Improvement of protein structure comparison using a structural alphabet

Biochimie

Volumn 93, Issue 9, 2011, Pages 1434-1445

  Joseph, Agnel Praveen ^a,b,c   Srinivasan, N ^d   De Brevern, Alexandre G ^a,b,c  

^a Institut National de la Transfusion Sanguine   (France)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c INSTITUT NATIONAL DE LA TRANSFUSION SANGUINE   (France)

^d INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Amino acid; Anchor based alignment; Protein blocks; Protein data bank; Protein folds; Protein structure mining; Semi global alignment; Structural alphabet; Structural comparison

Indexed keywords

ACYL CARRIER PROTEIN; BETA PROPELLER PROTEIN; CUPREDOXIN; GLOBIN; HYDROLASE; METALLOPROTEINASE; PHOSPHORYLASE; RING FINGER PROTEIN; UNCLASSIFIED DRUG;

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; PROTEIN DATABASE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL ALPHABET; STRUCTURE ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ALIGNMENT;

EID: 79959930240     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2011.04.010     Document Type: Article

References (103)

1. D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96 (Pubitemid 32952955)
2. D.M. Byers, and H. Gong Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family Biochem. Cell Biol. 85 2007 649 662 (Pubitemid 351198413)
3. A.R.H.J. Leach Structure-Based Drug Discovery 2007 Springer Berlin 1-4020-4406-2
4. G. Scapin Structural biology and drug discovery Curr. Pharm. Des 12 2006 2087 2097 (Pubitemid 43891405)
5. C.L. Verlinde, and W.G. Hol Structure-based drug design: progress, results and challenges Structure 2 1994 577 587
6. A. Bhaduri, G. Pugalenthi, and R. Sowdhamini PASS2: an automated database of protein alignments organised as structural superfamilies BMC Bioinformatics 5 2004 35
7. M.A. Marti-Renom, V.A. Ilyin, and A. Sali DBAli: a database of protein structure alignments Bioinformatics 17 2001 746 747 (Pubitemid 32851386)
8. K. Mizuguchi, C.M. Deane, T.L. Blundell, and J.P. Overington HOMSTRAD: a database of protein structure alignments for homologous families Protein Sci. 7 1998 2469 2471 (Pubitemid 28506965)
9. S. Sujatha, S. Balaji, and N. Srinivasan PALI: a database of alignments and phylogeny of homologous protein structures Bioinformatics 17 2001 375 376 (Pubitemid 32421935)
10. G. Agarwal, M. Rajavel, B. Gopal, and N. Srinivasan Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold PLoS One 4 2009 e5736
11. T. Akutsu, and K.L. Sim Protein threading based on multiple protein structure alignment Genome Inform. Ser. Workshop Genome Inform. 10 1999 23 29
12. D.M. Standley, V.A. Eyrich, Y. An, D.L. Pincus, J.R. Gunn, and R.A. Friesner Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment Proteins Suppl. 5 2001 133 139 (Pubitemid 34113176)
13. J. Skolnick, J.S. Fetrow, and A. Kolinski Structural genomics and its importance for gene function analysis Nat. Biotechnol. 18 2000 283 287 (Pubitemid 30159478)
14. J.F. Gibrat, T. Madej, and S.H. Bryant Surprising similarities in structure comparison Curr. Opin. Struct. Biol. 6 1996 377 385 (Pubitemid 26197439)
15. H. Hasegawa, and L. Holm Advances and pitfalls of protein structural alignment Curr. Opin. Struct. Biol. 19 2009 341 348
16. P. Koehl Protein structure similarities Curr. Opin. Struct. Biol. 11 2001 348 353 (Pubitemid 32568277)
17. M. Novotny, D. Madsen, and G.J. Kleywegt Evaluation of protein fold comparison servers Proteins 54 2004 260 270 (Pubitemid 38084067)
18. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138 (Pubitemid 23288916)
19. W.R. Taylor, and C.A. Orengo Protein structure alignment J. Mol. Biol. 208 1989 1 22 (Pubitemid 19191513)
20. I.N. Shindyalov, and P.E. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 11 1998 739 747 (Pubitemid 28434482)
21. Z.K. Feng, and M.J. Sippl Optimum superimposition of protein structures: ambiguities and implications Fold Des. 1 1996 123 132 (Pubitemid 126748167)
22. A. Godzik The structural alignment between two proteins: is there a unique answer? Protein Sci. 5 1996 1325 1338 (Pubitemid 26239440)
23. M. Shatsky, R. Nussinov, and H.J. Wolfson Flexible protein alignment and hinge detection Proteins 48 2002 242 256 (Pubitemid 34743414)
24. Y. Ye, and A. Godzik Flexible structure alignment by chaining aligned fragment pairs allowing twists Bioinformatics 19 Suppl. 2 2003 246 255 ii
25. A. Harrison, F. Pearl, R. Mott, J. Thornton, and C. Orengo Quantifying the similarities within fold space J. Mol. Biol. 323 2002 909 926 (Pubitemid 35341064)
26. E. Krissinel, and K. Henrick Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D Biol. Crystallogr. 60 2004 2256 2268 (Pubitemid 41742778)
27. G. Lu TOP: a new method for protein structure comparisons and similarity searches J. Appl. Cryst 33 2000 176 183 (Pubitemid 32142176)
28. A.G. de Brevern, C. Etchebest, and S. Hazout Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks Proteins 41 2000 271 287
29. R. Kolodny, P. Koehl, L. Guibas, and M. Levitt Small libraries of protein fragments model native protein structures accurately J. Mol. Biol. 323 2002 297 307 (Pubitemid 35283693)
30. C. Micheletti, F. Seno, and A. Maritan Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies Proteins 40 2000 662 674
31. M.J. Rooman, J. Rodriguez, and S.J. Wodak Automatic definition of recurrent local structure motifs in proteins J. Mol. Biol. 213 1990 327 336 (Pubitemid 20176543)
32. J. Schuchhardt, G. Schneider, J. Reichelt, D. Schomburg, and P. Wrede Local structural motifs of protein backbones are classified by self-organizing neural networks Protein Eng. 9 1996 833 842 (Pubitemid 26366508)
33. R. Unger, D. Harel, S. Wherland, and J.L. Sussman A 3D building blocks approach to analyzing and predicting structure of proteins Proteins 5 1989 355 373
34. O. Sander, I. Sommer, and T. Lengauer Local protein structure prediction using discriminative models BMC Bioinformatics 7 2006 14
35. C.H. Tung, J.W. Huang, and J.M. Yang Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database Genome Biol. 8 2007 R31
36. S.Y. Ku, and Y.J. Hu Protein structure search and local structure characterization BMC Bioinformatics 9 2008 349
37. J. Yang Comprehensive description of protein structures using protein folding shape code Proteins 71 2008 1497 1518 (Pubitemid 351564070)
38. B. Offmann, M. Tyagi, and A.G. de Brevern Local protein structures Curr. Bioinform. 3 2007 165 202
39. I. Friedberg, T. Harder, R. Kolodny, E. Sitbon, Z. Li, and A. Godzik Using an alignment of fragment strings for comparing protein structures Bioinformatics 23 2007 e219 224
40. F. Guyon, A.C. Camproux, J. Hochez, and P. Tuffery SA-Search: a web tool for protein structure mining based on a structural alphabet Nucleic Acids Res. 32 2004 W545 W548
41. A. Sacan, I.H. Toroslu, and H. Ferhatosmanoglu Integrated search and alignment of protein structures Bioinformatics 24 2008 2872 2879
42. S. Wang, and W.M. Zheng CLePAPS: fast pair alignment of protein structures based on conformational letters J. Bioinform. Comput. Biol. 6 2008 347 366 (Pubitemid 351712428)
43. A.G. de Brevern New assessment of a structural alphabet Silico Biol. 5 2005 283 289
44. A.G. de Brevern, C. Benros, R. Gautier, H. Valadie, S. Hazout, and C. Etchebest Local backbone structure prediction of proteins Silico Biol. 4 2004 381 386 (Pubitemid 39600484)
45. C. Etchebest, C. Benros, S. Hazout, and A.G. de Brevern A structural alphabet for local protein structures: improved prediction methods Proteins 59 2005 810 827 (Pubitemid 40695856)
46. O. Zimmermann, and U.H. Hansmann LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach J. Chem. Inf. Model. 48 2008 1903 1908
47. Q. Dong, X. Wang, L. Lin, and Y. Wang Analysis and prediction of protein local structure based on structure alphabets Proteins 72 2008 163 172 (Pubitemid 351809155)
48. C. Benros, A.G. de Brevern, and S. Hazout Analyzing the sequence-structure relationship of a library of local structural prototypes J. Theor. Biol. 256 2009 215 226
49. A.G. de Brevern, C. Etchebest, C. Benros, and S. Hazout "Pinning strateg": a novel approach for predicting the backbone structure in terms of protein blocks from sequence J. Biosci. 32 2007 51 70 (Pubitemid 46465757)
50. Q. Li, C. Zhou, and H. Liu Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities Proteins 74 2009 820 836
51. M. Tyagi, A. Bornot, B. Offmann, and A.G. de Brevern Protein short loop prediction in terms of a structural alphabet Comput. Biol. Chem. 33 2009 329 333
52. A.P. Joseph, A. Bornot, and A.G. de Brevern Local structural alphabet H. Rangwala, G. Karypis, Protein Structure Methods and Algorithms 2010 Wiley
53. M. Dudev, and C. Lim Discovering structural motifs using a structural alphabet: application to magnesium-binding sites BMC Bioinformatics 8 2007 106
54. G. Faure, A. Bornot, and A.G. de Brevern Analysis of protein contacts into protein units Biochimie 91 2009 876 887
55. M. Tyagi, A.G. de Brevern, N. Srinivasan, and B. Offmann Protein structure mining using a structural alphabet Proteins 71 2008 920 937 (Pubitemid 351430026)
56. Y.C. Zuo, and Q.Z. Li Using reduced amino acid composition to predict defensin family and subfamily: integrating similarity measure and structural alphabet Peptides 30 2009 1788 1793
57. A.P. Joseph, G. Agarwal, S. Mahajan, J.C. Gelly, L.S. Swapna, B. Offmann, and F. Cadet A short survey on protein blocks Biophys. Rev. 2 2010 137 145
58. M. Tyagi, V.S. Gowri, N. Srinivasan, A.G. de Brevern, and B. Offmann A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications Proteins 65 2006 32 39 (Pubitemid 44320613)
59. S. Balaji, S. Sujatha, S.S. Kumar, and N. Srinivasan PALI-a database of Phylogeny and ALIgnment of homologous protein structures Nucleic Acids Res. 29 2001 61 65 (Pubitemid 32054408)
60. V.S. Gowri, S.B. Pandit, P.S. Karthik, N. Srinivasan, and S. Balaji Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database Nucleic Acids Res. 31 2003 486 488 (Pubitemid 36150436)
61. M. Tyagi, P. Sharma, C.S. Swamy, F. Cadet, N. Srinivasan, A.G. de Brevern, and B. Offmann Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet Nucleic Acids Res. 34 2006 W119 W123
62. M. Carpentier, S. Brouillet, and J. Pothier YAKUSA: a fast structural database scanning method Proteins 61 2005 137 151 (Pubitemid 41262923)
63. A.P. Singh, and D.L. Brutlag Hierarchical protein structure superposition using both secondary structure and atomic representations Proc. Int. Conf. Intell. Syst. Mol. Biol. 5 1997 284 293
64. T. Kawabata MATRAS: a program for protein 3D structure comparison Nucleic Acids Res. 31 2003 3367 3369 (Pubitemid 37442161)
65. G.J. Kleywegt, and T.A. Jones Detecting folding motifs and similarities in protein structures Methods Enzymol. 277 1997 525 545 (Pubitemid 27390938)
66. 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
67. N. Bray, I. Dubchak, and L. Pachter AVID: a global alignment program Genome Res. 13 2003 97 102
68. M. Brudno, C.B. Do, G.M. Cooper, M.F. Kim, E. Davydov, E.D. Green, A. Sidow, and S. Batzoglou LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA Genome Res. 13 2003 721 731 (Pubitemid 36511930)
69. S. Chakrabarti, N. Bhardwaj, P.A. Anand, and R. Sowdhamini Improvement of alignment accuracy utilizing sequentially conserved motifs BMC Bioinformatics 5 2004 167
70. W. Huang, D.M. Umbach, and L. Li Accurate anchoring alignment of divergent sequences Bioinformatics 22 2006 29 34 (Pubitemid 43057005)
71. B. Morgenstern DIALIGN: multiple DNA and protein sequence alignment at BiBiServ Nucleic Acids Res. 32 2004 W33 W36
72. S.B. Needleman, and C.D. Wunsch A general method applicable to the search for similarities in the amino acid sequence of two proteins J. Mol. Biol. 48 1970 443 453
73. C. Notredame, D.G. Higgins, and J. Heringa T-Coffee: a novel method for fast and accurate multiple sequence alignment J. Mol. Biol. 302 2000 205 217
74. T. Kohonen Self-Organizing Maps third ed. 2001 Springer 501
75. L.R. Rabiner A tutorial on hidden Markov models and selected application in speech recognition P. IEEE 77 1989 257 286
76. R.B. Russell, and G.J. Barton Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels Proteins 14 1992 309 323
77. A.S. Konagurthu, J.C. Whisstock, P.J. Stuckey, and A.M. Lesk MUSTANG: a multiple structural alignment algorithm Proteins 64 2006 559 574 (Pubitemid 44100724)
78. M.S. Johnson, and J.P. Overington A structural basis for sequence comparisons. An evaluation of scoring methodologies J. Mol. Biol. 233 1993 716 738 (Pubitemid 23314782)
79. A. Martin, C. Porter, http://www.bioinf.org.uk/software/profit/, 2010.
80. A. Zemla LGA: a method for finding 3D similarities in protein structures Nucleic Acids Res. 31 2003 3370 3374 (Pubitemid 37442162)
81. A. Zemla, B. Geisbrecht, J. Smith, M. Lam, B. Kirkpatrick, M. Wagner, T. Slezak, and C.E. Zhou STRALCP - structure alignment-based clustering of proteins Nucleic Acids Res. 35 2007 e150
82. T.F. Smith, and M.S. Waterman Identification of common molecular subsequences J. Mol. Biol. 147 1981 195 197
83. X. Huang, and W. Miller A time-efficient linear-space local similarity algorithm Adv. Appl. Math. 12 1991 337 357
84. L. Holm, and J. Park DaliLite workbench for protein structure comparison Bioinformatics 16 2000 566 567
85. D.J. Leahy, W.A. Hendrickson, I. Aukhil, and H.P. Erickson Structure of a fibronectin type III domain from tenascin phased by MAD analysis of the selenomethionyl protein Science 258 1992 987 991
86. A.M. de Vos, M. Ultsch, and A.A. Kossiakoff Human growth hormone and extracellular domain of its receptor: crystal structure of the complex Science 255 1992 306 312
87. Y. Zhang, and J. Skolnick TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 33 2005 2302 2309 (Pubitemid 41439897)
88. A. Guerler, and E.W. Knapp Novel protein folds and their nonsequential structural analogs Protein Sci. 17 2008 1374 1382
89. I. Van Walle, I. Lasters, and L. Wyns SABmark - a benchmark for sequence alignment that covers the entire known fold space Bioinformatics 21 2005 1267 1268 (Pubitemid 40467955)
90. L.H. Greene, T.E. Lewis, S. Addou, A. Cuff, T. Dallman, M. Dibley, O. Redfern, F. Pearl, R. Nambudiry, A. Reid, I. Sillitoe, C. Yeats, J.M. Thornton, and C.A. Orengo The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution Nucleic Acids Res. 35 2007 D291 297
91. Z. Gaspari, K. Vlahovicek, and S. Pongor Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm Bioinformatics 21 2005 3322 3323 (Pubitemid 41418452)
92. E.A. Campbell, N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, and S.A. Darst Structural mechanism for rifampicin inhibition of bacterial rna polymerase Cell 104 2001 901 912 (Pubitemid 32289282)
93. C.E. Nichols, A.R. Hawkins, and D.K. Stammers Structure of the 'open' form of Aspergillus nidulans 3-dehydroquinate synthase at 1.7 A resolution from crystals grown following enzyme turnover Acta Crystallogr. D Biol. Crystallogr. 60 2004 971 973 (Pubitemid 41184806)
94. K.D. Westover, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center Cell 119 2004 481 489 (Pubitemid 39482348)
95. G. Bader, S. Schiffmann, A. Herrmann, M. Fischer, M. Gutlich, G. Auerbach, T. Ploom, A. Bacher, R. Huber, and T. Lemm Crystal structure of rat GTP cyclohydrolase I feedback regulatory protein, GFRP J. Mol. Biol. 312 2001 1051 1057 (Pubitemid 32980325)
96. A.L. Delcher, A. Phillippy, J. Carlton, and S.L. Salzberg Fast algorithms for large-scale genome alignment and comparison Nucleic Acids Res. 30 2002 2478 2483 (Pubitemid 34619000)
97. F. Birzele, J.E. Gewehr, G. Csaba, and R. Zimmer Vorolign-fast structural alignment using Voronoi contacts Bioinformatics 23 2007 e205 211
98. M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, and A. Sali Alignment of multiple protein structures based on sequence and structure features Protein Eng. Des Sel 22 2009 569 574
99. K. Watanabe, C. Khosla, R.M. Stroud, and S.C. Tsai Crystal structure of an Acyl-ACP dehydrogenase from the FK520 p.lyketide biosynthetic pathway: insights into extender unit biosynthesis J. Mol. Biol. 334 2003 435 444 (Pubitemid 37386345)
100. T. Kuroita, H. Matsumura, N. Yokota, M. Kitabayashi, H. Hashimoto, T. Inoue, T. Imanaka, and Y. Kai Structural mechanism for coordination of proofreading and polymerase activities in archaeal DNA polymerases J. Mol. Biol. 351 2005 291 298 (Pubitemid 41007748)
101. M.C. Franklin, J. Wang, and T.A. Steitz Structure of the replicating complex of a pol alpha family DNA polymerase Cell 105 2001 657 667 (Pubitemid 32524118)
102. Y. Yan, E. Winograd, A. Viel, T. Cronin, S.C. Harrison, and D. Branton Crystal structure of the repetitive segments of spectrin Science 262 1993 2027 2030 (Pubitemid 24041880)
103. J. Pascual, M. Pfuhl, D. Walther, M. Saraste, and M. Nilges Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil J. Mol. Biol. 273 1997 740 751 (Pubitemid 27488814)