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Volumn 3, Issue , 2007, Pages 27-35

The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks

Author keywords

Electrostatic potential; Hubs; Multipole expansion; Protein protein interaction networks; Surface charge

Indexed keywords


EID: 34547125807     PISSN: None     EISSN: 13492942     Source Type: Journal    
DOI: 10.2142/biophysics.3.27     Document Type: Article
Times cited : (9)

References (34)
  • 1
    • 33645214608 scopus 로고    scopus 로고
    • Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks
    • Patil, A. & Nakamura, H. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Lett. 580, 2041-2045 (2006).
    • (2006) FEBS Lett , vol.580 , pp. 2041-2045
    • Patil, A.1    Nakamura, H.2
  • 3
    • 27144464910 scopus 로고    scopus 로고
    • Flexible nets. The roles of intrinsic disorder in protein interaction networks
    • Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M. & Uversky, V. N. Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J. 272, 5129-5148 (2005).
    • (2005) FEBS J , vol.272 , pp. 5129-5148
    • Dunker, A.K.1    Cortese, M.S.2    Romero, P.3    Iakoucheva, L.M.4    Uversky, V.N.5
  • 4
    • 0036890316 scopus 로고    scopus 로고
    • Sinha, N. & Smith-Gill, S. J. Electrostatics in protein binding and function. Curr. Protein. Pept. Sci. 3, 601-614 (2002).
    • Sinha, N. & Smith-Gill, S. J. Electrostatics in protein binding and function. Curr. Protein. Pept. Sci. 3, 601-614 (2002).
  • 5
    • 0034039797 scopus 로고    scopus 로고
    • Electrostatic aspects of protein-protein interactions
    • Sheinerman, F. B., Norel, R. & Honig, B. Electrostatic aspects of protein-protein interactions. Curr. Opin. Struct. Biol. 10, 153-159 (2000).
    • (2000) Curr. Opin. Struct. Biol , vol.10 , pp. 153-159
    • Sheinerman, F.B.1    Norel, R.2    Honig, B.3
  • 6
    • 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, 1-9 (1998).
    • (1998) J. Mol. Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 7
    • 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. & Nussinov, R. Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl. Acad. Sci. U.S.A. 100, 5772-5777 (2003).
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 5772-5777
    • Ma, B.1    Elkayam, T.2    Wolfson, H.3    Nussinov, R.4
  • 11
    • 24044434446 scopus 로고    scopus 로고
    • Filtering high-throughput proteinprotein interaction data using a combination of genomic features
    • Patil, A. & Nakamura, H. Filtering high-throughput proteinprotein interaction data using a combination of genomic features. BMC Bioinformatics 6, 100 (2005).
    • (2005) BMC Bioinformatics , vol.6 , pp. 100
    • Patil, A.1    Nakamura, H.2
  • 12
    • 3042683893 scopus 로고    scopus 로고
    • eF-site and PDBjViewer: Database and viewer for protein functional sites
    • Kinoshita, K. & Nakamura, H. eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics 20, 1329-1330 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 1329-1330
    • Kinoshita, K.1    Nakamura, H.2
  • 13
    • 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 22, 2577-2637 (1983).
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 14
    • 12944257228 scopus 로고    scopus 로고
    • The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
    • Glaser, F., Rosenberg, Y., Kessel, A., Pupko, T. & Ben-Tal, N. The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58, 610-617 (2005).
    • (2005) Proteins , vol.58 , pp. 610-617
    • Glaser, F.1    Rosenberg, Y.2    Kessel, A.3    Pupko, T.4    Ben-Tal, N.5
  • 15
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J. & Doolittle, R. F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132 (1982).
    • (1982) J. Mol. Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 16
    • 16344389701 scopus 로고    scopus 로고
    • Cation-π interactions in proteinprotein interfaces
    • Crowley, P. B. & Golovin, A. Cation-π interactions in proteinprotein interfaces. Proteins 59, 231-239 (2005).
    • (2005) Proteins , vol.59 , pp. 231-239
    • Crowley, P.B.1    Golovin, A.2
  • 18
    • 33646064427 scopus 로고    scopus 로고
    • Structural complexity in ubiquitin recognition
    • Harper, J.W. & Schulman, B. A. Structural complexity in ubiquitin recognition. Cell 124, 1133-1136 (2006).
    • (2006) Cell , vol.124 , pp. 1133-1136
    • Harper, J.W.1    Schulman, B.A.2
  • 19
    • 33744515908 scopus 로고    scopus 로고
    • NMR Study of the Electron Transfer Complex of Plant Ferredoxin and Sulfite Reductase: Mapping the interaction sites of Ferredoxin
    • Saitoh, T., Ikegami, T., Nakayama, M., Teshima, K., Akutsu, H. & Hase, T. NMR Study of the Electron Transfer Complex of Plant Ferredoxin and Sulfite Reductase: Mapping the interaction sites of Ferredoxin. J. Biol. Chem. 281, 10482-10488 (2006).
    • (2006) J. Biol. Chem , vol.281 , pp. 10482-10488
    • Saitoh, T.1    Ikegami, T.2    Nakayama, M.3    Teshima, K.4    Akutsu, H.5    Hase, T.6
  • 20
    • 0031165571 scopus 로고    scopus 로고
    • Optimization of electrostatic binding free energy
    • Lee, L.-P. & Tidor, B. Optimization of electrostatic binding free energy. J. Chem. Phys. 106, 8681-8690 (1997).
    • (1997) J. Chem. Phys , vol.106 , pp. 8681-8690
    • Lee, L.-P.1    Tidor, B.2
  • 21
    • 0031891022 scopus 로고    scopus 로고
    • Computation of electrostatic complements to proteins: A case of charge stabilized binding
    • Chong, L. T., Dempster, S. E., Hendsch, Z. S., Lee, L. P. & Tidor, B. Computation of electrostatic complements to proteins: a case of charge stabilized binding. Protein Sci. 7, 206-210 (1998).
    • (1998) Protein Sci , vol.7 , pp. 206-210
    • Chong, L.T.1    Dempster, S.E.2    Hendsch, Z.S.3    Lee, L.P.4    Tidor, B.5
  • 22
    • 0035107570 scopus 로고    scopus 로고
    • Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex
    • Lee, L. P. & Tidor, B. Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex. Protein Sci. 10, 362-377 (2001).
    • (2001) Protein Sci , vol.10 , pp. 362-377
    • Lee, L.P.1    Tidor, B.2
  • 23
    • 17744390877 scopus 로고    scopus 로고
    • Action-at-a-distance interactions enhance protein binding affinity
    • Joughin, B. A., Green, D. F. & Tidor, B. Action-at-a-distance interactions enhance protein binding affinity. Protein Sci. 14, 1363-1369 (2005).
    • (2005) Protein Sci , vol.14 , pp. 1363-1369
    • Joughin, B.A.1    Green, D.F.2    Tidor, B.3
  • 25
    • 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, 53-64 (1997).
    • (1997) Protein Sci , vol.6 , pp. 53-64
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 27
    • 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, 331-342 (2000).
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 28
    • 24944549109 scopus 로고    scopus 로고
    • Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different
    • De, S., Krishnadev, O., Srinivasan, N. & Rekha, N. Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC Struct. Biol. 5, 15 (2005).
    • (2005) BMC Struct. Biol , vol.5 , pp. 15
    • De, S.1    Krishnadev, O.2    Srinivasan, N.3    Rekha, N.4
  • 29
    • 0041312697 scopus 로고    scopus 로고
    • Diversity of protein-protein interactions
    • Nooren, I. M. A. & Thornton, J. M. Diversity of protein-protein interactions. EMBO J. 22, 3486-3492 (2003).
    • (2003) EMBO J , vol.22 , pp. 3486-3492
    • Nooren, I.M.A.1    Thornton, J.M.2
  • 30
    • 33749337098 scopus 로고    scopus 로고
    • The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry
    • Kim, W. K., Henschel, A., Winter, C. & Schroeder, M. The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry. PLoS Comput. Biol. 2, e124 (2006).
    • (2006) PLoS Comput. Biol , vol.2
    • Kim, W.K.1    Henschel, A.2    Winter, C.3    Schroeder, M.4
  • 31
    • 33847768378 scopus 로고    scopus 로고
    • Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways
    • Keskin, O. & Nussinov, R. Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways. Structure 15, 341-354 (2007).
    • (2007) Structure , vol.15 , pp. 341-354
    • Keskin, O.1    Nussinov, R.2
  • 32
    • 5044244784 scopus 로고    scopus 로고
    • An examination of the conservation of surface patch polarity for proteins
    • Shanahan, H. P. & Thornton, J. M. An examination of the conservation of surface patch polarity for proteins. Bioinformatics 20, 2197-2204 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 2197-2204
    • Shanahan, H.P.1    Thornton, J.M.2
  • 33
    • 0026244229 scopus 로고    scopus 로고
    • Kraulis, P. J. MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures. J. Appl. Crystallogr. 24, 946-950 (1991).
    • Kraulis, P. J. MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures. J. Appl. Crystallogr. 24, 946-950 (1991).
  • 34
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic Molecular Graphics
    • Merritt, E. A. & Bacon, D. J. Raster3D: Photorealistic Molecular Graphics. Meth. Enzymol. 277, 505-524 (1997).
    • (1997) Meth. Enzymol , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.