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Volumn 12, Issue 6, 2004, Pages 1027-1038

Protein-protein interactions: Coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING KINETICS; BINDING SITE; CORRELATION ANALYSIS; DENSITY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 2942553723     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.04.009     Document Type: Article
Times cited : (130)

References (54)
  • 1
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins
    • Armon A., Grauer D., Ben-Tal N. ConSurf. an algorithmic tool for the identification of functional regions in proteins J. Mol. Biol. 307:2001;447-463
    • (2001) J. Mol. Biol. , vol.307 , pp. 447-463
    • Armon, A.1    Grauer, D.2    Ben-Tal, N.3
  • 3
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan A.A., Thorn K.S. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280:1998;1-9
    • (1998) J. Mol. Biol. , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 4
    • 0028247281 scopus 로고
    • Side-chain entropy and packing in proteins
    • Bromberg S., Dill K.A. Side-chain entropy and packing in proteins. Protein Sci. 3:1994;997-1009
    • (1994) Protein Sci. , vol.3 , pp. 997-1009
    • Bromberg, S.1    Dill, K.A.2
  • 5
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • Chakrabarti P., Janin J. Dissecting protein-protein recognition sites. Proteins. 47:2002;334-343
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 6
    • 0031599142 scopus 로고    scopus 로고
    • Mersenne twister: A 623-deimentionally equidistributed uniform pseudo random number generator
    • Chavez R.M., Cooper G.F. Mersenne twister. a 623-deimentionally equidistributed uniform pseudo random number generator ACM Trans. Model. Comput. Simul. 8:1998;1-30
    • (1998) ACM Trans. Model. Comput. Simul. , vol.8 , pp. 1-30
    • Chavez, R.M.1    Cooper, G.F.2
  • 7
    • 0016708122 scopus 로고
    • Principles of protein-protein recognition
    • Chothia C., Janin J. Principles of protein-protein recognition. Nature. 256:1975;705-708
    • (1975) Nature , vol.256 , pp. 705-708
    • Chothia, C.1    Janin, J.2
  • 8
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science. 267:1995;383-386
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 9
    • 0036469060 scopus 로고    scopus 로고
    • Unraveling hot spots in binding interfaces: Progress and challenges
    • DeLano W.L. Unraveling hot spots in binding interfaces. progress and challenges Curr. Opin. Struct. Biol. 12:2002;14-20
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 14-20
    • Delano, W.L.1
  • 10
    • 0034681465 scopus 로고    scopus 로고
    • Convergent solutions to binding at a protein-protein interface
    • DeLano W.L., Ultsch M.H., de Vos A.M., Wells J.A. Convergent solutions to binding at a protein-protein interface. Science. 287:2000;1279-1283
    • (2000) Science , vol.287 , pp. 1279-1283
    • Delano, W.L.1    Ultsch, M.H.2    De Vos, A.M.3    Wells, J.A.4
  • 12
    • 0037422589 scopus 로고    scopus 로고
    • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
    • Fernandez A., Scheraga H.A. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. USA. 100:2003;113-118
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 113-118
    • Fernandez, A.1    Scheraga, H.A.2
  • 13
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser F., Pupko T., Paz I., Bell R.E., Bechor-Shental D., Martz E., Ben-Tal N. ConSurf. identification of functional regions in proteins by surface-mapping of phylogenetic information Bioinformatics. 19:2003;163-164
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 14
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois R., Nielsen J.E., Serrano L. Predicting changes in the stability of proteins and protein complexes. a study of more than 1000 mutations J. Mol. Biol. 320:2002;369-387
    • (2002) J. Mol. Biol. , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 15
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of seach algorithms and a guide to scoring functions
    • Halperin I., Ma B., Wolfson H., Nussinov R. Principles of docking. an overview of seach algorithms and a guide to scoring functions Proteins. 47:2002;409-443
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 16
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? a continuum electrostatic analysis
    • Hendsch Z.S., Tidor B. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:1994;211-226
    • (1994) Protein Sci. , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 17
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot spots at protein interfaces
    • Hu Z., Ma B., Wolfson H., Nussinov R. Conservation of polar residues as hot spots at protein interfaces. Proteins. 39:2000;331-342
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 18
    • 0025123333 scopus 로고
    • The structure of protein-protein recognition sites
    • Janin J., Chothia C. The structure of protein-protein recognition sites. J. Biol. Chem. 256:1990;16027-16030
    • (1990) J. Biol. Chem. , vol.256 , pp. 16027-16030
    • Janin, J.1    Chothia, C.2
  • 20
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
    • Keskin O., Tsai C.J., Wolfson H., Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci. 13:2004;1043-1055
    • (2004) Protein Sci. , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 21
    • 0026079134 scopus 로고
    • Distribution and complementarity of hyropathy in mulisubunit proteins
    • Korn A.P., Burnett R.M. Distribution and complementarity of hyropathy in mulisubunit proteins. Proteins. 9:1991;37-55
    • (1991) Proteins , vol.9 , pp. 37-55
    • Korn, A.P.1    Burnett, R.M.2
  • 22
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme T., Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. USA. 99:2002;14116-14121
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 23
    • 0035476687 scopus 로고    scopus 로고
    • Structural basis for the high-affinity interaction of nidogen-1 with immunoglobulin-like domain 3 of perlecan
    • Kvansakul M., Hopf M., Ries A., Timpl R., Hohenester E. Structural basis for the high-affinity interaction of nidogen-1 with immunoglobulin-like domain 3 of perlecan. EMBO J. 19:2001;5342-5346
    • (2001) EMBO J. , vol.19 , pp. 5342-5346
    • Kvansakul, M.1    Hopf, M.2    Ries, A.3    Timpl, R.4    Hohenester, E.5
  • 24
    • 0032522670 scopus 로고    scopus 로고
    • Morphology of protein-protein interfaces
    • Larsen T.A., Olson A.J., Goodsell D.S. Morphology of protein-protein interfaces. Structure. 6:1998;421-427
    • (1998) Structure , vol.6 , pp. 421-427
    • Larsen, T.A.1    Olson, A.J.2    Goodsell, D.S.3
  • 25
    • 0028224689 scopus 로고
    • Modeling compact denatured states of proteins
    • Lattman E.E., Fiebig K.M., Dill K.A. Modeling compact denatured states of proteins. Biochemistry. 33:1994;6158-6166
    • (1994) Biochemistry , vol.33 , pp. 6158-6166
    • Lattman, E.E.1    Fiebig, K.M.2    Dill, K.A.3
  • 26
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge O., Sowa M.E. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12:2001;21-27
    • (2001) Curr. Opin. Struct. Biol. , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 27
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O., Bourne H.R., Cohen F.E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:1996;342-358
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 28
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • LoConte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198
    • (1999) J. Mol. Biol. , vol.285 , pp. 2177-2198
    • Loconte, L.1    Chothia, C.2    Janin, J.3
  • 29
    • 0037340493 scopus 로고    scopus 로고
    • Development of unified statistical potentials describing protein-protein interactions
    • Lu H., Lu L., Skolnick J. Development of unified statistical potentials describing protein-protein interactions. Biophys. J. 84:2003;1895-1901
    • (2003) Biophys. J. , vol.84 , pp. 1895-1901
    • Lu, H.1    Lu, L.2    Skolnick, J.3
  • 30
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma B., Shatsky M., Wolfson H., Nussinov R. Multiple diverse ligands binding at a single protein site. a matter of pre-existing populations Protein Sci. 11:2002;184-197
    • (2002) Protein Sci. , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.3    Nussinov, R.4
  • 31
    • 0037609791 scopus 로고    scopus 로고
    • Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
    • Ma B., Elkayam T., Wolfson H.J., Nussinov R. Protein-protein interactions. structurally conserved residues distinguish between binding sites and exposed protein surfaces Proc. Natl. Acad. Sci. USA. 100:2003;5772-5777
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.J.3    Nussinov, R.4
  • 32
    • 0031867090 scopus 로고    scopus 로고
    • A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies
    • Michnick S.W., Shakhnovich E. A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. Fold. Des. 3:1998;239-251
    • (1998) Fold. Des. , vol.3 , pp. 239-251
    • Michnick, S.W.1    Shakhnovich, E.2
  • 33
    • 0035957514 scopus 로고    scopus 로고
    • Evolutionary conservation of the folding nucleus
    • Mirny L., Shakhnovich E. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308:2001;123-129
    • (2001) J. Mol. Biol. , vol.308 , pp. 123-129
    • Mirny, L.1    Shakhnovich, E.2
  • 34
    • 0034769223 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
    • Norel R., Sheinerman F.B., Petry D., Honig B. Electrostatic contributions to protein-protein interactions. fast energetic filters for docking and their physical basis Protein Sci. 10:2001;2147-2161
    • (2001) Protein Sci. , vol.10 , pp. 2147-2161
    • Norel, R.1    Sheinerman, F.B.2    Petry, D.3    Honig, B.4
  • 35
    • 0025719208 scopus 로고
    • Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
    • Nussinov R., Wolfson H. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. USA. 88:1991;10495-10499
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.2
  • 36
    • 0037229456 scopus 로고    scopus 로고
    • Analyzing six types of protein-protein interfaces
    • Ofran Y., Rost B. Analyzing six types of protein-protein interfaces. J. Mol. Biol. 325:2003;377-387
    • (2003) J. Mol. Biol. , vol.325 , pp. 377-387
    • Ofran, Y.1    Rost, B.2
  • 37
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko T., Bell R.E., Mayrose I., Glaser F., Ben-Tal N. Rate4Site. an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues ISMB. 71:2002;71-77
    • (2002) ISMB , vol.71 , pp. 71-77
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 38
    • 84956971981 scopus 로고    scopus 로고
    • MultiProt: A multiple protein structural alignment algorithm
    • Shatsky M., Wolfson H.J., Nussinov R. MultiProt. a multiple protein structural alignment algorithm Lect. Notes Comput. Sci. 2452:2002;235-250
    • (2002) Lect. Notes Comput. Sci. , vol.2452 , pp. 235-250
    • Shatsky, M.1    Wolfson, H.J.2    Nussinov, R.3
  • 39
    • 2942629753 scopus 로고    scopus 로고
    • A method for simultaneous alignment of multiple protein structures
    • Shatsky M., Wolfson H.J., Nussinov R. A method for simultaneous alignment of multiple protein structures. Proteins. in press:2004
    • (2004) Proteins
    • Shatsky, M.1    Wolfson, H.J.2    Nussinov, R.3
  • 42
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn K.S., Bogan A.A. ASEdb. a database of alanine mutations and their effects on the free energy of binding in protein interactions Bioinformatics. 17:2001;284-285
    • (2001) Bioinformatics , vol.17 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2
  • 43
    • 0030602896 scopus 로고    scopus 로고
    • A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
    • Tsai C.J., Lin S.L., Wolfson H.J., Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol. 260:1996;604-620
    • (1996) J. Mol. Biol. , vol.260 , pp. 604-620
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 44
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
    • Tsai C.J., Lin S.L., Wolfson H.J., Nussinov R. Studies of protein-protein interfaces. a statistical analysis of the hydrophobic effect Protein Sci. 6:1997;53-64
    • (1997) Protein Sci. , vol.6 , pp. 53-64
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 45
    • 0031868211 scopus 로고    scopus 로고
    • Protein folding via binding and vice versa
    • Tsai C.J., Xu D., Nussinov R. Protein folding via binding and vice versa. Fold. Des. 3:1998;R71-R80
    • (1998) Fold. Des. , vol.3 , pp. 71-R80
    • Tsai, C.J.1    Xu, D.2    Nussinov, R.3
  • 46
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers
    • Valdar W.S.J., Thornton J.M. Protein-protein interfaces. analysis of amino acid conservation in homodimers Proteins. 42:2001;108-124
    • (2001) Proteins , vol.42 , pp. 108-124
    • Valdar, W.S.J.1    Thornton, J.M.2
  • 47
    • 0028575449 scopus 로고
    • Hydrophobic docking: A proposed enhancement to molecular recognition techniques
    • Vakser I.A., Aflalo C. Hydrophobic docking. a proposed enhancement to molecular recognition techniques Proteins. 20:1994;320-329
    • (1994) Proteins , vol.20 , pp. 320-329
    • Vakser, I.A.1    Aflalo, C.2
  • 48
    • 0036601150 scopus 로고    scopus 로고
    • Computational methods for prediction of protein interactions
    • Valencia A., Pazos F. Computational methods for prediction of protein interactions. Curr. Opin. Struct. Biol. 12:2002;368-373
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 368-373
    • Valencia, A.1    Pazos, F.2
  • 49
    • 0029564595 scopus 로고
    • Are buried salt bridges important for protein stability and conformational specificity?
    • Waldburger C.D., Schildbach J.F., Sauer R.T. Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2:1995;122-128
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 122-128
    • Waldburger, C.D.1    Schildbach, J.F.2    Sauer, R.T.3
  • 50
    • 0031893269 scopus 로고    scopus 로고
    • The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect
    • Xu J., Baase W.A., Baldwin E., Matthews B.W. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci. 7:1998;158-177
    • (1998) Protein Sci. , vol.7 , pp. 158-177
    • Xu, J.1    Baase, W.A.2    Baldwin, E.3    Matthews, B.W.4
  • 52
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young L., Jernigan R.L., Covell D.G. A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3:1994;717-729
    • (1994) Protein Sci. , vol.3 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 54
    • 0023660653 scopus 로고
    • Prediction of protein secondary structure and active sites using the alignment of homologous sequences
    • Zvelebil M.J., Barton G.J., Taylor W.R., Sternberg M.J. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol. 195:1987;957-961
    • (1987) J. Mol. Biol. , vol.195 , pp. 957-961
    • Zvelebil, M.J.1    Barton, G.J.2    Taylor, W.R.3    Sternberg, M.J.4


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