Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability

Journal of Molecular Biology

Volumn 426, Issue 4, 2014, Pages 962-979

  Mudgal, Richa ^a   Sowdhamini, Ramanathan ^b   Chandra, Nagasuma ^a   Srinivasan, Narayanaswamy ^a   Sandhya, Sankaran ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b UNIVERSITY OF AGRICULTURAL SCIENCES   (India)

Author keywords

in silico protein design; protein evolution; remote homology detection; sequence analysis

Indexed keywords

CBL PROTEIN; COCARBOXYLASE; COPPER PROTEIN; CUPREDOXIN; CYTIDINE DEAMINASE; DNA BINDING PROTEIN; DNA GLYCOSYLTRANSFERASE; GLUTAMATE AMMONIA LIGASE; GLYCOSIDASE; NUCLEASE; PEPTIDASE; PHOSPHATASE; PHOSPHOLIPASE D; SINGLE STRANDED DNA BINDING PROTEIN; SONIC HEDGEHOG PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; PROTEIN FAMILY; SENSITIVITY AND SPECIFICITY;

HIDDEN MARKOV MODEL; HMM; IN SILICO PROTEIN DESIGN; POSITION-SPECIFIC SCORING MATRIX; PROTEIN EVOLUTION; PSSM; REMOTE HOMOLOGY DETECTION; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; METHIONYL AMINOPEPTIDASES; MOLECULAR SEQUENCE DATA; PHOSPHOLIPASES A2; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84893690666     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.11.026     Document Type: Article

References (42)

1. P. Bork, and E.V. Koonin Predicting functions from protein sequences - where are the bottlenecks? Nat Genet 18 1998 313 318 (Pubitemid 28158157)
2. L. Holm Unification of protein families Curr Opin Struct Biol 8 1998 372 379 (Pubitemid 28321366)
3. S.R. Eddy Hidden Markov models Curr Opin Struct Biol 6 1996 361 365 (Pubitemid 26197437)
4. R.C. Edgar, and K. Sjolander COACH: profile-profile alignment of protein families using hidden Markov models Bioinformatics 20 2004 1309 1318 (Pubitemid 38811421)
5. M. Remmert, A. Biegert, A. Hauser, and J. Soding HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment Nat Methods 9 2012 173 175
6. J. Park, S.A. Teichmann, T. Hubbard, and C. Chothia Intermediate sequences increase the detection of homology between sequences J Mol Biol 273 1997 349 354 (Pubitemid 27460235)
7. A.A. Salamov, M. Suwa, C.A. Orengo, and M.B. Swindells Combining sensitive database searches with multiple intermediates to detect distant homologues Protein Eng 12 1999 95 100 (Pubitemid 29103687)
8. S. Sandhya, S. Chakrabarti, K.R. Abhinandan, R. Sowdhamini, and N. Srinivasan Assessment of a rigorous transitive profile based search method to detect remotely similar proteins J Biomol Struct Dyn 23 2005 283 298 (Pubitemid 41642432)
9. S. Sandhya, R. Mudgal, C. Jayadev, K.R. Abhinandan, R. Sowdhamini, and N. Srinivasan Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins Mol BioSyst 8 2012 2076 2084
10. B.I. Dahiyat, and S.L. Mayo De novo protein design: fully automated sequence selection Science 278 1997 82 87 (Pubitemid 27446279)
11. M. Soskine, and D.S. Tawfik Mutational effects and the evolution of new protein functions Nat Rev Genet 11 2010 572 582
12. N. Halabi, O. Rivoire, S. Leibler, and R. Ranganathan Protein sectors: evolutionary units of three-dimensional structure Cell 138 2009 774 786
13. M. Socolich, S.W. Lockless, W.P. Russ, H. Lee, K.H. Gardner, and R. Ranganathan Evolutionary information for specifying a protein fold Nature 437 2005 512 518 (Pubitemid 41613543)
14. W. Cai, J. Pei, and N.V. Grishin Reconstruction of ancestral protein sequences and its applications BMC Evol Biol 4 2004 33
15. J. Pei, N.V. Dokholyan, E.I. Shakhnovich, and N.V. Grishin Using protein design for homology detection and active site searches Proc Natl Acad Sci USA 100 2003 11361 11366 (Pubitemid 37205940)
16. A. Kumar, and L. Cowen Augmented training of hidden Markov models to recognize remote homologs via simulated evolution Bioinformatics 25 2009 1602 1608
17. O. Krishnadev, and N. Srinivasan AlignHUSH: alignment of HMMs using structure and hydrophobicity information BMC Bioinf 12 2011 275
18. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, and W. Miller et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 1997 3389 3402 (Pubitemid 27359211)
19. D.R. Flower, A.C. North, and C.E. Sansom The lipocalin protein family: structural and sequence overview Biochim Biophys Acta 1482 2000 9 24
20. A.M. Burroughs, S. Balaji, L.M. Iyer, and L. Aravind Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold Biol Direct 2 2007 18
21. L. Aravind, V. Anantharaman, S. Balaji, M.M. Babu, and L.M. Iyer The many faces of the helix-turn-helix domain: transcription regulation and beyond FEMS Microbiol Rev 29 2005 231 262 (Pubitemid 40439243)
22. P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, and D. Ramage et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res 13 2003 2498 2504 (Pubitemid 37428274)
23. R.B. Pethica, M. Levitt, and J. Gough Evolutionarily consistent families in SCOP: sequence, structure and function BMC Struct Biol 12 2012 27
24. A.M. Lesk, and C. Chothia How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins J Mol Biol 136 1980 225 270
25. L. Holm, and C. Sander Dali: a network tool for protein structure comparison Trends Biochem Sci 20 1995 478 480
26. A. Lobley, M.I. Sadowski, and D.T. Jones pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination Bioinformatics 25 2009 1761 1767
27. L.S. Johnson, S.R. Eddy, and E. Portugaly Hidden Markov model speed heuristic and iterative HMM search procedure BMC Bioinf 11 2010 431
28. E.L. Sonnhammer, S.R. Eddy, E. Birney, A. Bateman, and R. Durbin Pfam: multiple sequence alignments and HMM-profiles of protein domains Nucleic Acids Res 26 1998 320 322 (Pubitemid 28291550)
29. V. Agrawal, and K.V. Kishan OB-fold: growing bigger with functional consistency Curr Protein Pept Sci 4 2003 195 206 (Pubitemid 36656733)
30. 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
31. I. Sillitoe, A.L. Cuff, B.H. Dessailly, N.L. Dawson, N. Furnham, and D. Lee et al. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures Nucleic Acids Res 41 2013 D490 D498
32. L. Holm, and C. Sander The FSSP database of structurally aligned protein fold families Nucleic Acids Res 22 1994 3600 3609 (Pubitemid 24299833)
33. 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 Bioinf 5 2004 28
34. S.B. Pandit, D. Gosar, S. Abhiman, S. Sujatha, S.S. Dixit, and N.S. Mhatre et al. SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes Nucleic Acids Res 30 2002 289 293 (Pubitemid 34679566)
35. J.M. Chandonia, N.S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S.E. Brenner ASTRAL compendium enhancements Nucleic Acids Res 30 2002 260 263 (Pubitemid 34679559)
36. B.E. Suzek, H. Huang, P. McGarvey, R. Mazumder, and C.H. Wu UniRef: comprehensive and non-redundant UniProt reference clusters Bioinformatics 23 2007 1282 1288 (Pubitemid 47050545)
37. W. Li, and A. Godzik Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 2006 1658 1659 (Pubitemid 43985301)
38. A. Biegert, and J. Soding Sequence context-specific profiles for homology searching Proc Natl Acad Sci USA 106 2009 3770 3775
39. S.R. Eddy Profile hidden Markov models Bioinformatics 14 1998 755 763 (Pubitemid 28552108)
40. M. Gribskov, A.D. McLachlan, and D. Eisenberg Profile analysis: detection of distantly related proteins Proc Natl Acad Sci USA 84 1987 4355 4358
41. V.S. Gowri, O. Krishnadev, C.S. Swamy, and N. Srinivasan MulPSSM: a database of multiple position-specific scoring matrices of protein domain families Nucleic Acids Res 34 2006 D243 D246
42. V.S. Gowri, K.G. Tina, O. Krishnadev, and N. Srinivasan Strategies for the effective identification of remotely related sequences in multiple PSSM search approach Proteins 67 2007 789 794 (Pubitemid 46753929)