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Volumn 113, Issue 12, 2016, Pages 3269-3274

Allosteric switch regulates protein-protein binding through collective motion

Author keywords

Allostery; Concerted motion; Nuclear magnetic resonance; Protein dynamics; Relaxation dispersion

Indexed keywords

ALLOSTERISM; ARTICLE; BINDING AFFINITY; COLLECTIVE MOTION; CRYSTAL STRUCTURE; DISPERSION; MOLECULAR DYNAMICS; MOTION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; REGULATORY MECHANISM; TEMPERATURE DEPENDENCE; AMINO ACID SEQUENCE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS;

EID: 84962217637     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1519609113     Document Type: Article
Times cited : (58)

References (42)
  • 1
    • 0014958182 scopus 로고
    • Stereochemistry of cooperative effects in haemoglobin
    • Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228(5273):726-739.
    • (1970) Nature , vol.228 , Issue.5273 , pp. 726-739
    • Perutz, M.F.1
  • 2
    • 84880174882 scopus 로고    scopus 로고
    • The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals
    • Watson LC, et al. (2013) The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat Struct Mol Biol 20(7):876-883.
    • (2013) Nat Struct Mol Biol , vol.20 , Issue.7 , pp. 876-883
    • Watson, L.C.1
  • 3
    • 84919477203 scopus 로고    scopus 로고
    • Evolution of oligomeric state through allosteric pathways that mimic ligand binding
    • Perica T, et al. (2014) Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science 346(6216):1254346.
    • (2014) Science , vol.346 , Issue.6216 , pp. 1254346
    • Perica, T.1
  • 4
    • 84939522532 scopus 로고    scopus 로고
    • Universal allosteric mechanism for Gα activation by GPCRs
    • Flock T, et al. (2015) Universal allosteric mechanism for Gα activation by GPCRs. Nature 524(7564):173-179.
    • (2015) Nature , vol.524 , Issue.7564 , pp. 173-179
    • Flock, T.1
  • 5
    • 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(5882):1471-1475.
    • (2008) Science , vol.320 , Issue.5882 , pp. 1471-1475
    • Lange, O.F.1
  • 6
    • 67849133810 scopus 로고    scopus 로고
    • Toward an accurate determination of free energy landscapes in solution states of proteins
    • De Simone A, Richter B, Salvatella X, Vendruscolo M (2009) Toward an accurate determination of free energy landscapes in solution states of proteins. J Am Chem Soc 131(11):3810-3811.
    • (2009) J Am Chem Soc , vol.131 , Issue.11 , pp. 3810-3811
    • De Simone, A.1    Richter, B.2    Salvatella, X.3    Vendruscolo, M.4
  • 7
    • 70450237199 scopus 로고    scopus 로고
    • Toward a unified representation of protein structural dynamics in solution
    • Markwick PR, et al. (2009) Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc 131(46):16968-16975.
    • (2009) J Am Chem Soc , vol.131 , Issue.46 , pp. 16968-16975
    • Markwick, P.R.1
  • 8
    • 72249104272 scopus 로고    scopus 로고
    • Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups
    • Vögeli B, et al. (2009) Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups. J Am Chem Soc 131(47):17215-17225.
    • (2009) J Am Chem Soc , vol.131 , Issue.47 , pp. 17215-17225
    • Vögeli, B.1
  • 9
    • 79960044304 scopus 로고    scopus 로고
    • Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition
    • Fenwick RB, et al. (2011) Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition. J Am Chem Soc 133(27):10336-10339.
    • (2011) J Am Chem Soc , vol.133 , Issue.27 , pp. 10336-10339
    • Fenwick, R.B.1
  • 10
    • 84868090870 scopus 로고    scopus 로고
    • Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection
    • Peters JH, de Groot BL (2012) Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLOS Comput Biol 8(10):e1002704.
    • (2012) PLOS Comput Biol , vol.8 , Issue.10 , pp. e1002704
    • Peters, J.H.1    De Groot, B.L.2
  • 11
    • 14144250990 scopus 로고    scopus 로고
    • Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments
    • Massi F, Grey MJ, Palmer AG, 3rd (2005) Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci 14(3):735-742.
    • (2005) Protein Sci , vol.14 , Issue.3 , pp. 735-742
    • Massi, F.1    Grey, M.J.2    Palmer, A.G.3
  • 12
    • 84864210811 scopus 로고    scopus 로고
    • Exceeding the limit of dynamics studies on biomolecules using high spin-lock field strengths with a cryogenically cooled probehead
    • Ban D, et al. (2012) Exceeding the limit of dynamics studies on biomolecules using high spin-lock field strengths with a cryogenically cooled probehead. J Magn Reson 221:1-4.
    • (2012) J Magn Reson , vol.221 , pp. 1-4
    • Ban, D.1
  • 13
    • 84920121497 scopus 로고    scopus 로고
    • Population shuffling of protein conformations
    • Smith CA, et al. (2015) Population shuffling of protein conformations. Angew Chem Int Ed Engl 54(1):207-210.
    • (2015) Angew Chem Int Ed Engl , vol.54 , Issue.1 , pp. 207-210
    • Smith, C.A.1
  • 14
    • 81755177781 scopus 로고    scopus 로고
    • Kinetics of conformational sampling in ubiquitin
    • Ban D, et al. (2011) Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl 50(48):11437-11440.
    • (2011) Angew Chem Int Ed Engl , vol.50 , Issue.48 , pp. 11437-11440
    • Ban, D.1
  • 15
    • 80052401629 scopus 로고    scopus 로고
    • Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
    • Bouvignies G, et al. (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477(7362):111-114.
    • (2011) Nature , vol.477 , Issue.7362 , pp. 111-114
    • Bouvignies, G.1
  • 16
    • 84860013075 scopus 로고    scopus 로고
    • Structure of an intermediate state in protein folding and aggregation
    • Neudecker P, et al. (2012) Structure of an intermediate state in protein folding and aggregation. Science 336(6079):362-366.
    • (2012) Science , vol.336 , Issue.6079 , pp. 362-366
    • Neudecker, P.1
  • 17
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 A resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194(3):531-544.
    • (1987) J Mol Biol , vol.194 , Issue.3 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 18
    • 79952143817 scopus 로고    scopus 로고
    • The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch
    • Huang KY, Amodeo GA, Tong L, McDermott A (2011) The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch. Protein Sci 20(3):630-639.
    • (2011) Protein Sci , vol.20 , Issue.3 , pp. 630-639
    • Huang, K.Y.1    Amodeo, G.A.2    Tong, L.3    McDermott, A.4
  • 19
    • 80051666404 scopus 로고    scopus 로고
    • A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip
    • Sidhu A, Surolia A, Robertson AD, Sundd M (2011) A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip. J Mol Biol 411(5):1037-1048.
    • (2011) J Mol Biol , vol.411 , Issue.5 , pp. 1037-1048
    • Sidhu, A.1    Surolia, A.2    Robertson, A.D.3    Sundd, M.4
  • 20
    • 84856707634 scopus 로고    scopus 로고
    • Time scales of slow motions in ubiquitin explored by heteronuclear double resonance
    • Salvi N, Ulzega S, Ferrage F, Bodenhausen G (2012) Time scales of slow motions in ubiquitin explored by heteronuclear double resonance. J Am Chem Soc 134(5):2481-2484.
    • (2012) J Am Chem Soc , vol.134 , Issue.5 , pp. 2481-2484
    • Salvi, N.1    Ulzega, S.2    Ferrage, F.3    Bodenhausen, G.4
  • 21
    • 84898965855 scopus 로고    scopus 로고
    • Probing transient conformational states of proteins by solid-state R(1ρ) relaxation-dispersion NMR spectroscopy
    • Ma P, et al. (2014) Probing transient conformational states of proteins by solid-state R(1ρ) relaxation-dispersion NMR spectroscopy. Angew Chem Int Ed Engl 53(17):4312-4317.
    • (2014) Angew Chem Int Ed Engl , vol.53 , Issue.17 , pp. 4312-4317
    • Ma, P.1
  • 23
    • 14644424521 scopus 로고    scopus 로고
    • NMR snapshots of a fluctuating protein structure: Ubiquitin at 30 bar-3 kbar
    • Kitahara R, Yokoyama S, Akasaka K (2005) NMR snapshots of a fluctuating protein structure: Ubiquitin at 30 bar-3 kbar. J Mol Biol 347(2):277-285.
    • (2005) J Mol Biol , vol.347 , Issue.2 , pp. 277-285
    • Kitahara, R.1    Yokoyama, S.2    Akasaka, K.3
  • 24
    • 33846649161 scopus 로고    scopus 로고
    • Elimination of the C-cap in ubiquitin - Structure, dynamics and thermodynamic consequences
    • Ermolenko DN, Dangi B, Gvritishvili A, Gronenborn AM, Makhatadze GI (2007) Elimination of the C-cap in ubiquitin - structure, dynamics and thermodynamic consequences. Biophys Chem 126(1-3):25-35.
    • (2007) Biophys Chem , vol.126 , Issue.1-3 , pp. 25-35
    • Ermolenko, D.N.1    Dangi, B.2    Gvritishvili, A.3    Gronenborn, A.M.4    Makhatadze, G.I.5
  • 25
    • 70049114950 scopus 로고    scopus 로고
    • Detection of functional modes in protein dynamics
    • Hub JS, de Groot BL (2009) Detection of functional modes in protein dynamics. PLOS Comput Biol 5(8):e1000480.
    • (2009) PLOS Comput Biol , vol.5 , Issue.8 , pp. e1000480
    • Hub, J.S.1    De Groot, B.L.2
  • 26
    • 84865396279 scopus 로고    scopus 로고
    • Partial least-squares functional mode analysis: Application to the membrane proteins AQP1, Aqy1, and CLC-ec1
    • Krivobokova T, Briones R, Hub JS, Munk A, de Groot BL (2012) Partial least-squares functional mode analysis: Application to the membrane proteins AQP1, Aqy1, and CLC-ec1. Biophys J 103(4):786-796.
    • (2012) Biophys J , vol.103 , Issue.4 , pp. 786-796
    • Krivobokova, T.1    Briones, R.2    Hub, J.S.3    Munk, A.4    De Groot, B.L.5
  • 27
    • 37349046664 scopus 로고    scopus 로고
    • Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins
    • Haririnia A, et al. (2008) Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins. J Mol Biol 375(4):979-996.
    • (2008) J Mol Biol , vol.375 , Issue.4 , pp. 979-996
    • Haririnia, A.1
  • 28
    • 84871298878 scopus 로고    scopus 로고
    • Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7
    • Zhang Y, et al. (2013) Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7. Nat Chem Biol 9(1):51-58.
    • (2013) Nat Chem Biol , vol.9 , Issue.1 , pp. 51-58
    • Zhang, Y.1
  • 29
    • 84879923631 scopus 로고    scopus 로고
    • Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling
    • Phillips AH, et al. (2013) Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling. Proc Natl Acad Sci USA 110(28):11379-11384.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.28 , pp. 11379-11384
    • Phillips, A.H.1
  • 30
    • 84908502680 scopus 로고    scopus 로고
    • A designed conformational shift to control protein binding specificity
    • Michielssens S, et al. (2014) A designed conformational shift to control protein binding specificity. Angew Chem Int Ed Engl 53(39):10367-10371.
    • (2014) Angew Chem Int Ed Engl , vol.53 , Issue.39 , pp. 10367-10371
    • Michielssens, S.1
  • 31
    • 84873085753 scopus 로고    scopus 로고
    • A strategy for modulation of enzymes in the ubiquitin system
    • Ernst A, et al. (2013) A strategy for modulation of enzymes in the ubiquitin system. Science 339(6119):590-595.
    • (2013) Science , vol.339 , Issue.6119 , pp. 590-595
    • Ernst, A.1
  • 32
    • 33746827805 scopus 로고    scopus 로고
    • Structural basis of ubiquitin recognition by the deubiquitinating protease USP2
    • Renatus M, et al. (2006) Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure 14(8):1293-1302.
    • (2006) Structure , vol.14 , Issue.8 , pp. 1293-1302
    • Renatus, M.1
  • 33
    • 12944278747 scopus 로고    scopus 로고
    • Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: An application to a Fyn SH3 domain
    • Korzhnev DM, Orekhov VY, Kay LE (2005) Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: An application to a Fyn SH3 domain. J Am Chem Soc 127(2):713-721.
    • (2005) J Am Chem Soc , vol.127 , Issue.2 , pp. 713-721
    • Korzhnev, D.M.1    Orekhov, V.Y.2    Kay, L.E.3
  • 34
    • 27244449155 scopus 로고    scopus 로고
    • A new amide proton R1rho experiment permits accurate characterization of microsecond time-scale conformational exchange
    • Eichmüller C, Skrynnikov NR (2005) A new amide proton R1rho experiment permits accurate characterization of microsecond time-scale conformational exchange. J Biomol NMR 32(4):281-293.
    • (2005) J Biomol NMR , vol.32 , Issue.4 , pp. 281-293
    • Eichmüller, C.1    Skrynnikov, N.R.2
  • 35
    • 0037355721 scopus 로고    scopus 로고
    • Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach
    • Ishima R, Torchia DA (2003) Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach. J Biomol NMR 25(3):243-248.
    • (2003) J Biomol NMR , vol.25 , Issue.3 , pp. 243-248
    • Ishima, R.1    Torchia, D.A.2
  • 36
    • 7544221415 scopus 로고    scopus 로고
    • A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15N relaxation experiment
    • Yip GN, Zuiderweg ER (2004) A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15N relaxation experiment. J Magn Reson 171(1):25-36.
    • (2004) J Magn Reson , vol.171 , Issue.1 , pp. 25-36
    • Yip, G.N.1    Zuiderweg, E.R.2
  • 37
    • 39749145723 scopus 로고    scopus 로고
    • Accurately probing slow motions on millisecond timescales with a robust NMR relaxation experiment
    • Long D, Liu M, Yang D (2008) Accurately Probing Slow Motions on Millisecond Timescales with a Robust NMR Relaxation Experiment. J Am Chem Soc 130(51):17629.
    • (2008) J Am Chem Soc , vol.130 , Issue.51 , pp. 17629
    • Long, D.1    Liu, M.2    Yang, D.3
  • 38
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly improved protein chemical shift prediction
    • Han B, Liu Y, Ginzinger SW, Wishart DS (2011) SHIFTX2: Significantly improved protein chemical shift prediction. J Biomol NMR 50(1):43-57.
    • (2011) J Biomol NMR , vol.50 , Issue.1 , pp. 43-57
    • Han, B.1    Liu, Y.2    Ginzinger, S.W.3    Wishart, D.S.4
  • 39
    • 14644420979 scopus 로고    scopus 로고
    • The Uppsala electron-density server
    • Kleywegt GJ, et al. (2004) The Uppsala electron-density server. Acta Crystallogr D Biol Crystallogr 60(12 Pt 1):2240-2249.
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , Issue.12 , pp. 2240-2249
    • Kleywegt, G.J.1
  • 40
    • 79959615159 scopus 로고    scopus 로고
    • RosettaScripts: A scripting language interface to the Rosetta macromolecular modeling suite
    • Fleishman SJ, et al. (2011) RosettaScripts: A scripting language interface to the Rosetta macromolecular modeling suite. PLoS One 6(6):e20161.
    • (2011) PLoS One , vol.6 , Issue.6 , pp. e20161
    • Fleishman, S.J.1
  • 41
    • 77949617607 scopus 로고    scopus 로고
    • PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta
    • Chaudhury S, Lyskov S, Gray JJ (2010) PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics 26(5): 689-691.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 689-691
    • Chaudhury, S.1    Lyskov, S.2    Gray, J.J.3
  • 42
    • 84899077364 scopus 로고    scopus 로고
    • ORIUM: Optimized RDC-based iterative and unified model-free analysis
    • Sabo TM, et al. (2014) ORIUM: Optimized RDC-based Iterative and Unified Model-free analysis. J Biomol NMR 58(4):287-301.
    • (2014) J Biomol NMR , vol.58 , Issue.4 , pp. 287-301
    • Sabo, T.M.1


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