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Volumn 19, Issue 3, 2009, Pages 349-356

Exploiting structural classifications for function prediction: towards a domain grammar for protein function

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; CLASSIFICATION; FUNCTIONAL PROTEOMICS; MOLECULAR EVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; SEQUENCE ANALYSIS; STRUCTURAL PROTEOMICS; STRUCTURE ANALYSIS;

EID: 66549096455     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2009.03.009     Document Type: Review
Times cited : (30)

References (68)
  • 1
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee D., Redfern O., and Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 8 (2007) 995-1005
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 4
    • 33846059668 scopus 로고    scopus 로고
    • The generation of new protein functions by the combination of domains
    • This paper provides a very complete and well-structured analysis of mechanisms by which acquisition of new domains and recombination of domains allow proteins to adopt novel functions.
    • Bashton M., and Chothia C. The generation of new protein functions by the combination of domains. Structure 15 (2007) 85-99. This paper provides a very complete and well-structured analysis of mechanisms by which acquisition of new domains and recombination of domains allow proteins to adopt novel functions.
    • (2007) Structure , vol.15 , pp. 85-99
    • Bashton, M.1    Chothia, C.2
  • 6
    • 33744805069 scopus 로고    scopus 로고
    • Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction
    • Kolodny R., Petrey D., and Honig B. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 16 (2006) 393-398
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 393-398
    • Kolodny, R.1    Petrey, D.2    Honig, B.3
  • 8
    • 40749148575 scopus 로고    scopus 로고
    • On distance and similarity in fold space
    • Sippl M.J. On distance and similarity in fold space. Bioinformatics 24 (2008) 872-873
    • (2008) Bioinformatics , vol.24 , pp. 872-873
    • Sippl, M.J.1
  • 9
    • 34347383961 scopus 로고    scopus 로고
    • Evolutionary transitions in protein fold space
    • Taylor W.R. Evolutionary transitions in protein fold space. Curr Opin Struct Biol 17 (2007) 354-361
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 354-361
    • Taylor, W.R.1
  • 10
    • 44949143819 scopus 로고    scopus 로고
    • Cradle-loop barrels and the concept of metafolds in protein classification by natural descent
    • Alva V., Koretke K.K., Coles M., and Lupas A.N. Cradle-loop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol 18 (2008) 358-365
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 358-365
    • Alva, V.1    Koretke, K.K.2    Coles, M.3    Lupas, A.N.4
  • 11
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo C.A., Jones D.T., and Thornton J.M. Protein superfamilies and domain superfolds. Nature 372 (1994) 631-634
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 12
    • 33745727120 scopus 로고    scopus 로고
    • Structural diversity of domain superfamilies in the CATH database
    • Reeves G.A., Dallman T.J., Redfern O.C., Akpor A., and Orengo C.A. Structural diversity of domain superfamilies in the CATH database. J Mol Biol 360 (2006) 725-741
    • (2006) J Mol Biol , vol.360 , pp. 725-741
    • Reeves, G.A.1    Dallman, T.J.2    Redfern, O.C.3    Akpor, A.4    Orengo, C.A.5
  • 13
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin N.V. Fold change in evolution of protein structures. J Struct Biol 134 (2001) 167-185
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 14
    • 33744783371 scopus 로고    scopus 로고
    • Evolution of protein fold in the presence of functional constraints
    • Andreeva A., and Murzin A.G. Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16 (2006) 399-408
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 399-408
    • Andreeva, A.1    Murzin, A.G.2
  • 15
    • 46649088364 scopus 로고    scopus 로고
    • Biochemistry. Metamorphic proteins
    • Interesting and well-documented short article exploring the notion of metamorphic proteins, that is, proteins whose structure changes during their lifetime.
    • Murzin A.G. Biochemistry. Metamorphic proteins. Science 320 (2008) 1725-1726. Interesting and well-documented short article exploring the notion of metamorphic proteins, that is, proteins whose structure changes during their lifetime.
    • (2008) Science , vol.320 , pp. 1725-1726
    • Murzin, A.G.1
  • 16
    • 45549109966 scopus 로고    scopus 로고
    • Functionally important segments in proteins dissected using gene ontology and geometric clustering of peptide fragments
    • Manikandan K., Pal D., Ramakumar S., Brener N.E., Iyengar S.S., and Seetharaman G. Functionally important segments in proteins dissected using gene ontology and geometric clustering of peptide fragments. Genome Biol 9 (2008) R52
    • (2008) Genome Biol , vol.9
    • Manikandan, K.1    Pal, D.2    Ramakumar, S.3    Brener, N.E.4    Iyengar, S.S.5    Seetharaman, G.6
  • 17
    • 0041317258 scopus 로고    scopus 로고
    • More than the sum of their parts: on the evolution of proteins from peptides
    • Soding J., and Lupas A.N. More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 25 (2003) 837-846
    • (2003) Bioessays , vol.25 , pp. 837-846
    • Soding, J.1    Lupas, A.N.2
  • 18
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • This paper presents a novel method for predicting similarity in ligand-binding sites. The authors compare their method with other published approaches and demonstrate its superiority for predicting the binding of adenine-containing compounds. Their results also suggest that these binding sites have arisen from divergent rather than convergent evolution, as similarities are found across different SCOP superfamilies.
    • Xie L., and Bourne P.E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105 (2008) 5441-5446. This paper presents a novel method for predicting similarity in ligand-binding sites. The authors compare their method with other published approaches and demonstrate its superiority for predicting the binding of adenine-containing compounds. Their results also suggest that these binding sites have arisen from divergent rather than convergent evolution, as similarities are found across different SCOP superfamilies.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 19
    • 34548806425 scopus 로고    scopus 로고
    • Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone
    • Reid A.J., Yeats C., and Orengo C.A. Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics 23 (2007) 2353-2360
    • (2007) Bioinformatics , vol.23 , pp. 2353-2360
    • Reid, A.J.1    Yeats, C.2    Orengo, C.A.3
  • 22
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds. Binding site similarity in the absence of homology
    • Russell R.B., Sasieni P.D., and Sternberg M.J. Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 282 (1998) 903-918
    • (1998) J Mol Biol , vol.282 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.3
  • 23
    • 0037500141 scopus 로고    scopus 로고
    • Evolution by gene duplication: an update
    • Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol 18 (2003) 292-298
    • (2003) Trends Ecol Evol , vol.18 , pp. 292-298
    • Zhang, J.1
  • 24
    • 56549119570 scopus 로고    scopus 로고
    • Turning a hobby into a job: how duplicated genes find new functions
    • An exhaustive review that provides an update on the mechanisms by which the function of proteins changes after duplication.
    • Conant G.C., and Wolfe K.H. Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9 (2008) 938-950. An exhaustive review that provides an update on the mechanisms by which the function of proteins changes after duplication.
    • (2008) Nat Rev Genet , vol.9 , pp. 938-950
    • Conant, G.C.1    Wolfe, K.H.2
  • 27
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd A.E., Orengo C.A., and Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307 (2001) 1113-1143
    • (2001) J Mol Biol , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 28
    • 33747872771 scopus 로고    scopus 로고
    • Origins and impact of constraints in evolution of gene families
    • Shakhnovich B.E., and Koonin E.V. Origins and impact of constraints in evolution of gene families. Genome Res 16 (2006) 1529-1536
    • (2006) Genome Res , vol.16 , pp. 1529-1536
    • Shakhnovich, B.E.1    Koonin, E.V.2
  • 31
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov I.N., and Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11 (1998) 739-747
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 32
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 233 (1993) 123-138
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 33
    • 36949008379 scopus 로고    scopus 로고
    • CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures
    • Redfern O.C., Harrison A., Dallman T., Pearl F.M., and Orengo C.A. CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLoS Comput Biol 3 (2007) e232
    • (2007) PLoS Comput Biol , vol.3
    • Redfern, O.C.1    Harrison, A.2    Dallman, T.3    Pearl, F.M.4    Orengo, C.A.5
  • 34
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y., and Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19 Suppl. 2 (2003) ii246-ii255
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Ye, Y.1    Godzik, A.2
  • 35
    • 41949103740 scopus 로고    scopus 로고
    • The structure of protein evolution and the evolution of protein structure
    • In this review, the author systematically explores the different hypotheses that attempt to explain why some superfamilies and folds have expanded and diverged much more than others during the course of evolution.
    • Goldstein R.A. The structure of protein evolution and the evolution of protein structure. Curr Opin Struct Biol 18 (2008) 170-177. In this review, the author systematically explores the different hypotheses that attempt to explain why some superfamilies and folds have expanded and diverged much more than others during the course of evolution.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 170-177
    • Goldstein, R.A.1
  • 37
    • 50949084090 scopus 로고    scopus 로고
    • Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies
    • This paper presents an automated method for annotating members of different superfamilies with likely substrates. The authors' analysis looks at the substructures of the substrates that are conserved among different relatives. It highlights the fact that different superfamilies often need to be treated individually to predict aspects of their function using structural data.
    • Chiang R.A., Sali A., and Babbitt P.C. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 4 (2008) e1000142. This paper presents an automated method for annotating members of different superfamilies with likely substrates. The authors' analysis looks at the substructures of the substrates that are conserved among different relatives. It highlights the fact that different superfamilies often need to be treated individually to predict aspects of their function using structural data.
    • (2008) PLoS Comput Biol , vol.4
    • Chiang, R.A.1    Sali, A.2    Babbitt, P.C.3
  • 38
    • 37449004656 scopus 로고    scopus 로고
    • Molecular docking for substrate identification: the short-chain dehydrogenases/reductases
    • Favia A.D., Nobeli I., Glaser F., and Thornton J.M. Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J Mol Biol 375 (2008) 855-874
    • (2008) J Mol Biol , vol.375 , pp. 855-874
    • Favia, A.D.1    Nobeli, I.2    Glaser, F.3    Thornton, J.M.4
  • 40
    • 34547603801 scopus 로고    scopus 로고
    • Evolution of function in the 'two dinucleotide binding domains' flavoproteins
    • Ojha S., Meng E.C., and Babbitt P.C. Evolution of function in the 'two dinucleotide binding domains' flavoproteins. PLoS Comput Biol 3 (2007) e121
    • (2007) PLoS Comput Biol , vol.3
    • Ojha, S.1    Meng, E.C.2    Babbitt, P.C.3
  • 42
    • 0036643477 scopus 로고    scopus 로고
    • Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA
    • Aravind L., Anantharaman V., and Koonin E.V. Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Proteins 48 (2002) 1-14
    • (2002) Proteins , vol.48 , pp. 1-14
    • Aravind, L.1    Anantharaman, V.2    Koonin, E.V.3
  • 44
  • 45
    • 34547939672 scopus 로고    scopus 로고
    • Structure-based activity prediction for an enzyme of unknown function
    • This paper describes the successful prediction of the activity of an enzyme that belongs to the very large and diverse amidohydrolase superfamily, by docking it against a list of high-energy intermediate forms of candidate metabolites. The list of these candidate metabolites is derived from a list of compounds appearing in reactions catalysed by other members of the superfamily.
    • Hermann J.C., Marti-Arbona R., Fedorov A.A., Fedorov E., Almo S.C., Shoichet B.K., and Raushel F.M. Structure-based activity prediction for an enzyme of unknown function. Nature 448 (2007) 775-779. This paper describes the successful prediction of the activity of an enzyme that belongs to the very large and diverse amidohydrolase superfamily, by docking it against a list of high-energy intermediate forms of candidate metabolites. The list of these candidate metabolites is derived from a list of compounds appearing in reactions catalysed by other members of the superfamily.
    • (2007) Nature , vol.448 , pp. 775-779
    • Hermann, J.C.1    Marti-Arbona, R.2    Fedorov, A.A.3    Fedorov, E.4    Almo, S.C.5    Shoichet, B.K.6    Raushel, F.M.7
  • 47
    • 38549133831 scopus 로고    scopus 로고
    • At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate
    • Nguyen T.T., Brown S., Fedorov A.A., Fedorov E.V., Babbitt P.C., Almo S.C., and Raushel F.M. At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate. Biochemistry 47 (2008) 1194-1206
    • (2008) Biochemistry , vol.47 , pp. 1194-1206
    • Nguyen, T.T.1    Brown, S.2    Fedorov, A.A.3    Fedorov, E.V.4    Babbitt, P.C.5    Almo, S.C.6    Raushel, F.M.7
  • 48
    • 35848958144 scopus 로고    scopus 로고
    • A protein structure (or function?) initiative
    • Gerlt J.A. A protein structure (or function?) initiative. Structure 15 (2007) 1353-1356
    • (2007) Structure , vol.15 , pp. 1353-1356
    • Gerlt, J.A.1
  • 49
    • 0034923923 scopus 로고    scopus 로고
    • Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies
    • Gerlt J.A., and Babbitt P.C. Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. Annu Rev Biochem 70 (2001) 209-246
    • (2001) Annu Rev Biochem , vol.70 , pp. 209-246
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 50
    • 0036600740 scopus 로고    scopus 로고
    • Pathway evolution, structurally speaking
    • Rison S.C., and Thornton J.M. Pathway evolution, structurally speaking. Curr Opin Struct Biol 12 (2002) 374-382
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 374-382
    • Rison, S.C.1    Thornton, J.M.2
  • 51
    • 34548392746 scopus 로고    scopus 로고
    • Automated protein subfamily identification and classification
    • Brown D.P., Krishnamurthy N., and Sjolander K. Automated protein subfamily identification and classification. PLoS Comput Biol 3 (2007) e160
    • (2007) PLoS Comput Biol , vol.3
    • Brown, D.P.1    Krishnamurthy, N.2    Sjolander, K.3
  • 52
    • 44949137643 scopus 로고    scopus 로고
    • Determinants of protein function revealed by combinatorial entropy optimization
    • Reva B., Antipin Y., and Sander C. Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol 8 (2007) R232
    • (2007) Genome Biol , vol.8
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 53
    • 46249099576 scopus 로고    scopus 로고
    • Characterization and prediction of residues determining protein functional specificity
    • Capra J.A., and Singh M. Characterization and prediction of residues determining protein functional specificity. Bioinformatics 24 (2008) 1473-1480
    • (2008) Bioinformatics , vol.24 , pp. 1473-1480
    • Capra, J.A.1    Singh, M.2
  • 54
    • 37549049756 scopus 로고    scopus 로고
    • Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
    • Ye K., Anton F.K., Heringa J., Ijzerman A.P., and Marchiori E. Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinformatics 24 (2008) 18-25
    • (2008) Bioinformatics , vol.24 , pp. 18-25
    • Ye, K.1    Anton, F.K.2    Heringa, J.3    Ijzerman, A.P.4    Marchiori, E.5
  • 55
    • 0037423764 scopus 로고    scopus 로고
    • Functional fingerprints of folds: evidence for correlated structure-function evolution
    • Shakhnovich B.E., Dokholyan N.V., DeLisi C., and Shakhnovich E.I. Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol 326 (2003) 1-9
    • (2003) J Mol Biol , vol.326 , pp. 1-9
    • Shakhnovich, B.E.1    Dokholyan, N.V.2    DeLisi, C.3    Shakhnovich, E.I.4
  • 57
    • 33645098516 scopus 로고    scopus 로고
    • Automated discovery of 3D motifs for protein function annotation
    • Polacco B.J., and Babbitt P.C. Automated discovery of 3D motifs for protein function annotation. Bioinformatics 22 (2006) 723-730
    • (2006) Bioinformatics , vol.22 , pp. 723-730
    • Polacco, B.J.1    Babbitt, P.C.2
  • 58
    • 33748776559 scopus 로고    scopus 로고
    • Automated protein function prediction-the genomic challenge
    • Friedberg I. Automated protein function prediction-the genomic challenge. Brief Bioinform 7 (2006) 225-242
    • (2006) Brief Bioinform , vol.7 , pp. 225-242
    • Friedberg, I.1
  • 59
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: a server for predicting protein function from 3D structure
    • Laskowski R.A., Watson J.D., and Thornton J.M. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33 (2005) W89-W93
    • (2005) Nucleic Acids Res , vol.33
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 60
    • 11844292002 scopus 로고    scopus 로고
    • Inference of protein function from protein structure
    • Pal D., and Eisenberg D. Inference of protein function from protein structure. Structure 13 (2005) 121-130
    • (2005) Structure , vol.13 , pp. 121-130
    • Pal, D.1    Eisenberg, D.2
  • 61
    • 33747867004 scopus 로고    scopus 로고
    • JAFA: a protein function annotation meta-server
    • Friedberg I., Harder T., and Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res 34 (2006) W379-W381
    • (2006) Nucleic Acids Res , vol.34
    • Friedberg, I.1    Harder, T.2    Godzik, A.3
  • 62
    • 50849114838 scopus 로고    scopus 로고
    • Arrangements in the modular evolution of proteins
    • An interesting review of evolutionary insights into the diverse modes and origins of arrangements and combinations of domains in proteins.
    • Moore A.D., Bjorklund A.K., Ekman D., Bornberg-Bauer E., and Elofsson A. Arrangements in the modular evolution of proteins. Trends Biochem Sci 33 (2008) 444-451. An interesting review of evolutionary insights into the diverse modes and origins of arrangements and combinations of domains in proteins.
    • (2008) Trends Biochem Sci , vol.33 , pp. 444-451
    • Moore, A.D.1    Bjorklund, A.K.2    Ekman, D.3    Bornberg-Bauer, E.4    Elofsson, A.5
  • 65
    • 40449095056 scopus 로고    scopus 로고
    • Evolution of protein domain promiscuity in eukaryotes
    • Basu M.K., Carmel L., Rogozin I.B., and Koonin E.V. Evolution of protein domain promiscuity in eukaryotes. Genome Res 18 (2008) 449-461
    • (2008) Genome Res , vol.18 , pp. 449-461
    • Basu, M.K.1    Carmel, L.2    Rogozin, I.B.3    Koonin, E.V.4
  • 68
    • 33751091763 scopus 로고    scopus 로고
    • Cognate ligand domain mapping for enzymes
    • Bashton M., Nobeli I., and Thornton J.M. Cognate ligand domain mapping for enzymes. J Mol Biol 364 (2006) 836-852
    • (2006) J Mol Biol , vol.364 , pp. 836-852
    • Bashton, M.1    Nobeli, I.2    Thornton, J.M.3


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