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Volumn 77, Issue 4, 2009, Pages 796-811

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

Author keywords

Binding; Dynamics; Elastic network model; PDZ domain; Selectivity

Indexed keywords

PDZ PROTEIN;

EID: 70450065485     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22492     Document Type: Article
Times cited : (56)

References (113)
  • 1
    • 0036876382 scopus 로고    scopus 로고
    • Signaling complex organization by PDZ domain proteins
    • DOI 10.1159/000068256
    • Fan JS, Zhang M. Signaling complex organization by PDZ domain proteins. Neurosignals 2002;11:315-321. (Pubitemid 37494386)
    • (2002) NeuroSignals , vol.11 , Issue.6 , pp. 315-321
    • Fan, J.-S.1    Zhang, M.2
  • 3
    • 0037155199 scopus 로고    scopus 로고
    • PDZ domains: Structural modules for protein complex assembly
    • DOI 10.1074/jbc.R100065200
    • Hung AY, Sheng M. PDZ domains: structural modules for protein complex assembly. J Biol Chem 2002;277:5699-5702. (Pubitemid 34968344)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.8 , pp. 5699-5702
    • Hung, A.Y.1    Sheng, M.2
  • 4
    • 0037503653 scopus 로고    scopus 로고
    • PDZ domains-glue and guide
    • van Ham M, Hendriks W. PDZ domains-glue and guide. Mol Biol Rep 2003;30:69-82.
    • (2003) Mol Biol Rep , vol.30 , pp. 69-82
    • Van Ham, M.1    Hendriks, W.2
  • 5
    • 33746861956 scopus 로고    scopus 로고
    • Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1 Insights into determinants of PDZ domain specificity
    • DOI 10.1074/jbc.M602901200
    • Appleton BA, Zhang Y, Wu P, Yin JP, Hunziker W, Skelton NJ, Sidhu SS, Wiesmann C. Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity. J Biol Chem 2006;281:22312-22320. (Pubitemid 44181933)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.31 , pp. 22312-22320
    • Appleton, B.A.1    Zhang, Y.2    Wu, P.3    Yin, J.P.4    Hunziker, W.5    Skelton, N.J.6    Sidhu, S.S.7    Wiesmann, C.8
  • 6
    • 0037449799 scopus 로고    scopus 로고
    • Novel mode of ligand recognition by the Erbin PDZ domain
    • DOI 10.1074/jbc.C200571200
    • Birrane G, Chung J, Ladias JA. Novel mode of ligand recognition by the Erbin PDZ domain. J Biol Chem 2003;278:1399-1402. (Pubitemid 36801362)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.3 , pp. 1399-1402
    • Birrane, G.1    Chung, J.2    Ladias, J.A.A.3
  • 7
    • 34249800674 scopus 로고    scopus 로고
    • Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex
    • DOI 10.1110/ps.062440607
    • Chen Q, Niu X, Xu Y, Wu J, Shi Y. Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex. Protein Sci 2007;16:1053-1062. (Pubitemid 46849215)
    • (2007) Protein Science , vol.16 , Issue.6 , pp. 1053-1062
    • Chen, Q.1    Niu, X.2    Xu, Y.3    Wu, J.4    Shi, Y.5
  • 8
    • 0031960011 scopus 로고    scopus 로고
    • Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition
    • Daniels DL, Cohen AR, Anderson JM, Brunger AT. Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition. Nat Struct Biol 1998;5:317-325.
    • (1998) Nat Struct Biol , vol.5 , pp. 317-325
    • Daniels, D.L.1    Cohen, A.R.2    Anderson, J.M.3    Brunger, A.T.4
  • 9
    • 33846077132 scopus 로고    scopus 로고
    • PDZ domain protein-protein interactions: A case study with PICK1
    • Dev KK. PDZ domain protein-protein interactions: a case study with PICK1. Curr Top Med Chem 2007;7:3-20.
    • (2007) Curr Top Med Chem , vol.7 , pp. 3-20
    • Dev, K.K.1
  • 11
    • 0034740693 scopus 로고    scopus 로고
    • Mechanism and role of PDZ domains in signaling complex assembly
    • Harris BZ, Lim WA. Mechanism and role of PDZ domains in signaling complex assembly. J Cell Sci 2001;114(Part 18):3219-3231.
    • (2001) J Cell Sci , vol.114 , Issue.PART 18 , pp. 3219-3231
    • Harris, B.Z.1    Lim, W.A.2
  • 12
    • 0033617473 scopus 로고    scopus 로고
    • Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex
    • Hillier BJ, Christopherson KS, Prehoda KE, Bredt DS, Lim WA. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science 1999;284:812-815.
    • (1999) Science , vol.284 , pp. 812-815
    • Hillier, B.J.1    Christopherson, K.S.2    Prehoda, K.E.3    Bredt, D.S.4    Lim, W.A.5
  • 13
    • 0348111461 scopus 로고    scopus 로고
    • Crystal Structure of the Shank PDZ-Ligand Complex Reveals a Class I PDZ Interaction and a Novel PDZ-PDZ Dimerization
    • DOI 10.1074/jbc.M306919200
    • Im YJ, Lee JH, Park SH, Park SJ, Rho SH, Kang GB, Kim E, Eom SH. Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization. J Biol Chem 2003;278:48099-48104. (Pubitemid 37523261)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.48 , pp. 48099-48104
    • Im, Y.J.1    Lee, J.H.2    Park, S.H.3    Park, S.J.4    Rho, S.-H.5    Kang, G.B.6    Kim, E.7    Eom, S.H.8
  • 14
    • 0037424515 scopus 로고    scopus 로고
    • Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization
    • DOI 10.1074/jbc.M212263200
    • Im YJ, Park SH, Rho SH, Lee JH, Kang GB, Sheng M, Kim E, Eom SH. Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization. J Biol Chem 2003;278:8501-8507. (Pubitemid 36800602)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.10 , pp. 8501-8507
    • Im, Y.J.1    Park, S.H.2    Rho, S.-H.3    Lee, J.H.4    Kang, G.B.5    Sheng, M.6    Kim, E.7    Eom, S.H.8
  • 15
    • 0037816293 scopus 로고    scopus 로고
    • Molecular roots of degenerate specificity in syntenin's PDZ2 domain: Reassessment of the PDZ recognition paradigm
    • DOI 10.1016/S0969-2126(03)00125-4
    • Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS. Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm. Structure 2003;11:845-853. (Pubitemid 36833270)
    • (2003) Structure , vol.11 , Issue.7 , pp. 845-853
    • Kang, B.S.1    Cooper, D.R.2    Devedjiev, Y.3    Derewenda, U.4    Derewenda, Z.S.5
  • 16
    • 0035906714 scopus 로고    scopus 로고
    • + exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains
    • DOI 10.1006/jmbi.2001.4634
    • Karthikeyan S, Leung T, Birrane G, Webster G, Ladias JA. Crystal structure of the PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains. J Mol Biol 2001;308:963-973. (Pubitemid 32574372)
    • (2001) Journal of Molecular Biology , vol.308 , Issue.5 , pp. 963-973
    • Karthikeyan, S.1    Leung, T.2    Birrane, G.3    Webster, G.4    Ladias, J.A.A.5
  • 17
    • 0037166247 scopus 로고    scopus 로고
    • 2 adrenergic and platelet-derived growth factor receptors
    • DOI 10.1074/jbc.M201507200
    • Karthikeyan S, Leung T, Ladias JA. Structural determinants of the Na+/H+ exchanger regulatory factor interaction with the beta 2 adrenergic and platelet-derived growth factor receptors. J Biol Chem 2002;277:18973-18978. (Pubitemid 34952459)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.21 , pp. 18973-18978
    • Karthikeyan, S.1    Leung, T.2    Ladias, J.A.A.3
  • 19
    • 34247465989 scopus 로고    scopus 로고
    • Engineering modular protein interaction switches by sequence overlap
    • Sallee NA, Yeh BJ, Lim WA. Engineering modular protein interaction switches by sequence overlap. J Am Chem Soc 2007;129:4606-4611.
    • (2007) J Am Chem Soc , vol.129 , pp. 4606-4611
    • Sallee, N.A.1    Yeh, B.J.2    Lim, W.A.3
  • 20
    • 0034645726 scopus 로고    scopus 로고
    • Solution structure and backbone dynamics of the second PDZ domain of postsynaptic density-95
    • DOI 10.1006/jmbi.1999.3350
    • Tochio H, Hung F, Li M, Bredt DS, Zhang M. Solution structure and backbone dynamics of the second PDZ domain of postsynaptic density-95. J Mol Biol 2000;295:225-237. (Pubitemid 30045356)
    • (2000) Journal of Molecular Biology , vol.295 , Issue.2 , pp. 225-237
    • Tochio, H.1    Hung, F.2    Li, M.3    Bredt, D.S.4    Zhang, M.5
  • 21
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • DOI 10.1126/science.286.5438.295
    • Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999;286:295-299. (Pubitemid 29484693)
    • (1999) Science , vol.286 , Issue.5438 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 22
    • 33748313081 scopus 로고    scopus 로고
    • The prevalence and significance of PDZ domain-phosphoinositide interactions
    • DOI 10.1016/j.bbalip.2006.04.003, PII S138819810600117X
    • Zimmermann P. The prevalence and significance of PDZ domain- phophoinositide interactions. Biochim Biophys Acta 2006;1761:947-956. (Pubitemid 44332327)
    • (2006) Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids , vol.1761 , Issue.8 , pp. 947-956
    • Zimmermann, P.1
  • 26
    • 0035861856 scopus 로고    scopus 로고
    • Classification of PDZ domains
    • Bezprozvanny I, Maximov A. Classification of PDZ domains. FEBS Lett 2001;509:457-462.
    • (2001) FEBS Lett , vol.509 , pp. 457-462
    • Bezprozvanny, I.1    Maximov, A.2
  • 28
    • 0037070149 scopus 로고    scopus 로고
    • PDZ domains: Troubles in classification
    • Vaccaro P, Dente L. PDZ domains: troubles in classification. FEBS Lett 2002;512:345-346.
    • (2002) FEBS Lett , vol.512 , pp. 345-346
    • Vaccaro, P.1    Dente, L.2
  • 29
    • 0347753736 scopus 로고    scopus 로고
    • Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
    • Fuentes EJ, Der CJ, Lee AL. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J Mol Biol 2004;335:1105-1115.
    • (2004) J Mol Biol , vol.335 , pp. 1105-1115
    • Fuentes, E.J.1    Der, C.J.2    Lee, A.L.3
  • 30
    • 33749511033 scopus 로고    scopus 로고
    • Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study
    • DOI 10.1021/ja060830y
    • Basdevant N, Weinstein H, Ceruso M. Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc 2006;128:12766-12777. (Pubitemid 44527753)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.39 , pp. 12766-12777
    • Basdevant, N.1    Weinstein, H.2    Ceruso, M.3
  • 31
    • 34948852422 scopus 로고    scopus 로고
    • Diffusion-limited unbinding of small peptides from pdz domains
    • DOI 10.1021/jp0730390
    • Cecconi F, Rios PDL, Piazza F. Diffusion-limited unbinding of small peptides from PDZ domains. J Phys Chem B 2007;111:11057-11063. (Pubitemid 47522598)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.37 , pp. 11057-11063
    • Cecconi, F.1    De Los Rios, P.2    Piazza, F.3
  • 33
    • 47349099470 scopus 로고    scopus 로고
    • Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein
    • DOI 10.1021/ja0752080
    • Dhulesia A, Gsponer J, Vendruscolo M. Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein. J Am Chem Soc 2008;130:8931-8939. (Pubitemid 352000832)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.28 , pp. 8931-8939
    • Dhulesia, A.1    Gsponer, J.2    Vendruscolo, M.3
  • 35
    • 33746067899 scopus 로고    scopus 로고
    • Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6
    • DOI 10.1016/j.ejcb.2006.03.003, PII S0171933506000653
    • Kempkens O, Medina E, Fernandez-Ballester G, Ozuyaman S, Le Bivic A, Serrano L, Knust E. Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur J Cell Biol 2006;85:753-767. (Pubitemid 44070573)
    • (2006) European Journal of Cell Biology , vol.85 , Issue.8 , pp. 753-767
    • Kempkens, O.1    Medina, E.2    Fernandez-Ballester, G.3    Ozuyaman, S.4    Le Bivic, A.5    Serrano, L.6    Knust, E.7
  • 36
    • 26444604826 scopus 로고    scopus 로고
    • A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains
    • DOI 10.1021/ja054195s
    • Niv MY, Weinstein H. A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. J Am Chem Soc 2005;127:14072-14079. (Pubitemid 41437055)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.40 , pp. 14072-14079
    • Niv, M.Y.1    Weinstein, H.2
  • 37
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • DOI 10.1016/j.jmb.2005.05.043, PII S002228360500598X
    • Ota N, Agard DA. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol 2005;351:345-354. (Pubitemid 41007753)
    • (2005) Journal of Molecular Biology , vol.351 , Issue.2 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 39
    • 33749029273 scopus 로고    scopus 로고
    • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    • DOI 10.1002/prot.21146
    • Sharp K, Skinner JJ. Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling. Proteins 2006;65:347-361. (Pubitemid 44454109)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.2 , pp. 347-361
    • Sharp, K.1    Skinner, J.J.2
  • 40
    • 35548976322 scopus 로고    scopus 로고
    • Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
    • DOI 10.1038/nature06232, PII NATURE06232
    • Tang C, Schwieters CD, Clore GM. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 2007;449:1078-1082. (Pubitemid 350014601)
    • (2007) Nature , vol.449 , Issue.7165 , pp. 1078-1082
    • Tang, C.1    Schwieters, C.D.2    Clore, G.M.3
  • 42
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • DOI 10.1126/science.291.5512.2429
    • Volkman BF, Lipson D, Wemmer DE, Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 2001;291:2429-2433. (Pubitemid 32231808)
    • (2001) Science , vol.291 , Issue.5512 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 44
    • 0000496772 scopus 로고    scopus 로고
    • Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability
    • Bahar I, Atilgan AR, Demirel MC, Erman B. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett 1998;80:2733-2736. (Pubitemid 128621654)
    • (1998) Physical Review Letters , vol.80 , Issue.12 , pp. 2733-2736
    • Bahar, I.1    Atilgan, A.R.2    Demirel, M.C.3    Erman, B.4
  • 45
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181. (Pubitemid 127740467)
    • (1997) Folding and Design , vol.2 , Issue.3 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 46
    • 0037080323 scopus 로고    scopus 로고
    • Molecular mechanisms of chaperonin GroEL-GroES function
    • DOI 10.1021/bi011393x
    • Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry 2002;41:491-501. (Pubitemid 34062018)
    • (2002) Biochemistry , vol.41 , Issue.2 , pp. 491-501
    • Keskin, O.1    Bahar, I.2    Flatow, D.3    Covell, D.G.4    Jernigan, R.L.5
  • 47
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • Keskin O, Jernigan RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J 2000;78:2093-2106. (Pubitemid 30183603)
    • (2000) Biophysical Journal , vol.78 , Issue.4 , pp. 2093-2106
    • Keskin, O.1    Jernigan, R.L.2    Bahar, I.3
  • 48
    • 33749521415 scopus 로고    scopus 로고
    • Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data
    • DOI 10.1529/biophysj.106.085894
    • Kondrashov DA, Cui Q, Phillips GN, Jr. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J 2006;91:2760-2767. (Pubitemid 44526467)
    • (2006) Biophysical Journal , vol.91 , Issue.8 , pp. 2760-2767
    • Kondrashov, D.A.1    Cui, Q.2    Phillips Jr., G.N.3
  • 49
    • 14844300852 scopus 로고    scopus 로고
    • Maturation dynamics of bacteriophage HK97 capsid
    • DOI 10.1016/j.str.2004.12.015
    • Rader AJ, Vlad DH, Bahar I. Maturation dynamics of bacteriophage HK97 capsid. Structure 2005;13:413-421. (Pubitemid 40342881)
    • (2005) Structure , vol.13 , Issue.3 , pp. 413-421
    • Rader, A.J.1    Vlad, D.H.2    Bahar, I.3
  • 50
    • 33748189629 scopus 로고    scopus 로고
    • The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models
    • Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL. The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J Chem Theory Comput 2006;2:696-704.
    • (2006) J Chem Theory Comput , vol.2 , pp. 696-704
    • Sen, T.Z.1    Feng, Y.2    Garcia, J.V.3    Kloczkowski, A.4    Jernigan, R.L.5
  • 51
    • 78049283691 scopus 로고    scopus 로고
    • Optimizing cutoff distances and spring constants for the Gaussian Network Model of ATP-binding proteins
    • Cui IBaQ, editor. Boca Raton: Chapman and Hall/CRC
    • Sen TZ, Jernigan RL. Optimizing cutoff distances and spring constants for the Gaussian Network Model of ATP-binding proteins. In: Cui IBaQ, editor. Normal mode analysis: theory and applications to biological and chemical systems. Boca Raton: Chapman and Hall/CRC; 2006. pp 171-186.
    • (2006) Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems , pp. 171-186
    • Sen, T.Z.1    Jernigan, R.L.2
  • 52
    • 0036307741 scopus 로고    scopus 로고
    • The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
    • DOI 10.1016/S0022-2836(02)00135-3
    • Tama F, Brooks CL. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol 2002;318:733-747. (Pubitemid 34729365)
    • (2002) Journal of Molecular Biology , vol.318 , Issue.3 , pp. 733-747
    • Tama, F.1    Brooks III, C.L.2
  • 53
    • 9644266693 scopus 로고    scopus 로고
    • Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
    • DOI 10.1016/j.jmb.2004.10.054, PII S0022283604013609
    • Tama F, Brooks CL. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol 2005;345:299-314. (Pubitemid 39574852)
    • (2005) Journal of Molecular Biology , vol.345 , Issue.2 , pp. 299-314
    • Tama, F.1    Brooks III, C.L.2
  • 54
    • 0036077875 scopus 로고    scopus 로고
    • Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The Elastic Network Model
    • DOI 10.1016/S0022-2836(02)00562-4
    • Delarue M, Sanejouand YH. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J Mol Biol 2002;320:1011-1024. (Pubitemid 34808821)
    • (2002) Journal of Molecular Biology , vol.320 , Issue.5 , pp. 1011-1024
    • Delarue, M.1    Sanejouand, Y.-H.2
  • 55
    • 18144418170 scopus 로고    scopus 로고
    • Protein structural change upon ligand binding: Linear response theory
    • Ikeguchi M, Ueno J, Sato M, Kidera A. Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 2005;94:078102.
    • (2005) Phys Rev Lett , vol.94 , pp. 078102
    • Ikeguchi, M.1    Ueno, J.2    Sato, M.3    Kidera, A.4
  • 56
    • 34250001164 scopus 로고    scopus 로고
    • Binding induced conformational changes of proteins correlate with their intrinsic fluctuations
    • Keskin O. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations. BMC Struct Biol 2007;7:31.
    • (2007) BMC Struct Biol , vol.7 , pp. 31
    • Keskin, O.1
  • 57
    • 2942638203 scopus 로고    scopus 로고
    • Molecular mechanism of domain swapping in proteins: An analysis of slower motions
    • DOI 10.1529/biophysj.103.034736
    • Kundu S, Jernigan RL. Molecular mechanism of domain swapping in proteins: an analysis of slower motions. Biophys J 2004;86:3846-3854. (Pubitemid 38780261)
    • (2004) Biophysical Journal , vol.86 , Issue.6 , pp. 3846-3854
    • Kundu, S.1    Jernigan, R.L.2
  • 58
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001;14:1-6. (Pubitemid 32318932)
    • (2001) Protein Engineering , vol.14 , Issue.1 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.-H.2
  • 59
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • DOI 10.1073/pnas.0507603102
    • Tobi D, Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 2005;102:18908-18913. (Pubitemid 43049540)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.52 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 60
    • 17844411211 scopus 로고    scopus 로고
    • Normal-modes-based prediction of protein conformational changes guided by distance constraints
    • DOI 10.1529/biophysj.104.058453
    • Zheng W, Brooks BR. Normal-modes-based prediction of protein conformational changes guided by distance constraints. Biophys J 2005;88:3109-3117. (Pubitemid 40586565)
    • (2005) Biophysical Journal , vol.88 , Issue.5 , pp. 3109-3117
    • Zheng, W.1    Brooks, B.R.2
  • 62
    • 21244506296 scopus 로고    scopus 로고
    • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
    • DOI 10.1529/biophysj.104.051342
    • Haliloglu T, Keskin O, Ma B, Nussinov R. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J 2005;88:1552-1559. (Pubitemid 40976173)
    • (2005) Biophysical Journal , vol.88 , Issue.3 , pp. 1552-1559
    • Haliloglu, T.1    Keskin, O.2    Ma, B.3    Nussinov, R.4
  • 63
    • 44949215646 scopus 로고    scopus 로고
    • Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model
    • Haliloglu T, Seyrek E, Erman B. Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. Phys Rev Lett 2008;100:228102.
    • (2008) Phys Rev Lett , vol.100 , pp. 228102
    • Haliloglu, T.1    Seyrek, E.2    Erman, B.3
  • 65
    • 0035815305 scopus 로고    scopus 로고
    • Ephrin-B reverse signaling is mediated by a novel PDZ-RGS protein and selectively inhibits G protein-coupled chemoattraction
    • DOI 10.1016/S0092-8674(01)00297-5
    • Lu Q, Sun EE, Klein RS, Flanagan JG. Ephrin-B reverse signaling is mediated by a novel PDZ-RGS protein and selectively inhibits G protein-coupled chemoattraction. Cell 2001;105:69-79. (Pubitemid 32323917)
    • (2001) Cell , vol.105 , Issue.1 , pp. 69-79
    • Lu, Q.1    Sun, E.E.2    Klein, R.S.3    Flanagan, J.G.4
  • 69
    • 0037442915 scopus 로고    scopus 로고
    • Potentials of mean force between ionizable amino acid side chains in water
    • DOI 10.1021/ja025521w
    • Masunov A, Lazaridis T. Potentials of mean force between ionizable amino acid side chains in water. J Am Chem Soc 2003;125:1722-1730. (Pubitemid 36232567)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.7 , pp. 1722-1730
    • Masunov, A.1    Lazaridis, T.2
  • 71
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996;77:1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 72
    • 80054861084 scopus 로고    scopus 로고
    • The Gaussian Network Model: Theory and applications
    • Cui Q, Bahar I, editors. Chapman and Hall/CRC Mathematical and Computational Biology Series, Taylor and Francis Group: Boca Raton
    • Rader AJ, Chennubhotla C, Yang L-W, Bahar I. The Gaussian Network Model: theory and applications. In: Cui Q, Bahar I, editors. Normal mode analysis theory and applications to biological and chemical systems, Chapman and Hall/CRC Mathematical and Computational Biology Series, Taylor and Francis Group: Boca Raton; 2006. pp 41-64.
    • (2006) Normal Mode Analysis Theory and Applications to Biological and Chemical Systems , pp. 41-64
    • Rader, A.J.1    Chennubhotla, C.2    Yang, L.-W.3    Bahar, I.4
  • 73
    • 34249945151 scopus 로고    scopus 로고
    • Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions
    • DOI 10.1016/j.str.2007.04.014, PII S0969212607001839
    • Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure 2007;15:741-749. (Pubitemid 46876711)
    • (2007) Structure , vol.15 , Issue.6 , pp. 741-749
    • Yang, L.-W.1    Eyal, E.2    Chennubhotla, C.3    Jee, J.4    Gronenborn, A.M.5    Bahar, I.6
  • 74
    • 0037197254 scopus 로고    scopus 로고
    • Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
    • Tsodikov OV, Record MT, Jr, Sergeev YV. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem 2002;23:600-609.
    • (2002) J Comput Chem , vol.23 , pp. 600-609
    • Tsodikov, O.V.1    Record Jr., M.T.2    Sergeev, Y.V.3
  • 75
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • DOI 10.1006/jmbi.1996.0114
    • Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256:623-644. (Pubitemid 26107211)
    • (1996) Journal of Molecular Biology , vol.256 , Issue.3 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 76
    • 0029909384 scopus 로고    scopus 로고
    • An iterative method for extracting energy-like quantities from protein structures
    • Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci USA 1996;93:11628-11633.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 11628-11633
    • Thomas, P.D.1    Dill, K.A.2
  • 80
    • 39149108868 scopus 로고    scopus 로고
    • Structural flexibility in proteins: Impact of the crystal environment
    • DOI 10.1093/bioinformatics/btm625
    • Hinsen K. Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 2008;24:521-528. (Pubitemid 351256296)
    • (2008) Bioinformatics , vol.24 , Issue.4 , pp. 521-528
    • Hinsen, K.1
  • 81
    • 58849116413 scopus 로고    scopus 로고
    • Application of elastic network models to proteins in the crystalline state
    • Riccardi D, Cui Q, Phillips GN, Jr. Application of elastic network models to proteins in the crystalline state. Biophys J 2009;96:464-475.
    • (2009) Biophys J , vol.96 , pp. 464-475
    • Riccardi, D.1    Cui, Q.2    Phillips Jr., G.N.3
  • 82
    • 48949119100 scopus 로고    scopus 로고
    • Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors
    • DOI 10.1088/1478-3975/5/2/026008, PII S1478397508747733
    • Soheilifard R, Makarov DE, Rodin GJ. Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors. Phys Biol 2008;5:26008. (Pubitemid 352020321)
    • (2008) Physical Biology , vol.5 , Issue.2 , pp. 026008
    • Soheilifard, R.1    Makarov, D.E.2    Rodin, G.J.3
  • 83
    • 34248182936 scopus 로고    scopus 로고
    • VGNM: A Better Model for Understanding the Dynamics of Proteins in Crystals
    • DOI 10.1016/j.jmb.2007.03.059, PII S002228360700424X
    • Song G, Jernigan RL. vGNM: a better model for understanding the dynamics of proteins in crystals. J Mol Biol 2007;369:880-893. (Pubitemid 46709923)
    • (2007) Journal of Molecular Biology , vol.369 , Issue.3 , pp. 880-893
    • Song, G.1    Jernigan, R.L.2
  • 84
    • 47749099638 scopus 로고    scopus 로고
    • Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes
    • Isin B, Schulten K, Tajkhorshid E, Bahar I. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophys J 2008;95:789-803.
    • (2008) Biophys J , vol.95 , pp. 789-803
    • Isin, B.1    Schulten, K.2    Tajkhorshid, E.3    Bahar, I.4
  • 85
    • 23244450294 scopus 로고    scopus 로고
    • Exploring the common dynamics of homologous proteins. Application to the globin family
    • Maguid S, Fernandez-Alberti S, Ferrelli L, Echave J. Exploring the common dynamics of homologous proteins. Application to the globin family. Biophys J 2005;89:3-13.
    • (2005) Biophys J , vol.89 , pp. 3-13
    • Maguid, S.1    Fernandez-Alberti, S.2    Ferrelli, L.3    Echave, J.4
  • 87
    • 20444384605 scopus 로고    scopus 로고
    • Mining frequent patterns in protein structures: A study of protease families
    • DOI 10.1093/bioinformatics/bth912
    • Chen SC, Bahar I. Mining frequent patterns in protein structures: a study of protease families. Bioinformatics 2004;20(Suppl 1):i77-i85. (Pubitemid 41296674)
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Chen, S.-C.1    Bahar, I.2
  • 88
    • 20444409186 scopus 로고    scopus 로고
    • Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes
    • DOI 10.1016/j.str.2005.03.015, PII S096921260500167X
    • Yang LW, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 2005;13:893-904. (Pubitemid 40804392)
    • (2005) Structure , vol.13 , Issue.6 , pp. 893-904
    • Yang, L.-W.1    Bahar, I.2
  • 89
    • 84860168546 scopus 로고    scopus 로고
    • ClustalW, WWW Service at the European Bioinformatics
    • ClustalW, WWW Service at the European Bioinformatics (http://www.ebi.ac. uk/Tools/clustalw2).
  • 90
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 91
    • 0030955263 scopus 로고    scopus 로고
    • Understanding the recognition of protein structural classes by amino acid composition
    • DOI 10.1002/(SICI)1097-0134(199710)29:2<172::AID-PROT5>3.0.CO;2-F
    • Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 1997;29:172-185. (Pubitemid 27430932)
    • (1997) Proteins: Structure, Function and Genetics , vol.29 , Issue.2 , pp. 172-185
    • Bahar, I.1    Atilgan, A.R.2    Jernigan, R.L.3    Erman, B.4
  • 92
    • 0034097869 scopus 로고    scopus 로고
    • Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure
    • Keskin O, Bahar I, Jernigan RL, Beutler JA, Shoemaker RH, Sausville EA, Covell DG. Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure. Anticancer Drug Des 2000;15:79-98. (Pubitemid 30410467)
    • (2000) Anti-Cancer Drug Design , vol.15 , Issue.2 , pp. 79-98
    • Keskin, O.1    Bahar, I.2    Jernigan, R.L.3    Beutler, J.A.4    Shoemaker, R.H.5    Sausville, E.A.6    Covell, D.G.7
  • 93
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • DOI 10.1002/elps.1150181505
    • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723. (Pubitemid 28059943)
    • (1997) Electrophoresis , vol.18 , Issue.15 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 95
    • 0002098417 scopus 로고    scopus 로고
    • The development/application of a "Minimalist" organic/biochemical molecular mechanical force field using a combination of ab initio calculations and experimental data
    • van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Boston: Kluwer
    • Kollman PA, Dixon R, Cornell W, Vox T, Chipot C, Pohorille A. The development/application of a "Minimalist" organic/biochemical molecular mechanical force field using a combination of ab initio calculations and experimental data. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Computer simulation of biomolecular systems theoretical and experimental applications. Boston: Kluwer; 1997. pp 83-96.
    • (1997) Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications , pp. 83-96
    • Kollman, P.A.1    Dixon, R.2    Cornell, W.3    Vox, T.4    Chipot, C.5    Pohorille, A.6
  • 98
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • DOI 10.1093/bioinformatics/btg124
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018. (Pubitemid 36675823)
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 100
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815. (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 101
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • DOI 10.1110/ps.062416606
    • Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006;15:2507-2524. (Pubitemid 44771688)
    • (2006) Protein Science , vol.15 , Issue.11 , pp. 2507-2524
    • Shen, M.-Y.1    Sali, A.2
  • 104
    • 0034733733 scopus 로고    scopus 로고
    • Syntenin-syndecan binding requires syndecan-synteny and the co-operation of both PDZ domains of syntenin
    • DOI 10.1074/jbc.M002459200
    • Grootjans JJ, Reekmans G, Ceulemans H, David G. Syntenin-syndecan binding requires syndecan-synteny and the co-operation of both PDZ domains of syntenin. J Biol Chem 2000;275:19933-19941. (Pubitemid 30441599)
    • (2000) Journal of Biological Chemistry , vol.275 , Issue.26 , pp. 19933-19941
    • Grootjans, J.J.1    Reekmans, G.2    Ceulemans, H.3    David, G.4
  • 105
    • 0037452950 scopus 로고    scopus 로고
    • Role of electrostatic interactions in PDZ domain ligand recognition
    • DOI 10.1021/bi027061p
    • Harris BZ, Lau FW, Fujii N, Guy RK, Lim WA. Role of electrostatic interactions in PDZ domain ligand recognition. Biochemistry 2003;42:2797-2805. (Pubitemid 36331523)
    • (2003) Biochemistry , vol.42 , Issue.10 , pp. 2797-2805
    • Harris, B.Z.1    Lau, F.W.2    Fujii, N.3    Guy, R.K.4    Lim, W.A.5
  • 106
    • 0036479207 scopus 로고    scopus 로고
    • Ligand binding of the second PDZ domain regulates clustering of PSD-95 with the Kv1.4 potassium channel
    • DOI 10.1074/jbc.M106940200
    • Imamura F, Maeda S, Doi T, Fujiyoshi Y. Ligand binding of the second PDZ domain regulates clustering of PSD-95 with the Kv1.4 potassium channel. J Biol Chem 2002;277:3640-3646. (Pubitemid 34953237)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.5 , pp. 3640-3646
    • Imamura, F.1    Maeda, S.2    Doi, T.3    Fujiyoshi, Y.4
  • 108
    • 32544456096 scopus 로고    scopus 로고
    • Essential contribution of the ligand-binding beta B/beta C loop of PDZ1 and PDZ2 in the regulation of postsynaptic clustering, scaffolding, and localization of postsynaptic density-95
    • DOI 10.1523/JNEUROSCI.2489-05.2006
    • Nonaka M, Doi T, Fujiyoshi Y, Takemoto-Kimura S, Bito H. Essential contribution of the ligand-binding beta B/beta C loop of PDZ1 and PDZ2 in the regulation of postsynaptic clustering, scaffolding, and localization of postsynaptic density-95. J Neurosci 2006;26:763-774. (Pubitemid 43237069)
    • (2006) Journal of Neuroscience , vol.26 , Issue.3 , pp. 763-774
    • Nonaka, M.1    Doi, T.2    Fujiyoshi, Y.3    Takemoto-Kimura, S.4    Bito, H.5
  • 109
    • 0031465589 scopus 로고    scopus 로고
    • Specific interaction of the PDZ domain protein PICK1 with the COOH terminus of protein kinase C-alpha
    • DOI 10.1074/jbc.272.51.32019
    • Staudinger J, Lu J, Olson EN. Specific interaction of the PDZ domain protein PICK1 with the COOH terminus of protein kinase C-alpha. J Biol Chem 1997;272:32019-32024. (Pubitemid 28011869)
    • (1997) Journal of Biological Chemistry , vol.272 , Issue.51 , pp. 32019-32024
    • Staudinger, J.1    Lu, J.2    Olson, E.N.3
  • 110
    • 22844442823 scopus 로고    scopus 로고
    • Structural characterization of the intermolecular interactions of synapse-associated protein-97 with the NR2B subunit of N-methyl-D-aspartate receptors
    • DOI 10.1074/jbc.M503555200
    • Wang L, Piserchio A, Mierke DF. Structural characterization of the intermolecular interactions of synapse-associated protein-97 with the NR2B subunit of N-methyl-D-aspartate receptors. J Biol Chem 2005;280:26992-26996. (Pubitemid 41040735)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.29 , pp. 26992-26996
    • Wang, L.1    Piserchio, A.2    Mierke, D.F.3
  • 112
    • 4744341240 scopus 로고    scopus 로고
    • The PDZ domain of PICK1 differentially accepts protein kinase C-alpha and GluR2 as interacting ligands
    • DOI 10.1074/jbc.M404499200
    • Dev KK, Nakanishi S, Henley JM. The PDZ domain of PICK1 differentially accepts protein kinase C-alpha and GluR2 as interacting ligands. J Biol Chem 2004;279:41393-41397. (Pubitemid 39313579)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.40 , pp. 41393-41397
    • Dev, K.K.1    Nakanishi, S.2    Henley, J.M.3
  • 113
    • 10444276589 scopus 로고    scopus 로고
    • Making protein interactions druggable: Targeting PDZ domains
    • Dev KK. Making protein interactions druggable: targeting PDZ domains. Nat Rev Drug Discov 2004;3:1047-1056.
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 1047-1056
    • Dev, K.K.1


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