메뉴 건너뛰기




Volumn 40, Issue D1, 2012, Pages

PSCDB: A database for protein structural change upon ligand binding

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CONTROLLED STUDY; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; PSCDB DATABASE;

EID: 84857554750     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr966     Document Type: Article
Times cited : (45)

References (36)
  • 1
    • 0017411710 scopus 로고
    • The protein data bank: A computer based archival file for macromolecular structures
    • Bernstein,F.C., Koetzle,T.F., Williams,G.J., Meyer,E.F. Jr, Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542. (Pubitemid 8109216)
    • (1977) Journal of Molecular Biology , vol.112 , Issue.3 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 3
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama,F. and Sanejouand,Y.H. (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng., 14, 1-6. (Pubitemid 32318932)
    • (2001) Protein Engineering , vol.14 , Issue.1 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.-H.2
  • 4
    • 0037008011 scopus 로고    scopus 로고
    • Multiple conformational changes in enzyme catalysis
    • Hammes,G.G. (2002) Multiple conformational changes in enzyme catalysis. Biochemistry, 41, 8221-8228.
    • (2002) Biochemistry , vol.41 , pp. 8221-8228
    • Hammes, G.G.1
  • 5
    • 2442567233 scopus 로고    scopus 로고
    • Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements
    • Hayward,S. (2004) Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. J. Mol. Biol., 339, 1001-1021.
    • (2004) J. Mol. Biol. , vol.339 , pp. 1001-1021
    • Hayward, S.1
  • 6
    • 2542467720 scopus 로고    scopus 로고
    • Conformational change in substrate binding, catalysis and product release: An open and shut case?
    • DOI 10.1016/j.febslet.2004.03.067, PII S0014579304003643
    • Gutteridge,A. and Thornton,J. (2004) Conformational change in substrate binding, catalysis and product release: an open and shut case? FEBS Lett., 567, 67-73. (Pubitemid 38686425)
    • (2004) FEBS Letters , vol.567 , Issue.1 , pp. 67-73
    • Gutteridge, A.1    Thornton, J.2
  • 7
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • DOI 10.1016/j.jmb.2004.11.013, PII S0022283604014391
    • Gutteridge,A. and Thornton,J. (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J. Mol. Biol., 346, 21-28. (Pubitemid 40128303)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.1 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 8
    • 14144256567 scopus 로고    scopus 로고
    • Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool
    • DOI 10.1110/ps.04882105
    • Alexandrov,V., Lehnert,U., Echols,N., Milburn,D., Engelman,D. and Gerstein,M. (2005) Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci., 14, 633-643. (Pubitemid 40283901)
    • (2005) Protein Science , vol.14 , Issue.3 , pp. 633-643
    • Alexandrov, V.1    Lehnert, U.2    Echols, N.3    Milburn, D.4    Engelman, D.5    Gerstein, M.6
  • 9
    • 33751423377 scopus 로고    scopus 로고
    • How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding
    • DOI 10.1016/j.jmb.2006.09.062, PII S0022283606012861
    • Gunasekaran,K. and Nussinov,R. (2007) How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J. Mol. Biol., 365, 257-273. (Pubitemid 44821204)
    • (2007) Journal of Molecular Biology , vol.365 , Issue.1 , pp. 257-273
    • Gunasekaran, K.1    Nussinov, R.2
  • 10
    • 34250001164 scopus 로고    scopus 로고
    • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies
    • Keskin,O. (2007) Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Struct. Biol., 7, 1-11.
    • (2007) BMC Struct. Biol. , vol.7 , pp. 1-11
    • Keskin, O.1
  • 11
    • 34547666968 scopus 로고    scopus 로고
    • How well can we understand large-scale protein motions using normal modes of elastic network models?
    • DOI 10.1529/biophysj.106.095927
    • Yang,L., Song,G. and Jernigan,R.L. (2007) How well can we understand large-scale proteins motions using normal modes of elastic network models. Biophys. J., 93, 920-929. (Pubitemid 47219784)
    • (2007) Biophysical Journal , vol.93 , Issue.3 , pp. 920-929
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 12
    • 43449099725 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding correlates with enzymatic reaction mechanism
    • Koike,R., Amemiya,T., Ota,M. and Kidera,A. (2008) Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. J. Mol. Biol., 379, 397-401.
    • (2008) J. Mol. Biol. , vol.379 , pp. 397-401
    • Koike, R.1    Amemiya, T.2    Ota, M.3    Kidera, A.4
  • 13
    • 37849035176 scopus 로고    scopus 로고
    • What is the relationship between the global structures of apo and holo proteins?
    • Brylinski,M. and Skolnick,J. (2008) What is the relationship between the global structures of apo and holo proteins? Proteins, 70, 363-377.
    • (2008) Proteins , vol.70 , pp. 363-377
    • Brylinski, M.1    Skolnick, J.2
  • 14
    • 48749126860 scopus 로고    scopus 로고
    • Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
    • Dobbins,S.E., Lesk,V.I. and Sternberg,M.J. (2008) Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc. Natl Acad. Sci. USA, 105, 10390-10395.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 10390-10395
    • Dobbins, S.E.1    Lesk, V.I.2    Sternberg, M.J.3
  • 15
    • 65349173946 scopus 로고    scopus 로고
    • Database of ligand-induced domain movements in enzymes
    • Qi,G. and Hayward,S. (2009) Database of ligand-induced domain movements in enzymes. BMC Struct. Biol., 9, 13.
    • (2009) BMC Struct. Biol. , vol.9 , pp. 13
    • Qi, G.1    Hayward, S.2
  • 16
    • 70149090164 scopus 로고    scopus 로고
    • The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
    • Bakan,A. and Bahar,I. (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc. Natl Acad. Sci. USA, 106, 14349-14354.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 14349-14354
    • Bakan, A.1    Bahar, I.2
  • 17
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr,D.D., Nussinov,R. and Wright,P.E. (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol., 5, 789-796.
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 18
    • 77951270272 scopus 로고    scopus 로고
    • Large conformational changes in proteins: Signaling and other functions
    • Grant,B.J., Gorfe,A.A. and McCammon,J.A. (2010) Large conformational changes in proteins: signaling and other functions. Curr. Opin. Struct. Biol., 20, 142-147.
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 142-147
    • Grant, B.J.1    Gorfe, A.A.2    McCammon, J.A.3
  • 19
    • 77955627131 scopus 로고    scopus 로고
    • How to choose relevant multiple receptor conformations for virtual screening: A test case of Cdk2 and normal mode analysis
    • Sperandio,O., Mouawad,L., Pinto,E., Villoutreix,B.O., Perahia,D. and Miteva,M.A. (2010) How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur. Biophys. J., 39, 1365-1372.
    • (2010) Eur. Biophys. J. , vol.39 , pp. 1365-1372
    • Sperandio, O.1    Mouawad, L.2    Pinto, E.3    Villoutreix, B.O.4    Perahia, D.5    Miteva, M.A.6
  • 20
    • 79953905577 scopus 로고    scopus 로고
    • Classification and annotation of the relationship between protein structural change and ligand binding
    • Amemiya,T., Koike,R., Fuchigami,S., Ikeguchi,M. and Kidera,A. (2011) Classification and annotation of the relationship between protein structural change and ligand binding. J. Mol. Biol., 408, 568-584.
    • (2011) J. Mol. Biol. , vol.408 , pp. 568-584
    • Amemiya, T.1    Koike, R.2    Fuchigami, S.3    Ikeguchi, M.4    Kidera, A.5
  • 21
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • DOI 10.1093/nar/26.18.4280
    • Gerstein,M. and Krebs,W. (1998) A database of macromolecular motions. Nucleic Acids Res., 26, 4280-4290. (Pubitemid 28418388)
    • (1998) Nucleic Acids Research , vol.26 , Issue.18 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 23
    • 0038156098 scopus 로고    scopus 로고
    • The DynDom database of protein domain motions
    • DOI 10.1093/bioinformatics/btg137
    • Lee,R., Razaz,M. and Hayward,S. (2003) The DynDom database of protein domain motions. Bioinformatics, 19, 1290-1291. (Pubitemid 36850223)
    • (2003) Bioinformatics , vol.19 , Issue.10 , pp. 1290-1291
    • Lee, R.A.1    Razaz, M.2    Hayward, S.3
  • 24
    • 20844448232 scopus 로고    scopus 로고
    • A comprehensive and non-redundant database of protein domain movements
    • DOI 10.1093/bioinformatics/bti420
    • Qi,G., Lee,R. and Hayward,S. (2005) A comprehensive and non-redundant database of protein domain movements. Bioinformatics, 21, 2832-2838. (Pubitemid 40862280)
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2832-2838
    • Qi, G.1    Lee, R.2    Hayward, S.3
  • 25
    • 35748959334 scopus 로고    scopus 로고
    • PiQSi: Protein quaternary structure investigation
    • Levy,E.D. (2007) PiQSi: protein quaternary structure investigation. Structure, 15, 1364-1367.
    • (2007) Structure , vol.15 , pp. 1364-1367
    • Levy, E.D.1
  • 27
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    • DOI 10.1002/(SICI)1097-0134(19980201)30:2<144::AID-PROT4>3.0.CO;2-N
    • Hayward,S. and Berendsen,H.J.C. (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins, 30, 144-154. (Pubitemid 28080149)
    • (1998) Proteins: Structure, Function and Genetics , vol.30 , Issue.2 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.C.2
  • 28
    • 0036888353 scopus 로고    scopus 로고
    • Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50
    • DOI 10.1016/S1093-3263(02)00140-7, PII S1093326302001407
    • Hayward,S. and Lee,R.A. (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J. Mol. Graphics Model., 21, 181-183. (Pubitemid 35279848)
    • (2002) Journal of Molecular Graphics and Modelling , vol.21 , Issue.3 , pp. 181-183
    • Hayward, S.1    Lee, R.A.2
  • 29
    • 4944262604 scopus 로고    scopus 로고
    • Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose
    • DOI 10.1128/JB.186.20.6915-6927.2004
    • Lunin,V.V., Li,Y., Schrag,J.D., Iannuzzi,P., Cygler,M. and Matte,A. (2004) Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose. J. Bacteriol., 186, 6915-6927. (Pubitemid 39332131)
    • (2004) Journal of Bacteriology , vol.186 , Issue.20 , pp. 6915-6927
    • Lunin, V.V.1    Li, Y.2    Schrag, J.D.3    Iannuzzi, P.4    Cygler, M.5    Matte, A.6
  • 31
    • 0022412192 scopus 로고
    • Hydrophobicity of amino acid residues in globular proteins
    • Rose,G.D., Geselouitz,A.R., Lesser,G.J., Lee,R.H. and Zehfus,M.H. (1985) Hydrophobicity of amino acid residues in globular proteins. Science, 30, 834-838. (Pubitemid 16246583)
    • (1985) Science , vol.229 , Issue.4716 , pp. 834-838
    • Rose, G.D.1    Geselowitz, A.R.2    Lesser, G.J.3
  • 32
  • 34
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding: Linear response theory
    • DOI 10.1103/PhysRevLett.94.078102, 078102
    • Ikeguchi,M., Ueno,J., Sato,M. and Kidera,A. (2005) Protein structural change upon ligand binding: linear response theory. Phys. Rev. Lett., 94, 1-4. (Pubitemid 40620748)
    • (2005) Physical Review Letters , vol.94 , Issue.7 , pp. 1-4
    • Ikeguchi, M.1    Ueno, J.2    Sato, M.3    Kidera, A.4
  • 35
    • 70349913995 scopus 로고    scopus 로고
    • Linear response theory in dihedral angle space for protein structural change upon ligand binding
    • Omori,S., Fuchigami,S., Ikeguchi,M. and Kidera,A. (2009) Linear response theory in dihedral angle space for protein structural change upon ligand binding. J. Comput. Chem., 30, 2602-2608.
    • (2009) J. Comput. Chem. , vol.30 , pp. 2602-2608
    • Omori, S.1    Fuchigami, S.2    Ikeguchi, M.3    Kidera, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.