Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information

Journal of Molecular Biology

Volumn 346, Issue 3, 2005, Pages 875-894

  O'Donoghue, Patrick ^a   Luthey Schulten, Zaida ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Aminoacyl tRNA synthetase; Evolution; Non redundant set; OB fold; Protein structure profiles

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CALCULATION; CHEMICAL STRUCTURE; DATA BASE; MATHEMATICAL ANALYSIS; PHYLOGENY; PRIORITY JOURNAL; PROTEIN STRUCTURE; REGRESSION ANALYSIS;

EID: 13844266306     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.11.053     Document Type: Article

References (67)

1. W.T. Astbury Harvey Lectures 1950-51 1952 Thomas Springfield
2. E. Zuckerkandl, and L. Pauling Molecules as documents of evolutionary history J. Theor. Biol. 8 1965 357 366
3. E.F. DeLong, and N.R. Pace Environmental diversity of bacteria and archaea Syst. Biol. 50 2001 470 478
4. C.R. Woese, and G.E. Fox Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc. Natl Acad. Sci. USA 74 1977 5088 5090
5. C. Darwin The Life and Letters of Charles Darwin, Including an Autobiographical Chapter 1887 John Murray London
6. D.F. Feng, and R.F. Doolittle Progressive sequence alignment as a prerequisite to correct phylogenetic trees J. Mol. Evol. 25 1987 351 360
7. A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, and S. Griffiths-Jones The Pfam protein families database Nucl. Acids Res. 32 2004 D138 D141
8. S.B. Pandit, R. Bhadra, V.S. Gowri, S. Balaji, B. Anand, and N. Srinivasan Supfam: a database of sequence superfamilies of protein domains BMC Bioinformat. 5 2004 28
9. L.A. Stebbings, and K. Mizuguchi HOMSTRAD: recent developments in the homologous protein structure alignment database Nucl. Acids Res. 32 2004 D203 D207
10. M. Gribskov, M. McLachlan, and D. Eisenberg Profile analysis: detection of distantly related proteins Proc. Natl Acad. Sci. USA 84 1987 4355 4358
11. E.L.L. Sonnhammer, S.R. Eddy, and R. Durbin Pfam: a comprehensive database of protein domain families based on seed alignments Proteins: Struct. Funct. Genet. 28 1997 405 420
12. A.N. Lupas, C.P. Ponting, and R.B. Russell 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 2001 191 203
13. R. Sadreyev, and N. Grishin COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance J. Mol. Biol. 326 2003 317 336
14. C.L. Tang, L. Xie, I.Y.Y. Koh, S. Posy, E. Alexov, and B. Honig On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles J. Mol. Biol. 334 2003 1043 1062
15. O. O'Sullivan, K. Suhre, C. Abergel, D.G. Higgins, and C. Notredame 3DCoffee: combining protein sequences and structures within multiple sequence alignments J. Mol. Biol. 340 2004 385 395
16. A. Tramontano, and V. Morea Assessment of homology-based predictions in CASP5 Proteins: Struct. Funct. Genet. 53 2003 352 368
17. D. Petrey, Z. Xiang, C.L. Tang, L. Xie, M. Gimpelev, T. Mitros, and C.S. Soto Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling Proteins: Struct. Funct. Genet. 53 2003 430 435
18. P.J. Bickel, K.J. Kechris, P.C. Spector, G.J. Wedemayer, and A.N. Glazer Finding important sites in protein sequences Proc. Natl Acad. Sci. USA 99 2002 14764 14771
19. B.E. Shakhnovich, N.V. Dokholyan, C. DeLisi, and E.I. Shakhnovich Functional fingerprints of folds: evidence for correlated structure-function evolution J. Mol. Biol. 326 2003 1 9
20. C. Hardin, T.V. Pogorelov, and Z. Luthey-Schulten Ab initio protein structure prediction Curr. Opin. Struct. Biol. 12 2002 176 181
21. W.P. Russ, and R. Ranganathan Knowledge-based potential functions in protein design Curr. Opin. Struct. Biol. 12 2002 447 452
22. R.I. Amann, W. Ludwig, and K.H. Schleifer Phylogenetic identification and in situ detection of individual microbial cells without cultivation Microbiol. Rev. 59 1995 143 169
23. N.R. Pace A molecular view of microbial diversity and the biosphere Science 276 1997 734 740
24. G.W. Tyson, J. Chapman, P. Hugenholtz, E. Allen, R.J. Ram, and P.M. Richardson Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 428 2004 37 43
25. J.C. Venter, K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, and J.A. Eisen Environmental genome shotgun sequencing of the Sargasso Sea Science 304 2004 66 74
26. L. Holm, and C. Sander Removing near-neighbour redundancy from large protein sequence collections Bioinformatics 14 1998 423 429
27. C. O'Donovan, M.J. Martin, E. Glemet, J.-J. Codani, and R. Apweiler Removing redundancy in SWISS-PROT and TrEMBL Bioinformatics 15 1999 258 259
28. G. Wang, and R.L. Dunbrack Jr PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591
29. J. Park, L. Holm, A. Heger, and C. Chothia RSDB: representative protein sequence databases have high information content Bioinformatics 16 2000 458 464
30. M. Vingron, and P. Argos A fast and sensitive multiple sequence alignment algorithm Comput. Appl. Biosci. 5 1989 115 121
31. S. Heniko, and J.G. Heniko Position-based sequence weights J. Mol. Biol. 243 1994 574 578
32. A.C.W. May Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics Protein Eng. 14 2001 209 217
33. P. O'Donoghue, and Z. Luthey-Schulten Evolution of structure in aminoacyl-tRNA synthetases Microbiol. Mol. Biol. Rev. 67 2003 550 573
34. R.B. Russell, and G.J. Barton Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels Proteins: Struct. Funct. Genet. 14 1992 309 323
35. W. Humphrey, A. Dalke, and K. Schulten VMD-visual molecular dynamics J. Mol. Graph. 14.1 1996 33 38
36. M.P. Eastwood, C. Hardin, Z. Luthey-Schulten, and P.G. Wolynes Evaluating protein structure-prediction schemes using energy landscape theory, IBM J. Res. Dev. 45 2001 475 497
37. K. Koretke, Z. Luthey-Schulten, and P. Wolynes Self-consistently optimized statistical mechanical energy functions for sequence structure alignment Protein Sci. 5 1996 1043 1059
38. G.H. Golub, and H.A. Van der Vorst Eigenvalue computation in the 20th century J. Comput. Appl. Math. 123 2000 35 65
39. A.S. Householder Unitary triangularization of a nonsymmetric matrix JACM 5 1958 339 342
40. M.T. Heath 2nd edit. Scientific Computing: An Introductory Survey 2002 McGraw-Hill New York
41. G. Golub Numerical methods for solving linear least squares problems Numer. Math. 7 1965 206 216
42. J.H. Wilkinson The Algebraic Eigenvalue Problem 1965 Clarendon Press Oxford
43. P. Rogen, and H. Bohr A new family of global protein shape descriptors Math. Biosci. 182 2003 167 181
44. J.A. Olkin, L.P. Heck, and K. Naghshineh Automated placement of transducers for active noise control: performance measures IEEE Proceedings of International Conference on Acoustics, Speech, and Signal Processing, Atlanta, GA vol. 2 1996 969 972
45. L.P. Heck, J.A. Olkin, and K. Naghshineh Transducer placement for broadband active vibration control using a novel multidimensional qr factorization J. Vib. Acoust. 120 1998 663 670
46. A. Sethi, P. O'Donoghue, and Z. Luthey-Schulten Evolutionary profiles from the QR factorization of multiple sequence alignments Proc. Natl Acad. Sci. USA 2005 in the press
47. J. Felsenstein PHYLIP-phylogeny inference package (version 3.2) Cladistics 5 1989 164 166
48. R.R. Sokal, and C.D. Michener A statistical method for evaluating systematic relationships Univ. Kansas Sci. Bull. 28 1958 1409 1438
49. L. Pauling Molecular disease and evolution Bull. NY Acad. Med. 40 1964 334 342
50. C.R. Woese On the evolution of cells Proc. Natl Acad. Sci. USA 99 2002 8742 8747
51. C.R. Woese, G. Olsen, M. Ibba, and D. Söll Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process Microbiol. Mol. Bio. Rev. 64 2000 202 236
52. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 29 2000 291 325
53. C. Chothia, and A.M. Lesk The relation between the divergence of sequence and structure in proteins EMBO J. 5 1986 823 826
54. H.H. Gan, R.A. Perlow, S. Roy, J. Ko, M. Wu, and J. Huang Analysis of protein sequence/structure similarity relationships Biophys. J. 83 2002 2781 2791
55. N.C. Kyrpides, and C.R. Woese Universally conserved translation initiation factors Proc. Natl Acad. Sci. USA 95 1998 224 228
56. N.C. Kyrpides, and C.R. Woese Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2b alpha-beta-delta subunit families Proc. Natl Acad. Sci. USA 95 1998 3726 3730
57. D.L. Theobald, R.M. Mitton-Fry, and D.S. Wuttke Nucleic acid recognition by OB-fold proteins Annu. Rev. Biophys. Biomol. Struct. 32 2003 115 133
58. B. Al-Lazikani, F.B. Sheinerman, and B. Honig Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases Proc. Natl Acad. Sci. USA 98 2001 14796 14801
59. S.R. Eddy Profile hidden Markov models Bioinformatics 14 1998 755 763
60. B. Boeckmann, A. Bairoch, R. Apweiler, M.-C. Blatter, A. Estreicher, and E. Gasteiger The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucl. Acids Res. 31 2003 365 370
61. M.J. Sutcliffe Representing an ensemble of NMR-derived protein structures by a single structure Protein Sci. 2 1993 936 944
62. D.M.F. Van Aalten, B.L. de Groot, J.B.C. Findlay, H.J.C. Berendsen, and A. Amadei A comparison of techniques for calculating protein essential dynamics J. Comput. Chem. 18 1997 169 181
63. O. Lichtarge, H.R. Bourne, and F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358
64. V. Alexandrov, and M. Gerstein Using 3D hidden Markov models that explicitly represent spatial coordinates to model and compare protein structures BMC Bioinformat. 5 2004 2
65. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
66. J.M. Chandonia, G. Hon, N.S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S.E. Brenner The ASTRAL compendium in 2004 Nucl. Acids Res. 32 2004 D189 D192
67. T. Someya, N. Nameki, H. Hosoi, S. Suzuki, H. Hatanaka, and M. Fujii Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus FEBS Letters 535 2003 94 100