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Volumn 15, Issue 2, 2006, Pages 352-361

Finding biologically relevant protein domain interactions: Conserved binding mode analysis

Author keywords

Conserved binding modes; Homology modeling; Protein domain families; Protein structure; Protein protein interactions

Indexed keywords

GLOBIN;

EID: 31344459575     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051760806     Document Type: Article
Times cited : (63)

References (34)
  • 1
    • 5044235050 scopus 로고    scopus 로고
    • Ten thousand interactions for the molecular biologist
    • Aloy, P. and Russell, R.B. 2004. Ten thousand interactions for the molecular biologist. Nat. Biotechnol. 22: 1317-1321.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1317-1321
    • Aloy, P.1    Russell, R.B.2
  • 2
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy, P., Ceulemans, H., Stark, A., and Russell, R.B. 2003. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 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
  • 3
    • 1042275583 scopus 로고    scopus 로고
    • A dissection of specific and non-specific protein-protein interfaces
    • Bahadur, R.P., Chakrabarti, P., Rodier, F., and Janin, J. 2004. A dissection of specific and non-specific protein-protein interfaces. J. Mol. Biol. 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
    • 0036307754 scopus 로고    scopus 로고
    • The geometry of domain combination in proteins
    • Bashton, M. and Chothia, C. 2002. The geometry of domain combination in proteins. J. Mol. Biol. 315: 927-939.
    • (2002) J. Mol. Biol. , vol.315 , pp. 927-939
    • Bashton, M.1    Chothia, C.2
  • 5
    • 0030850230 scopus 로고    scopus 로고
    • Protein-protein crystal-packing contacts
    • Carugo, O. and Argos, P. 1997. Protein-protein crystal-packing contacts. Protein Sci. 6: 2261-2263.
    • (1997) Protein Sci. , vol.6 , pp. 2261-2263
    • Carugo, O.1    Argos, P.2
  • 6
    • 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, G.H., Bryant, S.H., Lawrence, C.E., and Bell, J.A. 1997. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 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
  • 7
    • 18744382508 scopus 로고    scopus 로고
    • PIBASE: A comprehensive database of structurally defined protein interfaces
    • Davis, F.P. and Sali, A. 2005. PIBASE: A comprehensive database of structurally defined protein interfaces. Bioinformatics 21: 1901-1907.
    • (2005) Bioinformatics , vol.21 , pp. 1901-1907
    • Davis, F.P.1    Sali, A.2
  • 8
    • 0035853028 scopus 로고    scopus 로고
    • Identification of protein oligomerization states by analysis of interface conservation
    • Elcock, A.H. and McCammon, J.A. 2001. Identification of protein oligomerization states by analysis of interface conservation. Proc. Natl. Acad. Sci. 98: 2990-2994.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 2990-2994
    • Elcock, A.H.1    McCammon, J.A.2
  • 9
  • 12
    • 0035854658 scopus 로고    scopus 로고
    • Crystalline ligand transitions in lamprey hemoglobin. Structural evidence for the regulation of oxygen affinity
    • Heaslet, H.A. and Royer Jr., W.E. 2001. Crystalline ligand transitions in lamprey hemoglobin. Structural evidence for the regulation of oxygen affinity. J. Biol. Chem. 276: 26230-26236.
    • (2001) J. Biol. Chem. , vol.276 , pp. 26230-26236
    • Heaslet, H.A.1    Royer Jr., W.E.2
  • 13
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569-4574.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4    Hattori, M.5    Sakaki, Y.6
  • 14
    • 0031297461 scopus 로고    scopus 로고
    • Specific versus non-specific contacts in protein crystals
    • Janin, J. 1997. Specific versus non-specific contacts in protein crystals. Nat. Struct. Biol. 4: 973-974.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 973-974
    • Janin, J.1
  • 15
    • 0029586759 scopus 로고
    • Protein-protein interaction at crystal contacts
    • Janin, J. and Rodier, F. 1995. Protein-protein interaction at crystal contacts. Proteins 23: 580-587.
    • (1995) Proteins , vol.23 , pp. 580-587
    • Janin, J.1    Rodier, F.2
  • 16
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D.T., Taylor, W.R., and Thornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8: 275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 17
    • 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., and Nussinov, R. 2004. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci. 13: 1043-1055.
    • (2004) Protein Sci. , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 18
    • 12144281353 scopus 로고    scopus 로고
    • Conservation of orientation and sequence in protein domain-domain interactions
    • Littler, S.J. and Hubbard, S.J. 2005. Conservation of orientation and sequence in protein domain-domain interactions. J. Mol. Biol. 345: 1265-1279.
    • (2005) J. Mol. Biol. , vol.345 , pp. 1265-1279
    • Littler, S.J.1    Hubbard, S.J.2
  • 19
    • 3242887157 scopus 로고    scopus 로고
    • CD-Search: Protein domain annotations on the fly
    • Marchler-Bauer, A. and Bryant, S.H. 2004. CD-Search: Protein domain annotations on the fly. Nucleic Acids Res. 32: W327-W331.
    • (2004) Nucleic Acids Res. , vol.32
    • Marchler-Bauer, A.1    Bryant, S.H.2
  • 22
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 24
    • 0037474541 scopus 로고    scopus 로고
    • Structural characterisation and functional significance of transient protein-protein interactions
    • Nooren, I.M. and Thornton, J.M. 2003. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325: 991-1018.
    • (2003) J. Mol. Biol. , vol.325 , pp. 991-1018
    • Nooren, I.M.1    Thornton, J.M.2
  • 25
    • 1842454912 scopus 로고    scopus 로고
    • Prediction of functional sites by analysis of sequence and structure conservation
    • Panchenko, A.R., Kondrashov, F., and Bryant, S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci. 13: 884-892.
    • (2004) Protein Sci. , vol.13 , pp. 884-892
    • Panchenko, A.R.1    Kondrashov, F.2    Bryant, S.3
  • 26
    • 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., and Teichmann, S.A. 2001. Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 307: 929-938.
    • (2001) J. Mol. Biol. , vol.307 , pp. 929-938
    • Park, J.1    Lappe, M.2    Teichmann, S.A.3
  • 27
    • 0034308172 scopus 로고    scopus 로고
    • Discriminating between homodimeric and monomeric proteins in the crystalline state
    • Ponstingl, H., Henrick, K., and Thornton, J.M. 2000. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 41: 47-57.
    • (2000) Proteins , vol.41 , pp. 47-57
    • Ponstingl, H.1    Henrick, K.2    Thornton, J.M.3
  • 28
    • 0032515101 scopus 로고    scopus 로고
    • A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions
    • Robert, C.H. and Janin, J. 1998. A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. J. Mol. Biol. 283: 1037-1047.
    • (1998) J. Mol. Biol. , vol.283 , pp. 1037-1047
    • Robert, C.H.1    Janin, J.2
  • 29
    • 0035336687 scopus 로고    scopus 로고
    • Cooperative hemoglobins: Conserved fold, diverse quaternary assemblies and allosteric mechanisms
    • Royer Jr., W.E., Knapp, J.E., Strand, K., and Heaslet, H.A. 2001. Cooperative hemoglobins: Conserved fold, diverse quaternary assemblies and allosteric mechanisms. Trends Biochem. Sci. 26: 297-304.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 297-304
    • Royer Jr., W.E.1    Knapp, J.E.2    Strand, K.3    Heaslet, H.A.4
  • 30
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 32
    • 0035907234 scopus 로고    scopus 로고
    • Conformational change of elongation factor Tu (EF-Tu) induced by antibiotic binding. Crystal structure of the complex between EF-Tu.GDP and aurodox
    • Vogeley, L., Palm, G.J., Mesters, J.R., and Hilgenfeld, R. 2001. Conformational change of elongation factor Tu (EF-Tu) induced by antibiotic binding. Crystal structure of the complex between EF-Tu.GDP and aurodox. J. Biol. Chem. 276: 17149-17155.
    • (2001) J. Biol. Chem. , vol.276 , pp. 17149-17155
    • Vogeley, L.1    Palm, G.J.2    Mesters, J.R.3    Hilgenfeld, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.