메뉴 건너뛰기




Volumn 63, Issue 4, 2006, Pages 976-985

Fold recognition and accurate sequence-structure alignment of sequences directing β-sheet proteins

Author keywords

Beta trefoil; Fold recognition; Parallel right handed beta helix; Protein structure prediction; Statistical prediction

Indexed keywords

ALLERGEN; AMINO ACID; CYTOKINE; PROTEIN; TOXIN; VIRULENCE FACTOR;

EID: 33646785677     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20942     Document Type: Article
Times cited : (22)

References (49)
  • 1
    • 0000977124 scopus 로고
    • Relative orientation of close-packed beta-pleated sheets in proteins
    • Chothia C, Janin J. Relative orientation of close-packed beta-pleated sheets in proteins. Proc Natl Acad Sci USA 1981;78:4146-4150.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 4146-4150
    • Chothia, C.1    Janin, J.2
  • 2
    • 0020485895 scopus 로고
    • Orthogonal packing of beta-pleated sheets in proteins
    • Chothia C, Janin J. Orthogonal packing of beta-pleated sheets in proteins. Biochemistry 1982;21:3955-3965.
    • (1982) Biochemistry , vol.21 , pp. 3955-3965
    • Chothia, C.1    Janin, J.2
  • 3
    • 0027918655 scopus 로고
    • Unusual structural features in the parallel beta-helix in pectate lyases
    • Yoder MD, Lietzke S, Jurnack F. Unusual structural features in the parallel beta-helix in pectate lyases. Structure 1993;1:241-251.
    • (1993) Structure , vol.1 , pp. 241-251
    • Yoder, M.D.1    Lietzke, S.2    Jurnack, F.3
  • 4
    • 0035543109 scopus 로고    scopus 로고
    • The architecture of parallel beta-helices and related folds
    • Jenkins J, Pickersgill R. The architecture of parallel beta-helices and related folds. Prog Biophys Mol Biol 2001;77:111-175.
    • (2001) Prog Biophys Mol Biol , vol.77 , pp. 111-175
    • Jenkins, J.1    Pickersgill, R.2
  • 5
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 6
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999;12:85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 7
    • 0033550256 scopus 로고    scopus 로고
    • Effective use of sequence correlation and conservation in fold recognition
    • Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:1221-1239.
    • (1999) J Mol Biol , vol.293 , pp. 1221-1239
    • Olmea, O.1    Rost, B.2    Valencia, A.3
  • 8
    • 0036681397 scopus 로고    scopus 로고
    • Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory
    • Steward RE, Thornton JM. Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins 2002;48;178-191.
    • (2002) Proteins , vol.48 , pp. 178-191
    • Steward, R.E.1    Thornton, J.M.2
  • 9
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
    • (1993) J Mol Biol , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 10
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:95-202.
    • (1999) J Mol Biol , vol.292 , pp. 95-202
    • Jones, D.T.1
  • 11
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in casp4: Predictions of three-dimensional structures, secondary structures and interresidue contacts
    • Lesk AM, LoConte L, Hubbard TJP. Assessment of novel fold targets in casp4: predictions of three-dimensional structures, secondary structures and interresidue contacts. Proteins Suppl 2001;5:98-118.
    • (2001) Proteins Suppl , vol.5 , pp. 98-118
    • Lesk, A.M.1    LoConte, L.2    Hubbard, T.J.P.3
  • 13
    • 0036606453 scopus 로고    scopus 로고
    • Ab initio prediction of protein structure using LINUS
    • Srinivasan R, Rose GD. Ab initio prediction of protein structure using LINUS. Proteins 2002;47:489-495.
    • (2002) Proteins , vol.47 , pp. 489-495
    • Srinivasan, R.1    Rose, G.D.2
  • 15
    • 4143058720 scopus 로고    scopus 로고
    • Predicting specificity in bZIP coiled-coil protein interactions
    • Fong J, Keating AE, Singh MS. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol 2004;5:R11.
    • (2004) Genome Biol , vol.5
    • Fong, J.1    Keating, A.E.2    Singh, M.S.3
  • 16
    • 0035910068 scopus 로고    scopus 로고
    • BETAWRAP: Successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens
    • Bradley P, Cowen L, Menke M, King J, Berger B. BETAWRAP: successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens. Proc Natl Acad Sci USA 2001;98:14819-14824.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14819-14824
    • Bradley, P.1    Cowen, L.2    Menke, M.3    King, J.4    Berger, B.5
  • 17
  • 21
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
    • Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002;315:1257-1275.
    • (2002) J Mol Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 22
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287:797-815.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 24
    • 0032613429 scopus 로고    scopus 로고
    • Threading with explicit models for evolutionary conservation of structure and sequence
    • Panchenko A, Marchler-Bauer A, Bryant SH. Threading with explicit models for evolutionary conservation of structure and sequence. Proteins Suppl 1999;3:133-140.
    • (1999) Proteins Suppl , vol.3 , pp. 133-140
    • Panchenko, A.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 25
    • 23844520274 scopus 로고    scopus 로고
    • Wrap-and-Pack: A new paradigm for beta structural motif recognition with application to recognizing beta trefoils
    • Menke M, King J, Berger B, Cowen L. Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. J Comput Biol 2005;12:777-795.
    • (2005) J Comput Biol , vol.12 , pp. 777-795
    • Menke, M.1    King, J.2    Berger, B.3    Cowen, L.4
  • 26
    • 0027160197 scopus 로고
    • A backbone dependent rotamer library for proteins: Application to side-chain prediction
    • Dunbrack RLJ, Karplus M. A backbone dependent rotamer library for proteins: application to side-chain prediction. J Mol Biol 1993;230:543-571.
    • (1993) J Mol Biol , vol.230 , pp. 543-571
    • Dunbrack, R.L.J.1    Karplus, M.2
  • 27
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu AA, Shelenkov AA, Dunbrack RLJ. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.J.3
  • 28
    • 0034663738 scopus 로고    scopus 로고
    • Protein threading using PROSPECT: Design and evaluation
    • Xu Y, Xu D. Protein threading using PROSPECT: design and evaluation. Proteins 2000;40:343-354.
    • (2000) Proteins , vol.40 , pp. 343-354
    • Xu, Y.1    Xu, D.2
  • 29
    • 0032605828 scopus 로고    scopus 로고
    • Processing and analysis of CASP3 protein structure predictions
    • Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999;37(S3):22-29.
    • (1999) Proteins , vol.37 , Issue.S3 , pp. 22-29
    • Zemla, A.1    Venclovas, C.2    Moult, J.3    Fidelis, K.4
  • 30
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein sice-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • Bower MJ, Cohen FE, Dunbrack RLJ. Prediction of protein sice-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack, R.L.J.3
  • 31
    • 0032613301 scopus 로고    scopus 로고
    • Comparative modeling of casp3 targets using PSI-BLAST and SCWRL
    • Dunbrack RLJ. Comparative modeling of casp3 targets using PSI-BLAST and SCWRL. Proteins Suppl 1999;3:81-87.
    • (1999) Proteins Suppl , vol.3 , pp. 81-87
    • Dunbrack, R.L.J.1
  • 32
    • 0031720234 scopus 로고    scopus 로고
    • Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods
    • Huang ES, Koehl P, Levitt M, Pappu RV, Ponder JW. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods. Proteins 1998;33:204-217.
    • (1998) Proteins , vol.33 , pp. 204-217
    • Huang, E.S.1    Koehl, P.2    Levitt, M.3    Pappu, R.V.4    Ponder, J.W.5
  • 33
    • 0242369082 scopus 로고    scopus 로고
    • RAPTOR: Optimal protein threading by linear programming
    • Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 2003;1:95-117.
    • (2003) J Bioinform Comput Biol , vol.1 , pp. 95-117
    • Xu, J.1    Li, M.2    Kim, D.3    Xu, Y.4
  • 34
    • 13544259023 scopus 로고    scopus 로고
    • Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core
    • Czerwinski EW, Midoro-Horiuti T, White MA, Brooks EG, Goldblum RM. Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core. J Biol Chem 2005;280:3740-3746.
    • (2005) J Biol Chem , vol.280 , pp. 3740-3746
    • Czerwinski, E.W.1    Midoro-Horiuti, T.2    White, M.A.3    Brooks, E.G.4    Goldblum, R.M.5
  • 35
    • 1942437434 scopus 로고    scopus 로고
    • The crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway
    • Clantin B, Hodak H, Willery E, Locht C, Jacob-Dubuisson F, Villeret V. The crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway. Proc Natl Acad Sci USA 2004;101:6194-6199.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 6194-6199
    • Clantin, B.1    Hodak, H.2    Willery, E.3    Locht, C.4    Jacob-Dubuisson, F.5    Villeret, V.6
  • 36
    • 0027463701 scopus 로고
    • Genes of variola and vaccinia viruses necessary to overcome the host protective mechanisms
    • Shchelkunov SN, BLinov VM, Sandakhchiev LS. Genes of variola and vaccinia viruses necessary to overcome the host protective mechanisms. FEBS Lett 1993;319:80-83.
    • (1993) FEBS Lett , vol.319 , pp. 80-83
    • Shchelkunov, S.N.1    Blinov, V.M.2    Sandakhchiev, L.S.3
  • 38
    • 0028095571 scopus 로고
    • Crystal structure of p22 tailspike protein: Interdigitated subunits in a thermostable trimer
    • Steinbacher S, Seckler R, Miller S, Steipe B, Huber R, Reinemer P. Crystal structure of p22 tailspike protein: interdigitated subunits in a thermostable trimer. Science 1994;265:383-386.
    • (1994) Science , vol.265 , pp. 383-386
    • Steinbacher, S.1    Seckler, R.2    Miller, S.3    Steipe, B.4    Huber, R.5    Reinemer, P.6
  • 39
    • 0031570284 scopus 로고    scopus 로고
    • Two crystal structures of pectin lyase a from aspergillus reveal a ph driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases
    • Mayans O, Scott M, Connerton I, Gravesen T, Benen J, Visser J, Pickersgill R, Jenkns J. Two crystal structures of pectin lyase A from aspergillus reveal a ph driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure 1997;5:677-689.
    • (1997) Structure , vol.5 , pp. 677-689
    • Mayans, O.1    Scott, M.2    Connerton, I.3    Gravesen, T.4    Benen, J.5    Visser, J.6    Pickersgill, R.7    Jenkns, J.8
  • 40
    • 0029988488 scopus 로고    scopus 로고
    • Structure of bordetella pertussis virulence factor p.69 pertactin
    • Emsley P, Charles IG, Fairweather NF, Isaacs NW. Structure of bordetella pertussis virulence factor p.69 pertactin. Nature 1996;381:90-92.
    • (1996) Nature , vol.381 , pp. 90-92
    • Emsley, P.1    Charles, I.G.2    Fairweather, N.F.3    Isaacs, N.W.4
  • 41
    • 0029764093 scopus 로고    scopus 로고
    • Crystal structure of phage p22 tailspike protein complexed with Salmonella Sp. o-antigen receptors
    • Steinbacher S, Baxa U, Miller S, Weintraub A, Seckler R, Huber R. Crystal structure of phage p22 tailspike protein complexed with Salmonella Sp. o-antigen receptors Proc Natl Acad Sci USA 1996;93:10584-10588.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 10584-10588
    • Steinbacher, S.1    Baxa, U.2    Miller, S.3    Weintraub, A.4    Seckler, R.5    Huber, R.6
  • 42
    • 0028280034 scopus 로고
    • Meal patterns in response to the intracerebroventricular administration of interleukin-1 beta in rats
    • Plata-Salaman CR. Meal patterns in response to the intracerebroventricular administration of interleukin-1 beta in rats. Physiol Behav 1994;55:727-733.
    • (1994) Physiol Behav , vol.55 , pp. 727-733
    • Plata-Salaman, C.R.1
  • 43
    • 0023216442 scopus 로고
    • Interleukin 1 is potent modulator of insulin secretion from isolated rat islets of Langerhans
    • Comens PG, Wolf BA, Unanue ER, Lacy PE, McDaniel ML. Interleukin 1 is potent modulator of insulin secretion from isolated rat islets of Langerhans. Diabetes 1987;36:963-970.
    • (1987) Diabetes , vol.36 , pp. 963-970
    • Comens, P.G.1    Wolf, B.A.2    Unanue, E.R.3    Lacy, P.E.4    McDaniel, M.L.5
  • 44
    • 0031056969 scopus 로고    scopus 로고
    • A purified protein from Salmonella typhimurium inhibits high-affinity interleukin-2 receptor expression on CTLL-2 cells
    • Arai T, Matsui K. A purified protein from Salmonella typhimurium inhibits high-affinity interleukin-2 receptor expression on CTLL-2 cells. FEMS Immunol Med Microbiol 1997;17:155-160.
    • (1997) FEMS Immunol Med Microbiol , vol.17 , pp. 155-160
    • Arai, T.1    Matsui, K.2
  • 46
    • 0035072551 scopus 로고    scopus 로고
    • Clustering of highly homologous sequences to reduce the size of large protein databases
    • Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 2001;17:282-283.
    • (2001) Bioinformatics , vol.17 , pp. 282-283
    • Li, W.1    Jaroszewski, L.2    Godzik, A.3
  • 47
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 49
    • 0032964297 scopus 로고    scopus 로고
    • Blast 2 sequences-a new tool for comparing protein and nucleotide sequences
    • Tatusova TA, Madden TL. Blast 2 sequences-a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999;174:247-250.
    • (1999) FEMS Microbiol Lett , vol.174 , pp. 247-250
    • Tatusova, T.A.1    Madden, T.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.