메뉴 건너뛰기




Volumn 27, Issue 4, 2019, Pages 566-578

Allostery in Its Many Disguises: From Theory to Applications

(39)  Wodak, Shoshana J a   Paci, Emanuele b   Dokholyan, Nikolay V c,ac   Berezovsky, Igor N d   Horovitz, Amnon e   Li, Jing f   Hilser, Vincent J f   Bahar, Ivet g   Karanicolas, John h   Stock, Gerhard i   Hamm, Peter j   Stote, Roland H k   Eberhardt, Jerome k   Chebaro, Yassmine k   Dejaegere, Annick k   Cecchini, Marco l   Changeux, Jean Pierre m   Bolhuis, Peter G n   Vreede, Jocelyne n   Faccioli, Pietro o   more..


Author keywords

allosteric drugs; allosteric material; allosteric switches; Allostery; elastic network models; energy landscape; molecular dynamics; protein conformational changes; protein function; regulation; signal transduction

Indexed keywords

PROTEIN;

EID: 85063381900     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2019.01.003     Document Type: Review
Times cited : (282)

References (122)
  • 1
    • 84935900800 scopus 로고    scopus 로고
    • A general approach to the design of allosteric, transcription factor-regulated DNAzymes
    • Adornetto, G., Porchetta, A., Palleschi, G., Plaxco, K.W., Ricci, F., A general approach to the design of allosteric, transcription factor-regulated DNAzymes. Chem. Sci. 6 (2015), 3692–3696.
    • (2015) Chem. Sci. , vol.6 , pp. 3692-3696
    • Adornetto, G.1    Porchetta, A.2    Palleschi, G.3    Plaxco, K.W.4    Ricci, F.5
  • 2
    • 33847609615 scopus 로고    scopus 로고
    • A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
    • Amaro, R.E., Sethi, A., Myers, R.S., Davisson, V.J., Luthey-Schulten, Z.A., A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry 46 (2007), 2156–2173.
    • (2007) Biochemistry , vol.46 , pp. 2156-2173
    • Amaro, R.E.1    Sethi, A.2    Myers, R.S.3    Davisson, V.J.4    Luthey-Schulten, Z.A.5
  • 3
    • 36549043024 scopus 로고    scopus 로고
    • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    • Bahar, I., Chennubhotla, C., Tobi, D., Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr. Opin. Struct. Biol. 17 (2007), 633–640.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 633-640
    • Bahar, I.1    Chennubhotla, C.2    Tobi, D.3
  • 4
    • 85043534113 scopus 로고    scopus 로고
    • Protein Actions: Principles & Modeling
    • Taylor & Francis Group
    • Bahar, I., Jernigan, R.L., Dill, K., Protein Actions: Principles & Modeling. 2017, Taylor & Francis Group.
    • (2017)
    • Bahar, I.1    Jernigan, R.L.2    Dill, K.3
  • 5
    • 77952938726 scopus 로고    scopus 로고
    • Global dynamics of proteins: bridging between structure and function
    • Bahar, I., Lezon, T.R., Yang, L.W., Eyal, E., Global dynamics of proteins: bridging between structure and function. Annu. Rev. Biophys. 39 (2010), 23–42.
    • (2010) Annu. Rev. Biophys. , vol.39 , pp. 23-42
    • Bahar, I.1    Lezon, T.R.2    Yang, L.W.3    Eyal, E.4
  • 7
    • 0036424048 scopus 로고    scopus 로고
    • Transition path sampling: throwing ropes over rough mountain passes, in the dark
    • Bolhuis, P.G., Chandler, D., Dellago, C., Geissler, P.L., Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53 (2002), 291–318.
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 8
    • 82655171926 scopus 로고    scopus 로고
    • Structural analysis of nuclear receptors: from isolated domains to integral proteins
    • Brelivet, Y., Rochel, N., Moras, D., Structural analysis of nuclear receptors: from isolated domains to integral proteins. Mol. Cell. Endocrinol. 348 (2012), 466–473.
    • (2012) Mol. Cell. Endocrinol. , vol.348 , pp. 466-473
    • Brelivet, Y.1    Rochel, N.2    Moras, D.3
  • 9
    • 84994043946 scopus 로고    scopus 로고
    • A one-way shooting algorithm for transition path sampling of asymmetric barriers
    • Brotzakis, Z.F., Bolhuis, P.G., A one-way shooting algorithm for transition path sampling of asymmetric barriers. J. Chem. Phys., 145, 2016, 164112.
    • (2016) J. Chem. Phys. , vol.145 , pp. 164112
    • Brotzakis, Z.F.1    Bolhuis, P.G.2
  • 10
    • 85027402370 scopus 로고    scopus 로고
    • Time-resolved observation of protein allosteric communication
    • Buchenberg, S., Sittel, F., Stock, G., Time-resolved observation of protein allosteric communication. Proc. Natl. Acad. Sci. U S A 114 (2017), E6804–E6811.
    • (2017) Proc. Natl. Acad. Sci. U S A , vol.114 , pp. E6804-E6811
    • Buchenberg, S.1    Sittel, F.2    Stock, G.3
  • 15
    • 73049119821 scopus 로고
    • The feedback control mechanisms of biosynthetic L-threonine deaminase by L-isoleucine
    • Changeux, J.P., The feedback control mechanisms of biosynthetic L-threonine deaminase by L-isoleucine. Cold Spring Harb. Symp. Quant. Biol. 26 (1961), 313–318.
    • (1961) Cold Spring Harb. Symp. Quant. Biol. , vol.26 , pp. 313-318
    • Changeux, J.P.1
  • 16
    • 79959334490 scopus 로고    scopus 로고
    • 50th anniversary of the word “allosteric”
    • Changeux, J.P., 50th anniversary of the word “allosteric”. Protein Sci. 20 (2011), 1119–1124.
    • (2011) Protein Sci. , vol.20 , pp. 1119-1124
    • Changeux, J.P.1
  • 17
    • 84861219631 scopus 로고    scopus 로고
    • Allostery and the Monod-Wyman-Changeux model after 50 years
    • Changeux, J.P., Allostery and the Monod-Wyman-Changeux model after 50 years. Annu. Rev. Biophys. 41 (2012), 103–133.
    • (2012) Annu. Rev. Biophys. , vol.41 , pp. 103-133
    • Changeux, J.P.1
  • 18
    • 20344370764 scopus 로고    scopus 로고
    • Allosteric mechanisms of signal transduction
    • Changeux, J.P., Edelstein, S.J., Allosteric mechanisms of signal transduction. Science 308 (2005), 1424–1428.
    • (2005) Science , vol.308 , pp. 1424-1428
    • Changeux, J.P.1    Edelstein, S.J.2
  • 19
    • 84876907320 scopus 로고    scopus 로고
    • Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics
    • Chebaro, Y., Amal, I., Rochel, N., Rochette-Egly, C., Stote, R.H., Dejaegere, A., Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics. PLoS Comput. Biol., 9, 2013, e1003012.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003012
    • Chebaro, Y.1    Amal, I.2    Rochel, N.3    Rochette-Egly, C.4    Stote, R.H.5    Dejaegere, A.6
  • 21
    • 85136801449 scopus 로고    scopus 로고
    • The chemistry of Cas9 and its CRISPR colleagues
    • Chen, J.S., Doudna, J.A., The chemistry of Cas9 and its CRISPR colleagues. Nat. Rev. Chem. 1 (2017), 1–15.
    • (2017) Nat. Rev. Chem. , vol.1 , pp. 1-15
    • Chen, J.S.1    Doudna, J.A.2
  • 22
    • 84900548447 scopus 로고    scopus 로고
    • Markov state models of biomolecular conformational dynamics
    • Chodera, J.D., Noe, F., Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol. 25 (2014), 135–144.
    • (2014) Curr. Opin. Struct. Biol. , vol.25 , pp. 135-144
    • Chodera, J.D.1    Noe, F.2
  • 24
    • 84962708550 scopus 로고    scopus 로고
    • Identifying allosteric hotspots with dynamics: application to inter- and intra-species conservation
    • Clarke, D., Sethi, A., Li, S., Kumar, S., Chang, R.W., Chen, J., Gerstein, M., Identifying allosteric hotspots with dynamics: application to inter- and intra-species conservation. Structure 24 (2016), 826–837.
    • (2016) Structure , vol.24 , pp. 826-837
    • Clarke, D.1    Sethi, A.2    Li, S.3    Kumar, S.4    Chang, R.W.5    Chen, J.6    Gerstein, M.7
  • 25
    • 0021726687 scopus 로고
    • Protein fluctuations and the thermodynamic uncertainty principle
    • Cooper, A., Protein fluctuations and the thermodynamic uncertainty principle. Prog. Biophys. Mol. Biol. 44 (1984), 181–214.
    • (1984) Prog. Biophys. Mol. Biol. , vol.44 , pp. 181-214
    • Cooper, A.1
  • 26
    • 0021658956 scopus 로고
    • Allostery without conformational change. A plausible model
    • Cooper, A., Dryden, D.T.F., Allostery without conformational change. A plausible model. Eur. Biophys. J. 11 (1984), 103–109.
    • (1984) Eur. Biophys. J. , vol.11 , pp. 103-109
    • Cooper, A.1    Dryden, D.T.F.2
  • 31
    • 84951743686 scopus 로고    scopus 로고
    • Comparing class A GPCRs to bitter taste receptors: structural motifs, ligand interactions and agonist-to-antagonist ratios
    • Di Pizio, A., Levit, A., Slutzki, M., Behrens, M., Karaman, R., Niv, M.Y., Comparing class A GPCRs to bitter taste receptors: structural motifs, ligand interactions and agonist-to-antagonist ratios. Methods Cell Biol. 132 (2016), 401–427.
    • (2016) Methods Cell Biol. , vol.132 , pp. 401-427
    • Di Pizio, A.1    Levit, A.2    Slutzki, M.3    Behrens, M.4    Karaman, R.5    Niv, M.Y.6
  • 32
    • 31344432159 scopus 로고    scopus 로고
    • Determination of network of residues that regulate allostery in protein families using sequence analysis
    • Dima, R.I., Thirumalai, D., Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 15 (2006), 258–268.
    • (2006) Protein Sci. , vol.15 , pp. 258-268
    • Dima, R.I.1    Thirumalai, D.2
  • 33
    • 84974577224 scopus 로고    scopus 로고
    • Controlling allosteric networks in proteins
    • Dokholyan, N.V., Controlling allosteric networks in proteins. Chem. Rev. 116 (2016), 6463–6487.
    • (2016) Chem. Rev. , vol.116 , pp. 6463-6487
    • Dokholyan, N.V.1
  • 35
    • 0025897094 scopus 로고
    • Application of linear free energy relations to protein conformational changes: the quaternary structural change of hemoglobin
    • Eaton, W.A., Henry, E.R., Hofrichter, J., Application of linear free energy relations to protein conformational changes: the quaternary structural change of hemoglobin. Proc. Natl. Acad. Sci. U S A 88 (1991), 4472–4475.
    • (1991) Proc. Natl. Acad. Sci. U S A , vol.88 , pp. 4472-4475
    • Eaton, W.A.1    Henry, E.R.2    Hofrichter, J.3
  • 36
    • 84908505379 scopus 로고    scopus 로고
    • Architecture and signal transduction mechanism of the bacterial chemosensory array: progress, controversies, and challenges
    • Falke, J.J., Piasta, K.N., Architecture and signal transduction mechanism of the bacterial chemosensory array: progress, controversies, and challenges. Curr. Opin. Struct. Biol. 29 (2014), 85–94.
    • (2014) Curr. Opin. Struct. Biol. , vol.29 , pp. 85-94
    • Falke, J.J.1    Piasta, K.N.2
  • 37
    • 84879327823 scopus 로고    scopus 로고
    • Modulation of allostery by protein intrinsic disorder
    • Ferreon, A.C., Ferreon, J.C., Wright, P.E., Deniz, A.A., Modulation of allostery by protein intrinsic disorder. Nature 498 (2013), 390–394.
    • (2013) Nature , vol.498 , pp. 390-394
    • Ferreon, A.C.1    Ferreon, J.C.2    Wright, P.E.3    Deniz, A.A.4
  • 38
    • 0026511656 scopus 로고
    • The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
    • Fersht, A.R., Matouschek, A., Serrano, L., The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224 (1992), 771–782.
    • (1992) J. Mol. Biol. , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 39
    • 85026879710 scopus 로고    scopus 로고
    • Design of elastic networks with evolutionary optimized long-range communication as mechanical models of allosteric proteins
    • Flechsig, H., Design of elastic networks with evolutionary optimized long-range communication as mechanical models of allosteric proteins. Biophys. J. 113 (2017), 558–571.
    • (2017) Biophys. J. , vol.113 , pp. 558-571
    • Flechsig, H.1
  • 43
    • 84921511844 scopus 로고    scopus 로고
    • Exploring a non-ATP pocket for potential allosteric modulation of PI3Kalpha
    • Gkeka, P., Papafotika, A., Christoforidis, S., Cournia, Z., Exploring a non-ATP pocket for potential allosteric modulation of PI3Kalpha. J. Phys. Chem. B 119 (2015), 1002–1016.
    • (2015) J. Phys. Chem. B , vol.119 , pp. 1002-1016
    • Gkeka, P.1    Papafotika, A.2    Christoforidis, S.3    Cournia, Z.4
  • 44
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., Noguti, T., Nishikawa, T., Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. U S A 80 (1983), 3696–3700.
    • (1983) Proc. Natl. Acad. Sci. U S A , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 45
    • 0034677524 scopus 로고    scopus 로고
    • Mapping the conformational wave of acetylcholine receptor channel gating
    • Grosman, C., Zhou, M., Auerbach, A., Mapping the conformational wave of acetylcholine receptor channel gating. Nature 403 (2000), 773–776.
    • (2000) Nature , vol.403 , pp. 773-776
    • Grosman, C.1    Zhou, M.2    Auerbach, A.3
  • 46
    • 84974555476 scopus 로고    scopus 로고
    • Allosteric mechanisms in chaperonin machines
    • Gruber, R., Horovitz, A., Allosteric mechanisms in chaperonin machines. Chem. Rev. 116 (2016), 6588–6606.
    • (2016) Chem. Rev. , vol.116 , pp. 6588-6606
    • Gruber, R.1    Horovitz, A.2
  • 47
    • 85046822154 scopus 로고    scopus 로고
    • Unpicking allosteric mechanisms of homo-oligomeric proteins by determining their successive ligand binding constants
    • Gruber, R., Horovitz, A., Unpicking allosteric mechanisms of homo-oligomeric proteins by determining their successive ligand binding constants. Philos. Trans. R. Soc. Lond. B Biol. Sci., 373, 2018, 10.1098/rstb.2017.0176.
    • (2018) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.373
    • Gruber, R.1    Horovitz, A.2
  • 48
    • 85019865811 scopus 로고    scopus 로고
    • Sequential allosteric mechanism of ATP hydrolysis by the CCT/TRiC chaperone is revealed through Arrhenius analysis
    • Gruber, R., Levitt, M., Horovitz, A., Sequential allosteric mechanism of ATP hydrolysis by the CCT/TRiC chaperone is revealed through Arrhenius analysis. Proc. Natl. Acad. Sci. U S A 114 (2017), 5189–5194.
    • (2017) Proc. Natl. Acad. Sci. U S A , vol.114 , pp. 5189-5194
    • Gruber, R.1    Levitt, M.2    Horovitz, A.3
  • 49
    • 84946906524 scopus 로고    scopus 로고
    • Allosteric sites: remote control in regulation of protein activity
    • Guarnera, E., Berezovsky, I.N., Allosteric sites: remote control in regulation of protein activity. Curr. Opin. Struct. Biol. 37 (2016), 1–8.
    • (2016) Curr. Opin. Struct. Biol. , vol.37 , pp. 1-8
    • Guarnera, E.1    Berezovsky, I.N.2
  • 50
    • 84962124121 scopus 로고    scopus 로고
    • Structure-based statistical mechanical model accounts for the causality and energetics of allosteric communication
    • Guarnera, E., Berezovsky, I.N., Structure-based statistical mechanical model accounts for the causality and energetics of allosteric communication. PLoS Comput. Biol., 12, 2016, e1004678.
    • (2016) PLoS Comput. Biol. , vol.12 , pp. e1004678
    • Guarnera, E.1    Berezovsky, I.N.2
  • 51
    • 85042817873 scopus 로고    scopus 로고
    • AlloSigMA: allosteric signaling and mutation analysis server
    • Guarnera, E., Tan, Z.W., Zheng, Z., Berezovsky, I.N., AlloSigMA: allosteric signaling and mutation analysis server. Bioinformatics 33 (2017), 3996–3998.
    • (2017) Bioinformatics , vol.33 , pp. 3996-3998
    • Guarnera, E.1    Tan, Z.W.2    Zheng, Z.3    Berezovsky, I.N.4
  • 52
    • 6344219895 scopus 로고    scopus 로고
    • Is allostery an intrinsic property of all dynamic proteins?
    • Gunasekaran, K., Ma, B., Nussinov, R., Is allostery an intrinsic property of all dynamic proteins?. Proteins 57 (2004), 433–443.
    • (2004) Proteins , vol.57 , pp. 433-443
    • Gunasekaran, K.1    Ma, B.2    Nussinov, R.3
  • 53
    • 84920950379 scopus 로고    scopus 로고
    • Two pathways mediate interdomain allosteric regulation in pin1
    • Guo, J., Pang, X., Zhou, H.X., Two pathways mediate interdomain allosteric regulation in pin1. Structure 23 (2015), 237–247.
    • (2015) Structure , vol.23 , pp. 237-247
    • Guo, J.1    Pang, X.2    Zhou, H.X.3
  • 54
    • 84974627299 scopus 로고    scopus 로고
    • Protein allostery and conformational dynamics
    • Guo, J., Zhou, H.X., Protein allostery and conformational dynamics. Chem. Rev. 116 (2016), 6503–6515.
    • (2016) Chem. Rev. , vol.116 , pp. 6503-6515
    • Guo, J.1    Zhou, H.X.2
  • 55
    • 19544377327 scopus 로고    scopus 로고
    • Coarse-grained model of entropic allostery
    • Hawkins, R.J., McLeish, T.C., Coarse-grained model of entropic allostery. Phys. Rev. Lett., 93, 2004, 098104.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 098104
    • Hawkins, R.J.1    McLeish, T.C.2
  • 56
    • 33748442882 scopus 로고    scopus 로고
    • Coupling of global and local vibrational modes in dynamic allostery of proteins
    • Hawkins, R.J., McLeish, T.C., Coupling of global and local vibrational modes in dynamic allostery of proteins. Biophys. J. 91 (2006), 2055–2062.
    • (2006) Biophys. J. , vol.91 , pp. 2055-2062
    • Hawkins, R.J.1    McLeish, T.C.2
  • 58
    • 84884914684 scopus 로고    scopus 로고
    • Looking at nuclear receptors from a new angle
    • Helsen, C., Claessens, F., Looking at nuclear receptors from a new angle. Mol. Cell. Endocrinol. 382 (2014), 97–106.
    • (2014) Mol. Cell. Endocrinol. , vol.382 , pp. 97-106
    • Helsen, C.1    Claessens, F.2
  • 60
    • 0021908041 scopus 로고
    • Reaction pathway for the quaternary structure change in hemoglobin
    • Janin, J., Wodak, S.J., Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers 24 (1985), 509–526.
    • (1985) Biopolymers , vol.24 , pp. 509-526
    • Janin, J.1    Wodak, S.J.2
  • 61
    • 0036721218 scopus 로고    scopus 로고
    • Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
    • Kass, I., Horovitz, A., Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48 (2002), 611–617.
    • (2002) Proteins , vol.48 , pp. 611-617
    • Kass, I.1    Horovitz, A.2
  • 62
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern, D., Zuiderweg, E.R., The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13 (2003), 748–757.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.2
  • 63
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • Koshland, D.E. Jr., Nemethy, G., Filmer, D., Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5 (1966), 365–385.
    • (1966) Biochemistry , vol.5 , pp. 365-385
    • Koshland, D.E.1    Nemethy, G.2    Filmer, D.3
  • 65
    • 85020325128 scopus 로고    scopus 로고
    • Toward allosterically increased catalytic activity of insulin-degrading enzyme against amyloid peptides
    • Kurochkin, I.V., Guarnera, E., Wong, J.H., Eisenhaber, F., Berezovsky, I.N., Toward allosterically increased catalytic activity of insulin-degrading enzyme against amyloid peptides. Biochemistry 56 (2017), 228–239.
    • (2017) Biochemistry , vol.56 , pp. 228-239
    • Kurochkin, I.V.1    Guarnera, E.2    Wong, J.H.3    Eisenhaber, F.4    Berezovsky, I.N.5
  • 67
  • 68
    • 82455220936 scopus 로고    scopus 로고
    • A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms
    • Livesay, D.R., Kreth, K.E., Fodor, A.A., A critical evaluation of correlated mutation algorithms and coevolution within allosteric mechanisms. Methods Mol. Biol. 796 (2012), 385–398.
    • (2012) Methods Mol. Biol. , vol.796 , pp. 385-398
    • Livesay, D.R.1    Kreth, K.E.2    Fodor, A.A.3
  • 69
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless, S.W., Ranganathan, R., Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999), 295–299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 70
    • 84856303585 scopus 로고    scopus 로고
    • Long-range modulation of chain motions within the intrinsically disordered transactivation domain of tumor suppressor p53
    • Lum, J.K., Neuweiler, H., Fersht, A.R., Long-range modulation of chain motions within the intrinsically disordered transactivation domain of tumor suppressor p53. J. Am. Chem. Soc. 134 (2012), 1617–1622.
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 1617-1622
    • Lum, J.K.1    Neuweiler, H.2    Fersht, A.R.3
  • 71
    • 85019256399 scopus 로고    scopus 로고
    • A DNA nanodevice that loads and releases a cargo with hemoglobin-like allosteric control and cooperativity
    • Mariottini, D., Idili, A., Vallee-Belisle, A., Plaxco, K.W., Ricci, F., A DNA nanodevice that loads and releases a cargo with hemoglobin-like allosteric control and cooperativity. Nano Lett. 17 (2017), 3225–3230.
    • (2017) Nano Lett. , vol.17 , pp. 3225-3230
    • Mariottini, D.1    Idili, A.2    Vallee-Belisle, A.3    Plaxco, K.W.4    Ricci, F.5
  • 72
    • 81255138340 scopus 로고    scopus 로고
    • Studying functional dynamics in bio-molecules using accelerated molecular dynamics
    • Markwick, P.R., McCammon, J.A., Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys. Chem. Chem. Phys. 13 (2011), 20053–20065.
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 20053-20065
    • Markwick, P.R.1    McCammon, J.A.2
  • 73
    • 85032730743 scopus 로고    scopus 로고
    • Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
    • Martin, N.E., Malik, S., Calimet, N., Changeux, J.P., Cecchini, M., Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics. PLoS Comput. Biol., 13, 2017, e1005784.
    • (2017) PLoS Comput. Biol. , vol.13 , pp. e1005784
    • Martin, N.E.1    Malik, S.2    Calimet, N.3    Changeux, J.P.4    Cecchini, M.5
  • 76
    • 80053142382 scopus 로고    scopus 로고
    • Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
    • Meireles, L., Gur, M., Bakan, A., Bahar, I., Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Sci. 20 (2011), 1645–1658.
    • (2011) Protein Sci. , vol.20 , pp. 1645-1658
    • Meireles, L.1    Gur, M.2    Bakan, A.3    Bahar, I.4
  • 77
    • 73049167504 scopus 로고
    • Teleonomic mechanisms in cellular metabolism, growth, and differentiation
    • Monod, J., Jacob, F., Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant. Biol. 26 (1961), 389–401.
    • (1961) Cold Spring Harb. Symp. Quant. Biol. , vol.26 , pp. 389-401
    • Monod, J.1    Jacob, F.2
  • 78
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: a plausible model
    • Monod, J., Wyman, J., Changeux, J.P., On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12 (1965), 88–118.
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 80
  • 81
    • 84856084072 scopus 로고    scopus 로고
    • FTSite: high accuracy detection of ligand binding sites on unbound protein structures
    • Ngan, C.H., Hall, D.R., Zerbe, B., Grove, L.E., Kozakov, D., Vajda, S., FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics 28 (2012), 286–287.
    • (2012) Bioinformatics , vol.28 , pp. 286-287
    • Ngan, C.H.1    Hall, D.R.2    Zerbe, B.3    Grove, L.E.4    Kozakov, D.5    Vajda, S.6
  • 83
    • 84916887461 scopus 로고    scopus 로고
    • Allostery without a conformational change? Revisiting the paradigm
    • Nussinov, R., Tsai, C.J., Allostery without a conformational change? Revisiting the paradigm. Curr. Opin. Struct. Biol. 30 (2015), 17–24.
    • (2015) Curr. Opin. Struct. Biol. , vol.30 , pp. 17-24
    • Nussinov, R.1    Tsai, C.J.2
  • 84
    • 84876275408 scopus 로고    scopus 로고
    • The underappreciated role of allostery in the cellular network
    • Nussinov, R., Tsai, C.J., Ma, B., The underappreciated role of allostery in the cellular network. Annu. Rev. Biophys. 42 (2013), 169–189.
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 169-189
    • Nussinov, R.1    Tsai, C.J.2    Ma, B.3
  • 85
    • 0001028835 scopus 로고
    • Allosteric effects: structural and thermodynamic origins of binding cooperativity in a subunit model
    • Onan, K., Rebek, J. Jr., Costello, T., Marshall, L., Allosteric effects: structural and thermodynamic origins of binding cooperativity in a subunit model. J. Am. Chem. Soc. 105 (1983), 6759–6760.
    • (1983) J. Am. Chem. Soc. , vol.105 , pp. 6759-6760
    • Onan, K.1    Rebek, J.2    Costello, T.3    Marshall, L.4
  • 86
    • 85027260636 scopus 로고    scopus 로고
    • Self-consistent calculation of protein folding pathways
    • Orioli, S., A Beccara, S., Faccioli, P., Self-consistent calculation of protein folding pathways. J. Chem. Phys., 147, 2017, 064108.
    • (2017) J. Chem. Phys. , vol.147 , pp. 064108
    • Orioli, S.1    A Beccara, S.2    Faccioli, P.3
  • 87
    • 85058749644 scopus 로고    scopus 로고
    • Key role of the REC lobe during CRISPR–Cas9 activation by 'sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain
    • Palermo, G., Chen, J.S., Ricci, C.G., Rivalta, I., Jinek, M., Batista, V.S., Doudna, J.A., McCammon, J.A., Key role of the REC lobe during CRISPR–Cas9 activation by 'sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain. Q. Rev. Biophys. 51 (2018), 1–11.
    • (2018) Q. Rev. Biophys. , vol.51 , pp. 1-11
    • Palermo, G.1    Chen, J.S.2    Ricci, C.G.3    Rivalta, I.4    Jinek, M.5    Batista, V.S.6    Doudna, J.A.7    McCammon, J.A.8
  • 88
    • 85016604142 scopus 로고    scopus 로고
    • Striking plasticity of CRISPR-Cas9 and key role of non-target DNA, as revealed by molecular simulations
    • Palermo, G., Miao, Y., Walker, R.C., Jinek, M., McCammon, J.A., Striking plasticity of CRISPR-Cas9 and key role of non-target DNA, as revealed by molecular simulations. ACS Cent. Sci. 2 (2016), 756–763.
    • (2016) ACS Cent. Sci. , vol.2 , pp. 756-763
    • Palermo, G.1    Miao, Y.2    Walker, R.C.3    Jinek, M.4    McCammon, J.A.5
  • 89
    • 85023197915 scopus 로고    scopus 로고
    • CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
    • Palermo, G., Miao, Y., Walker, R.C., Jinek, M., McCammon, J.A., CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc. Natl. Acad. Sci. U S A 114 (2017), 7260–7265.
    • (2017) Proc. Natl. Acad. Sci. U S A , vol.114 , pp. 7260-7265
    • Palermo, G.1    Miao, Y.2    Walker, R.C.3    Jinek, M.4    McCammon, J.A.5
  • 91
    • 77956220940 scopus 로고    scopus 로고
    • Everything you wanted to know about Markov State Models but were afraid to ask
    • Pande, V.S., Beauchamp, K., Bowman, G.R., Everything you wanted to know about Markov State Models but were afraid to ask. Methods 52 (2010), 99–105.
    • (2010) Methods , vol.52 , pp. 99-105
    • Pande, V.S.1    Beauchamp, K.2    Bowman, G.R.3
  • 93
    • 0014958182 scopus 로고
    • Stereochemistry of cooperative effects in haemoglobin
    • Perutz, M.F., Stereochemistry of cooperative effects in haemoglobin. Nature 228 (1970), 726–739.
    • (1970) Nature , vol.228 , pp. 726-739
    • Perutz, M.F.1
  • 96
    • 84921328502 scopus 로고    scopus 로고
    • Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator
    • Proctor, E.A., Kota, P., Aleksandrov, A.A., He, L., Riordan, J.R., Dokholyan, N.V., Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator. Chem. Sci. 6 (2015), 1237–1246.
    • (2015) Chem. Sci. , vol.6 , pp. 1237-1246
    • Proctor, E.A.1    Kota, P.2    Aleksandrov, A.A.3    He, L.4    Riordan, J.R.5    Dokholyan, N.V.6
  • 99
    • 84886412961 scopus 로고    scopus 로고
    • Chaperone machines for protein folding, unfolding and disaggregation. Nature reviews
    • Saibil, H., Chaperone machines for protein folding, unfolding and disaggregation. Nature reviews. Mol. Cell. Biol. 14 (2013), 630–642.
    • (2013) Mol. Cell. Biol. , vol.14 , pp. 630-642
    • Saibil, H.1
  • 100
    • 84984865333 scopus 로고    scopus 로고
    • Computational approaches to investigating allostery
    • Schueler-Furman, O., Wodak, S.J., Computational approaches to investigating allostery. Curr. Opin. Struct. Biol. 41 (2016), 159–171.
    • (2016) Curr. Opin. Struct. Biol. , vol.41 , pp. 159-171
    • Schueler-Furman, O.1    Wodak, S.J.2
  • 102
    • 79955685287 scopus 로고    scopus 로고
    • Allostery in a disordered protein: oxidative modifications to alpha-synuclein act distally to regulate membrane binding
    • Sevcsik, E., Trexler, A.J., Dunn, J.M., Rhoades, E., Allostery in a disordered protein: oxidative modifications to alpha-synuclein act distally to regulate membrane binding. J. Am. Chem. Soc. 133 (2011), 7152–7158.
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 7152-7158
    • Sevcsik, E.1    Trexler, A.J.2    Dunn, J.M.3    Rhoades, E.4
  • 104
    • 85046705129 scopus 로고    scopus 로고
    • A non-equilibrium approach to allosteric communication
    • Stock, G., Hamm, P., A non-equilibrium approach to allosteric communication. Philos. Trans. R. Soc. Lond. B Biol. Sci., 373, 2018, 10.1098/rstb.2017.0187.
    • (2018) Philos. Trans. R. Soc. Lond. B Biol. Sci. , vol.373
    • Stock, G.1    Hamm, P.2
  • 106
    • 85063408729 scopus 로고    scopus 로고
    • OpenPathSampling: a Python framework for path sampling simulations. I. Basics
    • Swenson, D.W.H., Prince, J.H., Noe, F., Codera, J.D., Bolhuis, P.G., OpenPathSampling: a Python framework for path sampling simulations. I. Basics. BioRxiv, 2018, 10.1101/351494.
    • (2018) BioRxiv
    • Swenson, D.W.H.1    Prince, J.H.2    Noe, F.3    Codera, J.D.4    Bolhuis, P.G.5
  • 108
    • 85049369467 scopus 로고    scopus 로고
    • Reversing allosteric communication: from detecting allosteric sites to inducing and tuning targeted allosteric response
    • Tee, W.V., Guarnera, E., Berezovsky, I.N., Reversing allosteric communication: from detecting allosteric sites to inducing and tuning targeted allosteric response. PLoS Comput. Biol., 14, 2018, e1006228.
    • (2018) PLoS Comput. Biol. , vol.14 , pp. e1006228
    • Tee, W.V.1    Guarnera, E.2    Berezovsky, I.N.3
  • 109
    • 6344231648 scopus 로고    scopus 로고
    • Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
    • Temiz, N.A., Meirovitch, E., Bahar, I., Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data. Proteins 57 (2004), 468–480.
    • (2004) Proteins , vol.57 , pp. 468-480
    • Temiz, N.A.1    Meirovitch, E.2    Bahar, I.3
  • 110
    • 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., Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. U S A 102 (2005), 18908–18913.
    • (2005) Proc. Natl. Acad. Sci. U S A , vol.102 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 111
    • 77956638746 scopus 로고    scopus 로고
    • Substrate-modulated thermal fluctuations affect long-range allosteric signaling in protein homodimers: exemplified in CAP
    • Toncrova, H., McLeish, T.C., Substrate-modulated thermal fluctuations affect long-range allosteric signaling in protein homodimers: exemplified in CAP. Biophys. J. 98 (2010), 2317–2326.
    • (2010) Biophys. J. , vol.98 , pp. 2317-2326
    • Toncrova, H.1    McLeish, T.C.2
  • 112
    • 84895745240 scopus 로고    scopus 로고
    • A unified view of “how allostery works”
    • Tsai, C.J., Nussinov, R., A unified view of “how allostery works”. PLoS Comput. Biol., 10, 2014, e1003394.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003394
    • Tsai, C.J.1    Nussinov, R.2
  • 113
    • 77249114204 scopus 로고    scopus 로고
    • Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein
    • Vreede, J., Juraszek, J., Bolhuis, P.G., Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proc. Natl. Acad. Sci. U S A 107 (2010), 2397–2402.
    • (2010) Proc. Natl. Acad. Sci. U S A , vol.107 , pp. 2397-2402
    • Vreede, J.1    Juraszek, J.2    Bolhuis, P.G.3
  • 114
    • 84925114160 scopus 로고    scopus 로고
    • Intrinsically disordered proteins in cellular signalling and regulation
    • Wright, P.E., Dyson, H.J., Intrinsically disordered proteins in cellular signalling and regulation. Nat. Rev. Mol. Cell Biol. 16 (2015), 18–29.
    • (2015) Nat. Rev. Mol. Cell Biol. , vol.16 , pp. 18-29
    • Wright, P.E.1    Dyson, H.J.2
  • 116
    • 85028778489 scopus 로고    scopus 로고
    • Edge mode amplification in disordered elastic networks
    • Yan, L., Bouchaud, J.P., Wyart, M., Edge mode amplification in disordered elastic networks. Soft Matter 13 (2017), 5795–5801.
    • (2017) Soft Matter , vol.13 , pp. 5795-5801
    • Yan, L.1    Bouchaud, J.P.2    Wyart, M.3
  • 118
    • 85047802483 scopus 로고    scopus 로고
    • Principles for optimal cooperativity in allosteric materials
    • Yan, L., Ravasio, R., Brito, C., Wyart, M., Principles for optimal cooperativity in allosteric materials. Biophys. J. 114 (2018), 2787–2798.
    • (2018) Biophys. J. , vol.114 , pp. 2787-2798
    • Yan, L.1    Ravasio, R.2    Brito, C.3    Wyart, M.4
  • 119
    • 0032561775 scopus 로고    scopus 로고
    • Mapping the transition state of the allosteric pathway of GroEL by protein engineering
    • Yifrach, O., Horovitz, A., Mapping the transition state of the allosteric pathway of GroEL by protein engineering. J. Am. Chem. Soc. 120 (1998), 13262–13263.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 13262-13263
    • Yifrach, O.1    Horovitz, A.2
  • 120
    • 84939864190 scopus 로고    scopus 로고
    • Conformational gating dynamics in the GluCl anion-selective chloride channel
    • Yoluk, O., Lindahl, E., Andersson, M., Conformational gating dynamics in the GluCl anion-selective chloride channel. ACS Chem. Neurosci. 6 (2015), 1459–1467.
    • (2015) ACS Chem. Neurosci. , vol.6 , pp. 1459-1467
    • Yoluk, O.1    Lindahl, E.2    Andersson, M.3
  • 121
    • 84963966407 scopus 로고    scopus 로고
    • A gating mechanism of the serotonin 5-HT3 receptor
    • Yuan, S., Filipek, S., Vogel, H., A gating mechanism of the serotonin 5-HT3 receptor. Structure 24 (2016), 816–825.
    • (2016) Structure , vol.24 , pp. 816-825
    • Yuan, S.1    Filipek, S.2    Vogel, H.3
  • 122
    • 79960629007 scopus 로고    scopus 로고
    • Role of fluctuations in ligand binding cooperativity of membrane receptors
    • Zhu, L., Frenkel, D., Bolhuis, P.G., Role of fluctuations in ligand binding cooperativity of membrane receptors. Phys. Rev. Lett., 106, 2011, 168103.
    • (2011) Phys. Rev. Lett. , vol.106 , pp. 168103
    • Zhu, L.1    Frenkel, D.2    Bolhuis, P.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.