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Volumn 106, Issue 46, 2009, Pages 19346-19351

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

Author keywords

Kolmogorov smirnov test; Protein recognition; Ubiquitin binding

Indexed keywords

UBIQUITIN;

EID: 73349117207     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0906966106     Document Type: Article
Times cited : (167)

References (51)
  • 1
    • 84892166712 scopus 로고
    • Einfluss der Konfiguration auf die Wirkung der Enzyme.
    • Fisher E (1894) Einfluss der Konfiguration auf die Wirkung der Enzyme. Ber Dt Chem Ges 27:2985-2993.
    • (1894) Ber Dt Chem Ges , vol.27 , pp. 2985-2993
    • Fisher, E.1
  • 2
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44:98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 3
    • 0035432947 scopus 로고    scopus 로고
    • Molecular recognition by induced fit: How fit is the concept?
    • Bosshard HR (2001) Molecular recognition by induced fit: How fit is the concept? News Physiol Sci 16:171-173.
    • (2001) News Physiol Sci , vol.16 , pp. 171-173
    • Bosshard, H.R.1
  • 5
    • 0033056708 scopus 로고    scopus 로고
    • Folding funnels, binding funnels, and protein function
    • Tsai CJ, Kumar S, Ma B, Nussinov R (1999) Folding funnels, binding funnels, and protein function. Protein Sci 8:1181-1190.
    • (1999) Protein Sci , vol.8 , pp. 1181-1190
    • Tsai, C.J.1    Kumar, S.2    Ma, B.3    Nussinov, R.4
  • 6
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai CJ, Ma B, Nussinov R (1999) Folding and binding cascades: Shifts in energy landscapes. Proc Natl Acad Sci USA 96:9970-9972.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.2    Nussinov, R.3
  • 7
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R (2000) Folding and binding cascades: Dynamic landscapes and population shifts. Protein Sci 9:10-19.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 9
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma B, Shatsky M, Wolfson HJ, Nussinov R (2002) Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations. Protein Sci 11:184-197.
    • (2002) Protein Sci , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 10
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution: A 60-year-old hypothesis revisited
    • James LC, Tawfik DS (2003) Conformational diversity and protein evolution: A 60-year-old hypothesis revisited. Trends Biochem Sci 28:361-368.
    • (2003) Trends Biochem Sci , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 11
    • 9944237833 scopus 로고    scopus 로고
    • Complementarity of structure ensembles in protein-protein binding
    • Grünberg R, Leckner J, Nilges M (2004) Complementarity of structure ensembles in protein-protein binding. Structure (London) 12:2125-2136.
    • (2004) Structure (London) , vol.12 , pp. 2125-2136
    • Grünberg, R.1    Leckner, J.2    Nilges, M.3
  • 12
    • 27744499156 scopus 로고    scopus 로고
    • Intrinsic dynamics of an enzyme underlies catalysis
    • Eisenmesser EZ, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117-121.
    • (2005) Nature , vol.438 , pp. 117-121
    • Eisenmesser, E.Z.1
  • 13
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • Tobi D, Bahar I (2005) Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 102:18908-18913.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 14
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313:1638-1642.
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 15
    • 49649125285 scopus 로고    scopus 로고
    • Fit for an enzyme
    • Kapur S, Khosla C (2008) Fit for an enzyme. Nature 454:832-833.
    • (2008) Nature , vol.454 , pp. 832-833
    • Kapur, S.1    Khosla, C.2
  • 16
    • 45849095234 scopus 로고    scopus 로고
    • How do proteins interact?
    • Boehr DD, Wright PE (2008) How do proteins interact? Science 320:1429-1430.
    • (2008) Science , vol.320 , pp. 1429-1430
    • Boehr, D.D.1    Wright, P.E.2
  • 17
    • 65249090946 scopus 로고    scopus 로고
    • Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis
    • Weikl TR, von Deuster C (2009) Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis. Proteins 75:104-110.
    • (2009) Proteins , vol.75 , pp. 104-110
    • Weikl, T.R.1    von Deuster, C.2
  • 18
    • 49649084492 scopus 로고    scopus 로고
    • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
    • Okazaki K, Takada S (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms. Proc Natl Acad Sci USA 105:11182-11187.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 11182-11187
    • Okazaki, K.1    Takada, S.2
  • 19
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J, Milstein C (1994) Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA 91:10370-10374.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 10370-10374
    • Foote, J.1    Milstein, C.2
  • 20
    • 0032966864 scopus 로고    scopus 로고
    • Antigen recognition by conformational selection
    • Berger C, et al. (1999) Antigen recognition by conformational selection. FEBS Lett 450:149-153.
    • (1999) FEBS Lett , vol.450 , pp. 149-153
    • Berger, C.1
  • 21
    • 0037470496 scopus 로고    scopus 로고
    • Antibody multispecificity mediated by conformational diversity
    • James LC, Roversi P, Tawfik DS (2003) Antibody multispecificity mediated by conformational diversity. Science 299:1362-1367.
    • (2003) Science , vol.299 , pp. 1362-1367
    • James, L.C.1    Roversi, P.2    Tawfik, D.S.3
  • 23
    • 33644556820 scopus 로고    scopus 로고
    • Enzyme dynamics along the reaction coordinate: Critical role of a conserved residue
    • Kovrigin EL, Loria JP (2006) Enzyme dynamics along the reaction coordinate: Critical role of a conserved residue. Biochemistry 45:2636-2647.
    • (2006) Biochemistry , vol.45 , pp. 2636-2647
    • Kovrigin, E.L.1    Loria, J.P.2
  • 24
    • 49649122848 scopus 로고    scopus 로고
    • Structural basis for the selectivity of the external thioesterase of the surfactin synthetase
    • Koglin A, et al. (2008) Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature 454:907-911.
    • (2008) Nature , vol.454 , pp. 907-911
    • Koglin, A.1
  • 25
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE (2001) Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism. Biochemistry 40:9846-9859.
    • (2001) Biochemistry , vol.40 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 26
    • 58749094825 scopus 로고    scopus 로고
    • Small- and large-scale conformational changes of adenylate kinase: A molecular dynamics study of the subdomain motion and mechanics
    • Pontiggia F, Zen A, Micheletti C (2008) Small- and large-scale conformational changes of adenylate kinase: A molecular dynamics study of the subdomain motion and mechanics. Biophys J 95:5901-5912.
    • (2008) Biophys J , vol.95 , pp. 5901-5912
    • Pontiggia, F.1    Zen, A.2    Micheletti, C.3
  • 27
    • 35548976322 scopus 로고    scopus 로고
    • Open-to-closed transition in apo maltose-binding protein observed by paramagnetic nmr
    • Tang C, Schwieters CD, Clore GM (2007) Open-to-closed transition in apo maltose-binding protein observed by paramagnetic nmr. Nature 449:1078-1082.
    • (2007) Nature , vol.449 , pp. 1078-1082
    • Tang, C.1    Schwieters, C.D.2    Clore, G.M.3
  • 28
    • 41649105538 scopus 로고    scopus 로고
    • Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design
    • Xu Y, et al. (2008) Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Protein Sci 17:601-605.
    • (2008) Protein Sci , vol.17 , pp. 601-605
    • Xu, Y.1
  • 29
    • 34249945151 scopus 로고    scopus 로고
    • Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions
    • Yang L, et al. (2007) Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure (London) 15:741-749.
    • (2007) Structure (London) , vol.15 , pp. 741-749
    • Yang, L.1
  • 30
    • 42949129270 scopus 로고    scopus 로고
    • A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction
    • Gsponer J, et al. (2008) A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction. Structure (London) 16:736-746.
    • (2008) Structure (London) , vol.16 , pp. 736-746
    • Gsponer, J.1
  • 31
    • 0034656949 scopus 로고    scopus 로고
    • Side-chain flexibility in proteins upon ligand binding
    • Najmanovich R, Kuttner J, Sobolev V, Edelman M (2000) Side-chain flexibility in proteins upon ligand binding. Proteins 39:261-268.
    • (2000) Proteins , vol.39 , pp. 261-268
    • Najmanovich, R.1    Kuttner, J.2    Sobolev, V.3    Edelman, M.4
  • 32
    • 7944225979 scopus 로고    scopus 로고
    • Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that preorganized in the unbound states: Implications for docking
    • Li X, Keskin O, Ma B, Nussinov R, Liang J (2004) Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that preorganized in the unbound states: Implications for docking. J Mol Biol 344:781-795.
    • (2004) J Mol Biol , vol.344 , pp. 781-795
    • Li, X.1    Keskin, O.2    Ma, B.3    Nussinov, R.4    Liang, J.5
  • 34
    • 43649093747 scopus 로고    scopus 로고
    • Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
    • Yogurtcu ON, Erdemli SB, Nussinov R, Turkay M, Keskin O (2008) Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. Biophys J 94:3475-3485.
    • (2008) Biophys J , vol.94 , pp. 3475-3485
    • Yogurtcu, O.N.1    Erdemli, S.B.2    Nussinov, R.3    Turkay, M.4    Keskin, O.5
  • 35
    • 52949089027 scopus 로고    scopus 로고
    • Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection
    • Sullivan SM, Holyoak T (2008) Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection. Proc Natl Acad Sci USA 105:13829-13834.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 13829-13834
    • Sullivan, S.M.1    Holyoak, T.2
  • 36
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules
    • Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. J Am Chem Soc 104:4546-4570.
    • (1982) J Am Chem Soc , vol.104 , pp. 4546-4570
    • Lipari, G.1    Szabo, A.2
  • 37
    • 0001144784 scopus 로고    scopus 로고
    • 1 constant relaxation time NMR spectroscopy
    • 1 constant relaxation time NMR spectroscopy. J Am Chem Soc 118:911-912.
    • (1996) J Am Chem Soc , vol.118 , pp. 911-912
    • Akke, M.1    Palmer, A.G.2
  • 38
    • 0034820148 scopus 로고    scopus 로고
    • Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins
    • Meiler J, Prompers JJ, Peti W, Griesinger C, Brüschweiler R (2001) Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J Am Chem Soc 123:6098-6107.
    • (2001) J Am Chem Soc , vol.123 , pp. 6098-6107
    • Meiler, J.1    Prompers, J.J.2    Peti, W.3    Griesinger, C.4    Brüschweiler, R.5
  • 39
    • 45849131354 scopus 로고    scopus 로고
    • Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
    • Lange OF, et al. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471-1475.
    • (2008) Science , vol.320 , pp. 1471-1475
    • Lange, O.F.1
  • 40
    • 52949121796 scopus 로고    scopus 로고
    • Markwick PRL, Malliavin T, Nilges M (2008) Structural biology by NMR: Structure, dynamics, and interactions. PLoS Comput Biol 4:e1000168.
    • Markwick PRL, Malliavin T, Nilges M (2008) Structural biology by NMR: Structure, dynamics, and interactions. PLoS Comput Biol 4:e1000168.
  • 41
    • 59149097931 scopus 로고    scopus 로고
    • Residual dipolar couplings as a tool to study molecular recognition of ubiquitin
    • Lakomek N, et al. (2008) Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem Soc Trans 36:1433-1437.
    • (2008) Biochem Soc Trans , vol.36 , pp. 1433-1437
    • Lakomek, N.1
  • 43
    • 33646064427 scopus 로고    scopus 로고
    • Structural complexity in ubiquitin recognition
    • Harper JW, Schulman BA (2006) Structural complexity in ubiquitin recognition. Cell 124:1133-1136.
    • (2006) Cell , vol.124 , pp. 1133-1136
    • Harper, J.W.1    Schulman, B.A.2
  • 44
    • 33846471122 scopus 로고    scopus 로고
    • Proteasome-independent functions of ubiquitin in endocytosis and signaling
    • Mukhopadhyay D, Riezman H (2007) Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science 315:201-205.
    • (2007) Science , vol.315 , pp. 201-205
    • Mukhopadhyay, D.1    Riezman, H.2
  • 45
    • 44649101850 scopus 로고    scopus 로고
    • Atypical ubiquitin chains: New molecular signals
    • Ikeda F, Dikic I (2008) Atypical ubiquitin chains: New molecular signals. EMBO Rep 9:536-542.
    • (2008) EMBO Rep , vol.9 , pp. 536-542
    • Ikeda, F.1    Dikic, I.2
  • 47
    • 67049155677 scopus 로고    scopus 로고
    • Friedland GD, Lakomek N, Griesinger C, Meiler J, Kortemme T (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 5:e1000393.
    • Friedland GD, Lakomek N, Griesinger C, Meiler J, Kortemme T (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 5:e1000393.
  • 49
    • 48449094112 scopus 로고    scopus 로고
    • Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
    • Chaudhury S, Gray JJ (2008) Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol 381:1068-1087.
    • (2008) J Mol Biol , vol.381 , pp. 1068-1087
    • Chaudhury, S.1    Gray, J.J.2
  • 50
    • 2642574503 scopus 로고    scopus 로고
    • R Development Core Team , R Foundation for Statistical Computing, Vienna
    • R Development Core Team (2008) A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna).
    • (2008) A Language and Environment for Statistical Computing
  • 51
    • 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 (1996) A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 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


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