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Volumn 34, Issue 22, 2006, Pages 6450-6460

Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; MESSENGER RNA; RNA;

EID: 33845865515     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl819     Document Type: Article
Times cited : (106)

References (50)
  • 1
    • 0037123632 scopus 로고    scopus 로고
    • An expanding universe of noncoding RNAs
    • Storz,G. (2002) An expanding universe of noncoding RNAs. Science, 296, 1260-1263.
    • (2002) Science , vol.296 , pp. 1260-1263
    • Storz, G.1
  • 2
    • 24644443227 scopus 로고    scopus 로고
    • The functional genomics of noncoding RNA
    • Mattick,J.S. (2005) The functional genomics of noncoding RNA. Science, 309, 1527-1528.
    • (2005) Science , vol.309 , pp. 1527-1528
    • Mattick, J.S.1
  • 4
    • 0035966319 scopus 로고    scopus 로고
    • microRNAs: Tiny regulators with great potential
    • Ambros,V. (2001) microRNAs: Tiny regulators with great potential. Cell, 107, 823-826.
    • (2001) Cell , vol.107 , pp. 823-826
    • Ambros, V.1
  • 5
    • 0042671357 scopus 로고    scopus 로고
    • Pre-mRNA splicing: Awash in a sea of proteins
    • Jurica,M.S. and Moore,M.J. (2003) Pre-mRNA splicing: Awash in a sea of proteins. Mol. Cell, 12, 5-14.
    • (2003) Mol. Cell , vol.12 , pp. 5-14
    • Jurica, M.S.1    Moore, M.J.2
  • 6
    • 24644502657 scopus 로고    scopus 로고
    • From birth to death: The complex lives of eukaryotic mRNAs
    • Moore,M.J. (2005) From birth to death: The complex lives of eukaryotic mRNAs. Science, 309, 1514-1518.
    • (2005) Science , vol.309 , pp. 1514-1518
    • Moore, M.J.1
  • 7
    • 24644437810 scopus 로고    scopus 로고
    • RNA structure: Reading the ribosome
    • Noller,H.F. (2005) RNA structure: Reading the ribosome. Science, 309, 1508-1514.
    • (2005) Science , vol.309 , pp. 1508-1514
    • Noller, H.F.1
  • 9
    • 0033866085 scopus 로고    scopus 로고
    • Sense from nonsense: How the genetic information of chloroplasts is altered by RNA editing
    • Bock,R. (2000) Sense from nonsense: How the genetic information of chloroplasts is altered by RNA editing. Biochimie, 82, 549-557.
    • (2000) Biochimie , vol.82 , pp. 549-557
    • Bock, R.1
  • 10
    • 0035912793 scopus 로고    scopus 로고
    • Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome
    • Keene,J.D. (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc. Natl Acad. Sci. USA, 98, 7018-7024.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 7018-7024
    • Keene, J.D.1
  • 11
    • 0028839860 scopus 로고
    • Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
    • Mandel-Gutfreund,Y., Schueler,O. and Margalit,H. (1995) Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles. J. Mol. Biol., 253, 370-382.
    • (1995) J. Mol. Biol. , vol.253 , pp. 370-382
    • Mandel-Gutfreund, Y.1    Schueler, O.2    Margalit, H.3
  • 13
    • 0033573827 scopus 로고    scopus 로고
    • Structural features of protein-nucleic acid recognition sites
    • Nadassy,K., Wodak,S.J. and Janin,J. (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry, 38, 1999-2017.
    • (1999) Biochemistry , vol.38 , pp. 1999-2017
    • Nadassy, K.1    Wodak, S.J.2    Janin, J.3
  • 14
    • 0034682882 scopus 로고    scopus 로고
    • Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
    • Pabo,C.O. and Nekludova,L. (2000) Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition? J. Mol. Biol., 301, 597-624.
    • (2000) J. Mol. Biol. , vol.301 , pp. 597-624
    • Pabo, C.O.1    Nekludova, L.2
  • 15
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe,N.M., Laskowski,R.A. and Thornton,J.M. (2001) Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 16
    • 0346258292 scopus 로고    scopus 로고
    • Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
    • Jones,S., Shanahan,H.P., Berman,H.M. and Thornton,J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 7189-7198
    • Jones, S.1    Shanahan, H.P.2    Berman, H.M.3    Thornton, J.M.4
  • 17
    • 2542557409 scopus 로고    scopus 로고
    • Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
    • Tsuchiya,Y., Kinoshita,K. and Nakamura,H. (2004) Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 55, 885-894.
    • (2004) Proteins , vol.55 , pp. 885-894
    • Tsuchiya, Y.1    Kinoshita, K.2    Nakamura, H.3
  • 18
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig,B. and Nicholls,A. (1995) Classical electrostatics in biology and chemistry. Science, 268, 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 19
    • 0032727991 scopus 로고    scopus 로고
    • Themes in RNA-protein recognition
    • Draper,D.E. (1999) Themes in RNA-protein recognition. J. Mol. Biol., 293, 255-270.
    • (1999) J Mol. Biol. , vol.293 , pp. 255-270
    • Draper, D.E.1
  • 20
  • 21
    • 0037470573 scopus 로고    scopus 로고
    • Annotating nucleic acid-binding function based on protein structure
    • Stawiski,E.W., Gregoret,L.M. and Mandel-Gutfreund,Y. (2003) Annotating nucleic acid-binding function based on protein structure. J. Mol. Biol., 326, 1065-1079.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1065-1079
    • Stawiski, E.W.1    Gregoret, L.M.2    Mandel-Gutfreund, Y.3
  • 22
    • 18844421633 scopus 로고    scopus 로고
    • Decoding the decoding region: Analysis of eukaryotic release factor (eRF1) stop codon-binding residues
    • Liang,H., Wong,J.Y., Bao,Q., Cavalcanti,A.R. and Landweber,L.F. (2005) Decoding the decoding region: Analysis of eukaryotic release factor (eRF1) stop codon-binding residues. J. Mol. Evol., 60, 337-344.
    • (2005) J. Mol. Evol. , vol.60 , pp. 337-344
    • Liang, H.1    Wong, J.Y.2    Bao, Q.3    Cavalcanti, A.R.4    Landweber, L.F.5
  • 23
    • 14744303845 scopus 로고    scopus 로고
    • Newly sequenced eRF1s from ciliates: The diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions
    • Kim,O.T.P., Yura,K., Go,N. and Harumoto,T. (2005) Newly sequenced eRF1s from ciliates: The diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions. Gene, 346, 277-286.
    • (2005) Gene , vol.346 , pp. 277-286
    • Kim, O.T.P.1    Yura, K.2    Go, N.3    Harumoto, T.4
  • 25
    • 0034603210 scopus 로고    scopus 로고
    • The crystal structure of human eukaryotic release factor eRF1 - Mechanism of stop codon recognition and peptidyl-tRNA hydrolysis
    • Song,H., Mugnier,P., Das,A.K., Webb,H.M., Evans,D.R., Tuite,M.F., Hemmings,B.A. and Barford,D. (2000) The crystal structure of human eukaryotic release factor eRF1 - mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell, 100, 311-321.
    • (2000) Cell , vol.100 , pp. 311-321
    • Song, H.1    Mugnier, P.2    Das, A.K.3    Webb, H.M.4    Evans, D.R.5    Tuite, M.F.6    Hemmings, B.A.7    Barford, D.8
  • 28
    • 0034823943 scopus 로고    scopus 로고
    • Statistical analysis of atomic contacts at RNA-protein interfaces
    • Treger,M. and Westhof,E. (2001) Statistical analysis of atomic contacts at RNA-protein interfaces. J. Mol. Recognit., 14, 199-214.
    • (2001) J. Mol. Recognit. , vol.14 , pp. 199-214
    • Treger, M.1    Westhof, E.2
  • 29
    • 0141760496 scopus 로고    scopus 로고
    • Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns
    • Kim,H., Jeong,E., Lee,S.W. and Han,K. (2003) Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns. FEBS Lett., 552, 231-239.
    • (2003) FEBS Lett. , vol.552 , pp. 231-239
    • Kim, H.1    Jeong, E.2    Lee, S.W.3    Han, K.4
  • 30
    • 0035800599 scopus 로고    scopus 로고
    • Structure-based analysis of protein-RNA interactions using the program ENTANGLE
    • Allers,J. and Shamoo,Y. (2001) Structure-based analysis of protein-RNA interactions using the program ENTANGLE. J. Mol. Biol., 311, 75-86.
    • (2001) J. Mol. Biol. , vol.311 , pp. 75-86
    • Allers, J.1    Shamoo, Y.2
  • 31
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick,K. and Thornton,J.M. (1998) PQS: A protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 32
  • 35
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge,O. and Sowa,M.E. (2002) Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol., 12, 21-27.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 36
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: An overview
    • Baldi,P., Brunak,S., Chauvin,Y., Andersen,C.A. and Nielsen,H. (2000) Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics, 16, 412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 37
    • 26444619105 scopus 로고    scopus 로고
    • Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes
    • Jeong,E., Kim,H., Lee,S.W. and Han,K. (2003) Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes. Mol. Cells, 16, 161-167.
    • (2003) Mol. Cells , vol.16 , pp. 161-167
    • Jeong, E.1    Kim, H.2    Lee, S.W.3    Han, K.4
  • 38
    • 0036836642 scopus 로고    scopus 로고
    • Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence
    • Kloczkowski,A., Ting,K.L., Jernigan,R.L. and Garnier,J. (2002) Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins, 49, 154-166.
    • (2002) Proteins , vol.49 , pp. 154-166
    • Kloczkowski, A.1    Ting, K.L.2    Jernigan, R.L.3    Garnier, J.4
  • 39
    • 0037133188 scopus 로고    scopus 로고
    • The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor
    • Ho,D.N., Coburn,G.A., Kang,Y., Cullen,B.R. and Georgiadis,M.M. (2002) The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor. Proc. Natl Acad. Sci. USA, 99, 1888-1893.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 1888-1893
    • Ho, D.N.1    Coburn, G.A.2    Kang, Y.3    Cullen, B.R.4    Georgiadis, M.M.5
  • 40
    • 4143076853 scopus 로고    scopus 로고
    • Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export
    • Zhao,R., Shen,J., Green,M.R., MacMorris,M. and Blumenthal,T. (2004) Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. Structure, 12, 1373-1381.
    • (2004) Structure , vol.12 , pp. 1373-1381
    • Zhao, R.1    Shen, J.2    Green, M.R.3    MacMorris, M.4    Blumenthal, T.5
  • 41
    • 11144222543 scopus 로고    scopus 로고
    • Crystal structure of the human ATP-dependent splicing and export factor UAP56
    • Shi,H., Cordin,O., Minder,C.M., Linder,P. and Xu,R.M. (2004) Crystal structure of the human ATP-dependent splicing and export factor UAP56. Proc. Natl Acad. Sci. USA, 101, 17628-17633.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17628-17633
    • Shi, H.1    Cordin, O.2    Minder, C.M.3    Linder, P.4    Xu, R.M.5
  • 42
    • 0032766007 scopus 로고    scopus 로고
    • Identification of novel import and export signals of human TAP, the protein that binds to the constitutive transport element of the type D retrovirus mRNAs
    • Bear,J., Tan,W., Zolotukhin,A.S., Tabernero,C., Hudson,E.A. and Felber,B.K. (1999) Identification of novel import and export signals of human TAP, the protein that binds to the constitutive transport element of the type D retrovirus mRNAs. Mol. Cell. Biol., 19, 6306-6317.
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 6306-6317
    • Bear, J.1    Tan, W.2    Zolotukhin, A.S.3    Tabernero, C.4    Hudson, E.A.5    Felber, B.K.6
  • 43
    • 0033135976 scopus 로고    scopus 로고
    • The human Tap protein is a nuclear mRNA export factor that contains novel RNA-binding and nucleocytoplasmic transport sequences
    • Kang,Y. and Cullen,B.R. (1999) The human Tap protein is a nuclear mRNA export factor that contains novel RNA-binding and nucleocytoplasmic transport sequences. Genes Dev., 13, 1126-1139.
    • (1999) Genes Dev. , vol.13 , pp. 1126-1139
    • Kang, Y.1    Cullen, B.R.2
  • 44
    • 0345643313 scopus 로고    scopus 로고
    • The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human
    • Katahira,J., Strasser,K., Podtelejnikov,A., Mann,M., Jung,J.U. and Hurt,E. (1999) The Mex67p-mediated nuclear mRNA export pathway is conserved from yeast to human. EMBO J., 18, 2593-2609.
    • (1999) EMBO J. , vol.18 , pp. 2593-2609
    • Katahira, J.1    Strasser, K.2    Podtelejnikov, A.3    Mann, M.4    Jung, J.U.5    Hurt, E.6
  • 45
    • 0037443026 scopus 로고    scopus 로고
    • Nuclear RNA export
    • Cullen,B.R. (2003) Nuclear RNA export. J. Cell Sci., 116, 587-597.
    • (2003) J. Cell Sci. , vol.116 , pp. 587-597
    • Cullen, B.R.1
  • 46
    • 0035873246 scopus 로고    scopus 로고
    • Using viral species specificity to define a critical protein/RNA interaction surface
    • Coburn,G.A., Wiegand,H.L., Kang,Y., Ho,D.N., Georgiadis,M.M. and Cullen,B.R. (2001) Using viral species specificity to define a critical protein/RNA interaction surface. Genes Dev., 15, 1194-1205.
    • (2001) Genes Dev. , vol.15 , pp. 1194-1205
    • Coburn, G.A.1    Wiegand, H.L.2    Kang, Y.3    Ho, D.N.4    Georgiadis, M.M.5    Cullen, B.R.6
  • 47
    • 0030611640 scopus 로고    scopus 로고
    • U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction
    • Fleckner,J., Zhang,M., Valcarcel,J. and Green,M.R. (1997) U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes Dev., 11, 1864-1872.
    • (1997) Genes Dev. , vol.11 , pp. 1864-1872
    • Fleckner, J.1    Zhang, M.2    Valcarcel, J.3    Green, M.R.4
  • 48
    • 0035846138 scopus 로고    scopus 로고
    • Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly
    • Luo,M.L., Zhou,Z., Magni,K., Christoforides,C., Rappsilber,J., Mann,M. and Reed,R. (2001) Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature, 413, 644-647.
    • (2001) Nature , vol.413 , pp. 644-647
    • Luo, M.L.1    Zhou, Z.2    Magni, K.3    Christoforides, C.4    Rappsilber, J.5    Mann, M.6    Reed, R.7
  • 49
    • 0038719952 scopus 로고    scopus 로고
    • UAP56 levels affect viability and mRNA export in Caenorhabditis elegans
    • MacMorris,M., Brocker,C. and Blumenthal,T. (2003) UAP56 levels affect viability and mRNA export in Caenorhabditis elegans. RNA, 9, 847-857.
    • (2003) RNA , vol.9 , pp. 847-857
    • MacMorris, M.1    Brocker, C.2    Blumenthal, T.3
  • 50
    • 0032489021 scopus 로고    scopus 로고
    • Mechanical devices of the spliceosome: Motors, clocks, springs, and things
    • Staley,J.P. and Guthrie,C. (1998) Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell, 92, 315-326.
    • (1998) Cell , vol.92 , pp. 315-326
    • Staley, J.P.1    Guthrie, C.2


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