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Volumn 78, Issue 16, 2010, Pages 3304-3316

Geometrically centered region: A "wet" model of protein binding hot spots not excluding water molecules

Author keywords

Burial level; GCR; Hot spot; O ring; Water mediated contact

Indexed keywords

GLYCINE; SOLVENT; WATER;

EID: 78349271620     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22838     Document Type: Article
Times cited : (18)

References (43)
  • 1
    • 0024403619 scopus 로고
    • High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis
    • Cunningham BC, Wells JA. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science 1989; 244: 1081-1085.
    • (1989) Science , vol.244 , pp. 1081-1085
    • Cunningham, B.C.1    Wells, J.A.2
  • 2
    • 0026350498 scopus 로고
    • Methods in enzymology
    • In:Molecular design and modeling: concepts and applications part a: proteins, peptides, and enzymes, of, San Diego, California, Academic Press
    • Wells JA. Systematic mutational analyses of protein-protein interfaces. In:Molecular design and modeling: concepts and applications part a: proteins, peptides, and enzymes, volume 202 of Methods in enzymology. San Diego, California: Academic Press; 1991, pp. 390-411.
    • (1991) Systematic mutational analyses of protein-protein interfaces , vol.202 , pp. 390-411
    • Wells, J.A.1
  • 3
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson T, Wells JA. A hot spot of binding energy in a hormone-receptor interface. Science 1995; 267: 383-386.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 4
    • 0032540358 scopus 로고    scopus 로고
    • Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity
    • Clackson T, Ultsch MH, Wells JA, de Vos AM. Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. J Mol Biol 1998; 277: 1111-1128.
    • (1998) J Mol Biol , vol.277 , pp. 1111-1128
    • Clackson, T.1    Ultsch, M.H.2    Wells, J.A.3    de Vos, A.M.4
  • 6
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc 1999; 121: 8133-8143.
    • (1999) J Am Chem Soc , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 7
    • 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 2002; 99: 14116-14121.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 8
    • 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 JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002; 320: 369-387.
    • (2002) J Mol Biol , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 9
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • 2004
    • Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Sci STKE 2004:p l2 (2004).
    • (2004) Sci STKE
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 10
    • 14144256681 scopus 로고    scopus 로고
    • Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity
    • Pokala N, Handel TM. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 2005; 347: 203-227.
    • (2005) J Mol Biol , vol.347 , pp. 203-227
    • Pokala, N.1    Handel, T.M.2
  • 11
    • 34548764386 scopus 로고    scopus 로고
    • An automated decision-tree approach to predicting protein interaction hot spots
    • Darnell SJ, Page D, Mitchell JC. An automated decision-tree approach to predicting protein interaction hot spots. Proteins Struct Funct Bioinformatics 2007; 68: 813-823.
    • (2007) Proteins Struct Funct Bioinformatics , vol.68 , pp. 813-823
    • Darnell, S.J.1    Page, D.2    Mitchell, J.C.3
  • 12
    • 38549092067 scopus 로고    scopus 로고
    • Hotsprint: database of computational hot spots in protein interfaces
    • Guney E, Tuncbag N, Keskin O, Gursoy A. Hotsprint: database of computational hot spots in protein interfaces. Nucleic Acids Res 2007; 36: D662-D666.
    • (2007) Nucleic Acids Res , vol.36
    • Guney, E.1    Tuncbag, N.2    Keskin, O.3    Gursoy, A.4
  • 14
    • 65849158839 scopus 로고    scopus 로고
    • A feature-based approach to modeling protein-protein interaction hot spots
    • Cho K, Kim D, Lee D. A feature-based approach to modeling protein-protein interaction hot spots. Nucleic Acids Res 2009; 37: 2672-2687.
    • (2009) Nucleic Acids Res , vol.37 , pp. 2672-2687
    • Cho, K.1    Kim, D.2    Lee, D.3
  • 15
    • 70749125843 scopus 로고    scopus 로고
    • Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
    • Lise S, Archambeau C, Pontil M, Jones D. Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. BMC Bioinformatics 2009; 10: 365.
    • (2009) BMC Bioinformatics , vol.10 , pp. 365
    • Lise, S.1    Archambeau, C.2    Pontil, M.3    Jones, D.4
  • 16
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998; 280: 1-9.
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 17
    • 11844249426 scopus 로고    scopus 로고
    • Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues
    • Keskin O, Ma B, Nussinov R. Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol 2005; 345: 1281-1294.
    • (2005) J Mol Biol , vol.345 , pp. 1281-1294
    • Keskin, O.1    Ma, B.2    Nussinov, R.3
  • 18
    • 62549102939 scopus 로고    scopus 로고
    • Double water exclusion: a hypothesis refining the o-ring theory for the hot spots at protein interfaces
    • Li J, Liu Q. Double water exclusion: a hypothesis refining the o-ring theory for the hot spots at protein interfaces. Bioinformatics 2009; 25: 743-750.
    • (2009) Bioinformatics , vol.25 , pp. 743-750
    • Li, J.1    Liu, Q.2
  • 19
    • 8644234346 scopus 로고    scopus 로고
    • Water-mediated interaction at a protein-protein interface
    • Ikura T, Urakubo Y, Ito N. Water-mediated interaction at a protein-protein interface. Chem Phys 2004; 307: 111-119.
    • (2004) Chem Phys , vol.307 , pp. 111-119
    • Ikura, T.1    Urakubo, Y.2    Ito, N.3
  • 21
    • 38349152721 scopus 로고    scopus 로고
    • On the contribution of water-mediated interactions to protein-complex stability
    • Reichmann D, Phillip Y, Carmi A, Schreiber G. On the contribution of water-mediated interactions to protein-complex stability. Biochemistry 2008; 47: 1051-1060.
    • (2008) Biochemistry , vol.47 , pp. 1051-1060
    • Reichmann, D.1    Phillip, Y.2    Carmi, A.3    Schreiber, G.4
  • 22
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions
    • Thorn KS, Bogan AA. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 2001; 17: 284-285.
    • (2001) Bioinformatics , vol.17 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2
  • 23
    • 0027132013 scopus 로고
    • Comparison of a structural and a functional epitope
    • Cunningham BC, Wells JA. Comparison of a structural and a functional epitope. J Mol Biol 1993; 234: 554-563.
    • (1993) J Mol Biol , vol.234 , pp. 554-563
    • Cunningham, B.C.1    Wells, J.A.2
  • 24
    • 0031887368 scopus 로고    scopus 로고
    • Effects of substitutions in the binding surface of an antibody on antigen affinity
    • Dougan DA, Malby RL, Gruen LC, Kortt AA, Hudson PJ. Effects of substitutions in the binding surface of an antibody on antigen affinity. Protein Eng 1998; 11: 65-74.
    • (1998) Protein Eng , vol.11 , pp. 65-74
    • Dougan, D.A.1    Malby, R.L.2    Gruen, L.C.3    Kortt, A.A.4    Hudson, P.J.5
  • 25
    • 0037200049 scopus 로고    scopus 로고
    • The thrombin epitope recognizing thrombomodulin is a highly cooperative hot spot in exosite i
    • Pineda AO, Cantwell AM, Bush LA, Rose T, Di Cera E. The thrombin epitope recognizing thrombomodulin is a highly cooperative hot spot in exosite i. J Biol Chem 2002; 277: 32015-32019.
    • (2002) J Biol Chem , vol.277 , pp. 32015-32019
    • Pineda, A.O.1    Cantwell, A.M.2    Bush, L.A.3    Rose, T.4    Di Cera, E.5
  • 27
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998; 11: 739-747.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 28
    • 0015222647 scopus 로고
    • The interpretation of protein structures: estimation of static accessibility
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971; 55: 379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 29
    • 34147120474 scopus 로고
    • A note on two problems in connexion with graphs
    • Dijkstra EW. A note on two problems in connexion with graphs. Numerische Mathematik 1959; 1: 269-271.
    • (1959) Numerische Mathematik , vol.1 , pp. 269-271
    • Dijkstra, E.W.1
  • 30
    • 78349300798 scopus 로고
    • Weighted alpha shapes. Technical report, Champaign, IL
    • Edelsbrunner H. Weighted alpha shapes. Technical report, Champaign, IL 1992.
    • (1992)
    • Edelsbrunner, H.1
  • 32
    • 0037382258 scopus 로고    scopus 로고
    • Atom depth as a descriptor of the protein interior
    • Pintar A, Carugo O, Pongor S. Atom depth as a descriptor of the protein interior. Biophys J 2003; 84: 2553-2561.
    • (2003) Biophys J , vol.84 , pp. 2553-2561
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 33
    • 68049128318 scopus 로고    scopus 로고
    • Shelling the voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition
    • Bouvier B, Grünberg R, Nilges M, Cazals F. Shelling the voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition. Proteins Struct Funct Bioinformatics 2009; 76: 677-692.
    • (2009) Proteins Struct Funct Bioinformatics , vol.76 , pp. 677-692
    • Bouvier, B.1    Grünberg, R.2    Nilges, M.3    Cazals, F.4
  • 34
    • 0001884644 scopus 로고
    • Individual comparisons by ranking methods
    • Wilcoxon F. Individual comparisons by ranking methods. Biometrics Bull 1945; 1: 80-83.
    • (1945) Biometrics Bull , vol.1 , pp. 80-83
    • Wilcoxon, F.1
  • 36
    • 0002322469 scopus 로고
    • On a test of whether one of two random variables is stochastically larger than the other
    • Mann HB, Whitney DR. On a test of whether one of two random variables is stochastically larger than the other. Annals Math Stat 1947; 18: 50-60.
    • (1947) Annals Math Stat , vol.18 , pp. 50-60
    • Mann, H.B.1    Whitney, D.R.2
  • 37
    • 33748513468 scopus 로고    scopus 로고
    • Binding free energy contributions of interfacial waters in hiv-1 protease/inhibitor complexes
    • Lu Y, Yang CY, Wang S. Binding free energy contributions of interfacial waters in hiv-1 protease/inhibitor complexes. J Am Chem Soc 2006; 128: 11830-11839.
    • (2006) J Am Chem Soc , vol.128 , pp. 11830-11839
    • Lu, Y.1    Yang, C.Y.2    Wang, S.3
  • 39
    • 33750014560 scopus 로고    scopus 로고
    • Solvated docking: introducing water into the modelling of biomolecular complexes
    • van Dijk ADJD, Bonvin AMJJM. Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics 2006; 22: 2340-2347.
    • (2006) Bioinformatics , vol.22 , pp. 2340-2347
    • van Dijk, A.D.J.D.1    Bonvin, A.M.J.J.M.2
  • 40
    • 34248545940 scopus 로고    scopus 로고
    • Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description
    • Teyra J, Pisabarro MT. Characterization of interfacial solvent in protein complexes and contribution of wet spots to the interface description. Proteins Struct Funct Bioinformatics 2007; 67: 1087-1095.
    • (2007) Proteins Struct Funct Bioinformatics , vol.67 , pp. 1087-1095
    • Teyra, J.1    Pisabarro, M.T.2
  • 41
    • 52249096127 scopus 로고    scopus 로고
    • A molecular dynamics approach to study the importance of solvent in protein interactions
    • Samsonov S, Teyra J, Pisabarro TM. A molecular dynamics approach to study the importance of solvent in protein interactions. Proteins Struct Funct Bioinformatics 2008; 73: 515-525.
    • (2008) Proteins Struct Funct Bioinformatics , vol.73 , pp. 515-525
    • Samsonov, S.1    Teyra, J.2    Pisabarro, T.M.3
  • 42
    • 0037422589 scopus 로고    scopus 로고
    • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
    • Fernández A, Scheraga HA. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci USA 2003; 100: 113-118.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 113-118
    • Fernández, A.1    Scheraga, H.A.2
  • 43
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle R. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982; 157: 105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.2


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