메뉴 건너뛰기




Volumn 67, Issue 4, 2007, Pages 1060-1077

Comprehensive statistical analysis of residues interaction specificity at protein-protein interfaces

Author keywords

Protein interface; Protein protein interaction; Residue contact preferences; Voronoi tessellation

Indexed keywords

AMINO ACID; CYSTEINE; HOMODIMER; MATRIX PROTEIN; PROTEIN;

EID: 34248532098     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21363     Document Type: Article
Times cited : (22)

References (53)
  • 1
    • 0016708122 scopus 로고
    • Principles of protein-protein recognition
    • Chothia C, Janin J. Principles of protein-protein recognition. Nature 1975;256:705-708.
    • (1975) Nature , vol.256 , pp. 705-708
    • Chothia, C.1    Janin, J.2
  • 2
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93:13-20.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 3
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004;336:943-955.
    • (2004) J Mol Biol , vol.336 , pp. 943-955
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 4
    • 0037093645 scopus 로고    scopus 로고
    • Dissecting protein-protein recognition sites
    • Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
    • (2002) Proteins , vol.47 , pp. 334-343
    • Chakrabarti, P.1    Janin, J.2
  • 5
    • 0029988383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 1996;31:127-152.
    • (1996) Crit Rev Biochem Mol Biol , vol.31 , pp. 127-152
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 6
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: Analysis of amino acid conservation in homodimers
    • Valdar WS, Thornton JM. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001;42:108-124.
    • (2001) Proteins , vol.42 , pp. 108-124
    • Valdar, W.S.1    Thornton, J.M.2
  • 7
    • 0031561809 scopus 로고    scopus 로고
    • Protein binding versus protein folding: The role of hydrophilic bridges in protein associations
    • Xu D, Lin SL, Nussinov R. Protein binding versus protein folding: the role of hydrophilic bridges in protein associations. J Mol Biol 1997;265:68-84.
    • (1997) J Mol Biol , vol.265 , pp. 68-84
    • Xu, D.1    Lin, S.L.2    Nussinov, R.3
  • 9
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 10
    • 0242299201 scopus 로고    scopus 로고
    • Dissecting subunit interfaces in homodimeric proteins
    • Bahadur RP, Chakrabarti P, Rodier F, Janin J. Dissecting subunit interfaces in homodimeric proteins. Proteins 2003;53:708-719.
    • (2003) Proteins , vol.53 , pp. 708-719
    • Bahadur, R.P.1    Chakrabarti, P.2    Rodier, F.3    Janin, J.4
  • 11
    • 0034308172 scopus 로고    scopus 로고
    • Discriminating between homodimeric and monomelic proteins in the crystalline state
    • Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomelic proteins in the crystalline state. Proteins 2000;41:47-57.
    • (2000) Proteins , vol.41 , pp. 47-57
    • Ponstingl, H.1    Henrick, K.2    Thornton, J.M.3
  • 12
    • 0030877077 scopus 로고    scopus 로고
    • Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
    • Dasgupta S, Iyer GH, Bryant SH, Lawrence CE, Bell JA. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 1997;28:494-514.
    • (1997) Proteins , vol.28 , pp. 494-514
    • Dasgupta, S.1    Iyer, G.H.2    Bryant, S.H.3    Lawrence, C.E.4    Bell, J.A.5
  • 13
    • 0032054715 scopus 로고    scopus 로고
    • Predictive docking of protein-protein and protein-DNA complexes
    • Sternberg MJ, Gabb HA, Jackson RM. Predictive docking of protein-protein and protein-DNA complexes. Curr Opin Struct Biol 1998;8:250-256.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 250-256
    • Sternberg, M.J.1    Gabb, H.A.2    Jackson, R.M.3
  • 14
    • 0023155210 scopus 로고
    • Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder JW, Richards FM. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987;193:775-791.
    • (1987) J Mol Biol , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 15
    • 28644448657 scopus 로고    scopus 로고
    • Survey of the geometric association of domain-domain interfaces
    • Kim WK, Ison JC. Survey of the geometric association of domain-domain interfaces. Proteins 2005;61:1075-1088.
    • (2005) Proteins , vol.61 , pp. 1075-1088
    • Kim, W.K.1    Ison, J.C.2
  • 16
    • 0026079134 scopus 로고
    • Distribution and complementarity of hydropathy in multisubunit proteins
    • Korn AP, Burnett RM. Distribution and complementarity of hydropathy in multisubunit proteins. Proteins 1991;9:37-55.
    • (1991) Proteins , vol.9 , pp. 37-55
    • Korn, A.P.1    Burnett, R.M.2
  • 17
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 1994;3:717-729.
    • (1994) Protein Sci , vol.3 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 18
    • 0030997363 scopus 로고    scopus 로고
    • Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
    • Lijnzaad P, Argos P. Hydrophobic patches on protein subunit interfaces: characteristics and prediction. Proteins 1997;28:333-343.
    • (1997) Proteins , vol.28 , pp. 333-343
    • Lijnzaad, P.1    Argos, P.2
  • 19
    • 0031454652 scopus 로고    scopus 로고
    • Simulating the minimum core for hydrophobic collapse in globular proteins
    • Tsai J, Gerstein M, Levitt M. Simulating the minimum core for hydrophobic collapse in globular proteins. Protein Sci 1997;6:2606-2616.
    • (1997) Protein Sci , vol.6 , pp. 2606-2616
    • Tsai, J.1    Gerstein, M.2    Levitt, M.3
  • 20
    • 0028607523 scopus 로고
    • Cavities and packing at protein interfaces
    • Hubbard SJ, Argos P. Cavities and packing at protein interfaces. Protein Sci 1994;3:2194-2206.
    • (1994) Protein Sci , vol.3 , pp. 2194-2206
    • Hubbard, S.J.1    Argos, P.2
  • 21
    • 0024046505 scopus 로고
    • An investigation of protein subunit and domain interfaces
    • Argos P. An investigation of protein subunit and domain interfaces. Protein Eng 1988;2:101-113.
    • (1988) Protein Eng , vol.2 , pp. 101-113
    • Argos, P.1
  • 23
    • 0024246956 scopus 로고
    • Surface, subunit interfaces and interior of oligomeric proteins
    • Janin J, Miller S, Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 1988;204:155-164.
    • (1988) J Mol Biol , vol.204 , pp. 155-164
    • Janin, J.1    Miller, S.2    Chothia, C.3
  • 24
    • 0035970298 scopus 로고    scopus 로고
    • Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
    • Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 2001;307:929-938.
    • (2001) J Mol Biol , vol.307 , pp. 929-938
    • Park, J.1    Lappe, M.2    Teichmann, S.A.3
  • 25
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy P, Ceulemans H, Stark A, Russell RB. The relationship between sequence and interaction divergence in proteins. J Mol Biol 2003;332:989-998.
    • (2003) J Mol Biol , vol.332 , pp. 989-998
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 26
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
    • Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004;13:1043-1055.
    • (2004) Protein Sci , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 27
    • 0030602896 scopus 로고    scopus 로고
    • A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 1996;260:604-620.
    • (1996) J Mol Biol , vol.260 , pp. 604-620
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 28
    • 26444568633 scopus 로고    scopus 로고
    • Statistical analysis of predominantly transient protein-protein interfaces
    • Ansari S, Helms V. Statistical analysis of predominantly transient protein-protein interfaces. Proteins 2005;61:344-355.
    • (2005) Proteins , vol.61 , pp. 344-355
    • Ansari, S.1    Helms, V.2
  • 29
    • 0031678069 scopus 로고    scopus 로고
    • Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions
    • Keskin O, Bahar I, Badretdinov AY, Ptitsyn OB, Jernigan RL. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci 1998;7:2578-2586.
    • (1998) Protein Sci , vol.7 , pp. 2578-2586
    • Keskin, O.1    Bahar, I.2    Badretdinov, A.Y.3    Ptitsyn, O.B.4    Jernigan, R.L.5
  • 30
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
    • (1997) J Mol Biol , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 31
    • 0025008445 scopus 로고
    • Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
    • Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol 1990;216:167-180.
    • (1990) J Mol Biol , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floeckner, H.4    Froschauer, R.5    Gottsbacher, K.6    Casari, G.7    Sippl, M.J.8
  • 32
    • 0033835533 scopus 로고    scopus 로고
    • Structure-derived substitution matrices for alignment of distantly related sequences
    • Prlic A, Domingues FS, Sippl MJ. Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng 2000;13:545-550.
    • (2000) Protein Eng , vol.13 , pp. 545-550
    • Prlic, A.1    Domingues, F.S.2    Sippl, M.J.3
  • 33
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • Glaser F, Steinberg DM, Vakser IA, Ben-Tal N. Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 2001;43:89-102.
    • (2001) Proteins , vol.43 , pp. 89-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 34
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-5901.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 35
    • 0029089271 scopus 로고
    • Significance of bound water to local chain conformations in protein crystals
    • Robert CH, Ho PS. Significance of bound water to local chain conformations in protein crystals. Proc Natl Acad Sci USA 1995;92:7600-7604.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 7600-7604
    • Robert, C.H.1    Ho, P.S.2
  • 36
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • Richards FM. The interpretation of protein structures: total volume, group volume distributions and packing density. J Mol Biol 1974;82:1-14.
    • (1974) J Mol Biol , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 37
    • 1842850600 scopus 로고    scopus 로고
    • Voronoi and Voronoi-related tessellations in studies of protein structure and interaction
    • Poupon A. Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr Opin Struct Biol 2004;14:233-241.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 233-241
    • Poupon, A.1
  • 38
    • 0034287449 scopus 로고    scopus 로고
    • Voronoi tessellation reveals the condensed matter character of folded proteins
    • Soyer A, Chomilier J, Mornon JP, Jullien R, Sadoc JF. Voronoi tessellation reveals the condensed matter character of folded proteins. Phys Rev Lett 2000;85:3532-3535.
    • (2000) Phys Rev Lett , vol.85 , pp. 3532-3535
    • Soyer, A.1    Chomilier, J.2    Mornon, J.P.3    Jullien, R.4    Sadoc, J.F.5
  • 39
    • 0036892439 scopus 로고    scopus 로고
    • Nonatomic solvent-driven Voronoi tessellation of proteins: An open tool to analyze protein folds
    • Angelov B, Sadoc JF, Jullien R, Soyer A, Mornon JP, Chomilier J. Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds. Proteins 2002;49:446-456.
    • (2002) Proteins , vol.49 , pp. 446-456
    • Angelov, B.1    Sadoc, J.F.2    Jullien, R.3    Soyer, A.4    Mornon, J.P.5    Chomilier, J.6
  • 40
    • 0029004611 scopus 로고
    • The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra
    • Gerstein M, Tsai J, Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol 1995;249:955-966.
    • (1995) J Mol Biol , vol.249 , pp. 955-966
    • Gerstein, M.1    Tsai, J.2    Levitt, M.3
  • 41
    • 0006166868 scopus 로고    scopus 로고
    • Structure characterization and predictability by Voronoi analysis
    • Christensen SW, Thomas NW. Structure characterization and predictability by Voronoi analysis. Acta Crystallogr A 1999;55(Part 5):811-820.
    • (1999) Acta Crystallogr A , vol.55 , Issue.PART 5 , pp. 811-820
    • Christensen, S.W.1    Thomas, N.W.2
  • 43
    • 0034778102 scopus 로고    scopus 로고
    • Determining the minimum number of types necessary to represent the sizes of protein atoms
    • Tsai J, Voss N, Gerstein M. Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinformatics 2001;17:949-956.
    • (2001) Bioinformatics , vol.17 , pp. 949-956
    • Tsai, J.1    Voss, N.2    Gerstein, M.3
  • 45
    • 24344487344 scopus 로고    scopus 로고
    • Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
    • Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions. Proteins 2005;61:6-20.
    • (2005) Proteins , vol.61 , pp. 6-20
    • Mintz, S.1    Shulman-Peleg, A.2    Wolfson, H.J.3    Nussinov, R.4
  • 46
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTP and FASTA
    • Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 1990;183:63-98.
    • (1990) Methods Enzymol , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 47
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992;8:275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 48
    • 26844500695 scopus 로고    scopus 로고
    • Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimeric interface
    • Saha RP, Bahadur RP, Chakrabarti P. Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimeric interface. J Proteome Res 2005;4:1600-1609.
    • (2005) J Proteome Res , vol.4 , pp. 1600-1609
    • Saha, R.P.1    Bahadur, R.P.2    Chakrabarti, P.3
  • 49
    • 34248529053 scopus 로고    scopus 로고
    • Kendall M, Stuart A. Kendall's advanced theory of statistics. Arnold, London 2A Classical Inference and the linear Model. 6 th edition. 1998.
    • Kendall M, Stuart A. Kendall's advanced theory of statistics. Arnold, London Volume 2A Classical Inference and the linear Model. 6 th edition. 1998.
  • 50
    • 29344461522 scopus 로고    scopus 로고
    • Breaking symmetry in protein dimers: Designs and functions
    • Brown JH. Breaking symmetry in protein dimers: designs and functions. Protein Sci 2006;15:1-13.
    • (2006) Protein Sci , vol.15 , pp. 1-13
    • Brown, J.H.1
  • 51
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 52
    • 30544438396 scopus 로고    scopus 로고
    • The analysis of multiprotein complexes: The yeast and the human spliceosome as case studies
    • Neubauer G. The analysis of multiprotein complexes: the yeast and the human spliceosome as case studies. Methods Enzymol 2005;405:236-263.
    • (2005) Methods Enzymol , vol.405 , pp. 236-263
    • Neubauer, G.1
  • 53
    • 16644386648 scopus 로고    scopus 로고
    • The importance of disulfide bridging
    • Swaisgood HE. The importance of disulfide bridging. Biotechnol Adv 2005;23:71-73.
    • (2005) Biotechnol Adv , vol.23 , pp. 71-73
    • Swaisgood, H.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.