134(19991115)37:3%3C360::AID-PROT5%3E3.0.CO;2-Z 10591097
23. Dokholyan NV, Shakhnovich B, Shakhnovich EI, (2002) Expanding protein universe and its origin from the biological Big Bang. PNAS 99: 14132–14136. doi: 10.1073/pnas.202497999 12384571
24. Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI, (2003) Functional Fingerprints of Folds: Evidence for Correlated Structure–Function Evolution. J Mol Biol 326: 1–9. doi: 10.1016/S0022-2836(02)01362-1 12547186
25. Friedberg I, Godzik A, (2005) Connecting the protein structure universe by using sparse recurring fragments. Structure 13: 1213–1224. doi: 10.1016/j.str.2005.05.009 16084393
26. Sun ZB, Zou XW, Guan W, Jin ZZ, (2006) The architectonic fold similarity network in protein fold space. EPJ B 49: 127–134. doi: 10.1140/epjb/e2006-00026-0
27. Çamoğlu O, Can T, Singh AK, (2006) Integrating multi-attribute similarity networks for robust representation of the protein space. Bioinformatics 22: 1585–92. doi: 10.1093/bioinformatics/btl130 16595556
28. Skolnick J, Arakaki AK, Lee SY, Brylinski M, (2009) The continuity of protein structure space is an intrinsic property of proteins. PNAS 106: 15690–15695. doi: 10.1073/pnas.0907683106 19805219
29. Alva V, Remmert M, Biegert A, Lupas AN, Söding J, (2010) A galaxy of folds. Protein Sci 19: 124–130. doi: 10.1002/pro.297 19937658
30. Valavanis IK, Spyrou GM, Nikita KS, (2010) A comparative study of multi-classification methods for protein fold recognition. J Bioinform Comput Biol 1: 332–346.
31. Nepomnyachiy S, Ben-Tal N, Kolodny R, (2014) Global view of the protein universe. PNAS 111: 11691–11696. doi: 10.1073/pnas.1403395111 25071170
32. Osadchy M, Kolodny R, (2011) Maps of protein structure space reveal a fundamental relationship between protein structure and function. PNAS 108: 12301–6. doi: 10.1073/pnas.1102727108 21737750
33. 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. doi: 10.1016/j.sbi.2006.04.007 16678402
34. Pascual-García A, Abia D, Ortiz AR, Bastolla U, (2009) Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures. PLoS Comput Biol 5: e1000331. doi: 10.1371/journal.pcbi.1000331 19325884
35. Sadowski MI, Taylor WR, (2010) On the evolutionary origins of ‘Fold Space Continuity’: a study of topological convergence and divergence in mixed alpha-beta domains. J Struct Biol 172: 244–252. doi: 10.1016/j.jsb.2010.07.016 20691788
36. Chothia C, Lesk AM, (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823–826. 3709526
37. Andreeva A, Murzin AG, (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16: 399–408. doi: 10.1016/j.sbi.2006.04.003 16650981
38. Petrey D, Honig B, (2009) Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol 19: 363–8. doi: 10.1016/j.sbi.2009.02.001 19269161
39. Sadreyev RI, Kim BH, Grishin NV, (2009) Discrete–continuous duality of protein structure space. Curr Opin Struct Biol 19: 321–328. doi: 10.1016/j.sbi.2009.04.009 19482467
40. Andreeva A, Howorth D, Chothia C, Kulesha E, Murzin AG, (2014) SCOP2 prototype: a new approach to protein structure mining. Nucleic Acids Res 42: D310–D314. doi: 10.1093/nar/gkt1242 24293656
41. Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G, (1992) A database of protein structure families with common folding motifs. Protein Sci 1: 1691–1698. doi: 10.1002/pro.5560011217 1304898
42. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, et al. (2014) Pfam: the protein families database. Nucleic Acids Res 42: D222–D230. doi: 10.1093/nar/gkt1223 24288371
43. Hasegawa H, Holm L, (2009) Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 19: 341–348. doi: 10.1016/j.sbi.2009.04.003 19481444
44. Sadowski MI, Taylor WR, (2012) Evolutionary inaccuracy of pairwise structural alignments. Bioinformatics 28: 1209–1215. doi: 10.1093/bioinformatics/bts103 22399676
45. Winstanley HF, Abeln S, Deane CM, (2005) How old is your fold? Bioinformatics 21: i449–458. doi: 10.1093/bioinformatics/bti1008 15961490
46. Edwards H, Abeln S, Deane CM, (2013) Exploring fold space preferences of new-born and ancient protein superfamilies. PLoS Comput Biol 9: e1003325. doi: 10.1371/journal.pcbi.1003325 24244135
47. Brenner SE, Koehl P, Levitt M, (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 28: 254–256. doi: 10.1093/nar/28.1.254 10592239
48. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422–1423. doi: 10.1093/bioinformatics/btp163 19304878
49. Ortiz AR, Strauss CEM, Olmea O, (2002) MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison. Protein Sci 11: 2606–2621. doi: 10.1110/ps.0215902 12381844
50. Ye Y, Godzik A, (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19: ii246–ii255. doi: 10.1093/bioinformatics/btg1086 14534198
51. Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302–2309. doi: 10.1093/nar/gki524 15849316
52. Liu W, Srivastava A, Zhang J, (2011) A mathematical framework for protein structure comparison. PLoS Comput Biol 7: e1001075. doi: 10.1371/journal.pcbi.1001075 21304929
53. Xu J, Zhang Y, (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26: 889–895. doi: 10.1093/bioinformatics/btq066 20164152
54. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498–2504. doi: 10.1101/gr.1239303 14597658
55. Blondel VD, Guillaume JL, Lambiotte R, Lefebvre E, (2008) Fast unfolding of communities in large networks. J Stat Mech Theor Exp: P10008. doi: 10.1088/1742-5468/2008/10/P10008
56. Opsahl T, Agneessens F, Skvoretz J, (2010) Node centrality in weighted networks: Generalizing degree and shortest paths. Soc Networks 32: 245–251. doi: 10.1016/j.socnet.2010.03.006
57. R Core Team (2014) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
58. Dijkstra E, (1959) A note on two problems in connexion with graphs. Numer Math 1: 269–271. doi: 10.1007/BF01386390
59. Federhen S, (2012) The NCBI taxonomy database. Nucleic Acids Res 40: D136–D143. doi: 10.1093/nar/gkr1178 22139910
60. Mann HB, Whitney DR, (1947) On a test of whether one of two random variables is stochastically larger than the other. Ann Math Stat 18: 50–60. doi: 10.1214/aoms/1177730491
61. Osadchy M, Kolodny R, (2011) Maps of protein structure space reveal a fundamental relationship between protein structure and function. PNAS 208: 12301–12306. doi: 10.1073/pnas.1102727108