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Volumn 6, Issue , 2015, Pages

Design of protein switches based on an ensemble model of allostery

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; BETA LACTAMASE; BETA-LACTAMASE TEM-1; ENZYME; MALTOSE BINDING PROTEIN;

EID: 84928799061     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7968     Document Type: Article
Times cited : (64)

References (57)
  • 1
    • 23944444109 scopus 로고    scopus 로고
    • Engineering allosteric protein switches by domain insertion
    • Ostermeier, M. Engineering allosteric protein switches by domain insertion. Protein Eng. Des. Sel. 18, 359-364 (2005).
    • (2005) Protein Eng. Des. Sel. , vol.18 , pp. 359-364
    • Ostermeier, M.1
  • 2
    • 78650796409 scopus 로고    scopus 로고
    • Converting a protein into a switch for biosensing and functional regulation
    • Stratton, M. M. & Loh, S. N. Converting a protein into a switch for biosensing and functional regulation. Protein Sci. 20, 19-29 (2011).
    • (2011) Protein Sci. , vol.20 , pp. 19-29
    • Stratton, M.M.1    Loh, S.N.2
  • 3
    • 77955984136 scopus 로고    scopus 로고
    • Structure-switching biosensors: Inspired by Nature
    • Vallee-Belisle, A. & Plaxco, K. W. Structure-switching biosensors: inspired by Nature. Curr. Opin. Struct. Biol. 20, 518-526 (2010).
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 518-526
    • Vallee-Belisle, A.1    Plaxco, K.W.2
  • 5
    • 8844263869 scopus 로고    scopus 로고
    • A molecular switch created by in vitro recombination of nonhomologous genes
    • Guntas, G., Mitchell, S. F. & Ostermeier, M. A molecular switch created by in vitro recombination of nonhomologous genes. Chem. Biol. 11, 1483-1487 (2004).
    • (2004) Chem. Biol. , vol.11 , pp. 1483-1487
    • Guntas, G.1    Mitchell, S.F.2    Ostermeier, M.3
  • 6
    • 23844465160 scopus 로고    scopus 로고
    • Directed evolution of protein switches and their application to the creation of ligand-binding proteins
    • Guntas, G., Mansell, T. J., Kim, J. R. & Ostermeier, M. Directed evolution of protein switches and their application to the creation of ligand-binding proteins. Proc. Natl Acad. Sci. USA 102, 11224-11229 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 11224-11229
    • Guntas, G.1    Mansell, T.J.2    Kim, J.R.3    Ostermeier, M.4
  • 7
    • 77951215979 scopus 로고    scopus 로고
    • NMR characterization of an engineered domain fusion between maltose binding protein and TEM1 beta-lactamase provides insight into its structure and allosteric mechanism
    • Wright, C. M., Majumdar, A., Tolman, J. R. & Ostermeier, M. NMR characterization of an engineered domain fusion between maltose binding protein and TEM1 beta-lactamase provides insight into its structure and allosteric mechanism. Proteins 78, 1423-1430 (2009).
    • (2009) Proteins , vol.78 , pp. 1423-1430
    • Wright, C.M.1    Majumdar, A.2    Tolman, J.R.3    Ostermeier, M.4
  • 8
    • 31544462780 scopus 로고    scopus 로고
    • Modulation of effector affinity by hinge region mutations also modulates switching activity in an engineered allosteric TEM1 beta-lactamase switch
    • Kim, J. R. & Ostermeier, M. Modulation of effector affinity by hinge region mutations also modulates switching activity in an engineered allosteric TEM1 beta-lactamase switch. Arch. Biochem. Biophys. 446, 44-51 (2006).
    • (2006) Arch. Biochem. Biophys. , vol.446 , pp. 44-51
    • Kim, J.R.1    Ostermeier, M.2
  • 9
    • 80855139801 scopus 로고    scopus 로고
    • In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells
    • Heins, R. A., Choi, J. H., Sohka, T. & Ostermeier, M. In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells. PLoS One 6, e27302 (2011).
    • (2011) PLoS One , vol.6
    • Heins, R.A.1    Choi, J.H.2    Sohka, T.3    Ostermeier, M.4
  • 10
    • 84878323463 scopus 로고    scopus 로고
    • Non-allosteric enzyme switches possess larger effector-induced changes in thermodynamic stability than their non-switch analogs
    • Choi, J. H., San, A. & Ostermeier, M. Non-allosteric enzyme switches possess larger effector-induced changes in thermodynamic stability than their non-switch analogs. Protein Sci. 22, 475-485 (2013).
    • (2013) Protein Sci. , vol.22 , pp. 475-485
    • Choi, J.H.1    San, A.2    Ostermeier, M.3
  • 11
    • 84898993517 scopus 로고    scopus 로고
    • The ensemble nature of allostery
    • Motlagh, H. N., Wrabl, J. O., Li, J. & Hilser, V. J. The ensemble nature of allostery. Nature 508, 331-339 (2014).
    • (2014) Nature , vol.508 , pp. 331-339
    • Motlagh, H.N.1    Wrabl, J.O.2    Li, J.3    Hilser, V.J.4
  • 12
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • Cui, Q. & Karplus, M. Allostery and cooperativity revisited. Protein Sci. 17, 1295-1307 (2008).
    • (2008) Protein Sci. , vol.17 , pp. 1295-1307
    • Cui, Q.1    Karplus, M.2
  • 13
    • 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, 88-118 (1965).
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 14
    • 0042882982 scopus 로고
    • Enzyme flexibility and enzyme action
    • Koshland, Jr. D. E. Enzyme flexibility and enzyme action. J. Cell. Comp. Physiol. 54, 245-258 (1959).
    • (1959) J. Cell. Comp. Physiol. , vol.54 , pp. 245-258
    • Koshland, D.E.1
  • 15
    • 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, 103-133 (2012).
    • (2012) Annu. Rev. Biophys. , vol.41 , pp. 103-133
    • Changeux, J.P.1
  • 18
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr, D. D., Nussinov, R. & Wright, P. E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 5, 789-796 (2009).
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 19
    • 70350131719 scopus 로고    scopus 로고
    • Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins
    • Schrank, T. P., Bolen, D. W. & Hilser, V. J. Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins. Proc. Natl Acad. Sci. USA 106, 16984-16989 (2009).
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 16984-16989
    • Schrank, T.P.1    Bolen, D.W.2    Hilser, V.J.3
  • 20
    • 70450191983 scopus 로고    scopus 로고
    • Dynamic activation of an allosteric regulatory protein
    • Tzeng, S. R. & Kalodimos, C. G. Dynamic activation of an allosteric regulatory protein. Nature 462, 368-372 (2009).
    • (2009) Nature , vol.462 , pp. 368-372
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 21
    • 80052340812 scopus 로고    scopus 로고
    • The role of protein conformational fluctuations in allostery, function, and evolution
    • Wrabl, J. O. et al. The role of protein conformational fluctuations in allostery, function, and evolution. Biophys. Chem. 159, 129-141 (2011).
    • (2011) Biophys. Chem. , vol.159 , pp. 129-141
    • Wrabl, J.O.1
  • 22
  • 23
    • 84864651001 scopus 로고    scopus 로고
    • Protein activity regulation by conformational entropy
    • Tzeng, S. R. & Kalodimos, C. G. Protein activity regulation by conformational entropy. Nature 488, 236-240 (2012).
    • (2012) Nature , vol.488 , pp. 236-240
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 24
    • 84879392599 scopus 로고    scopus 로고
    • Structural biology: Signalling from disordered proteins
    • Hilser, V. J. Structural biology: signalling from disordered proteins. Nature 498, 308-310 (2013).
    • (2013) Nature , vol.498 , pp. 308-310
    • Hilser, V.J.1
  • 25
    • 84879411842 scopus 로고    scopus 로고
    • Allosteric inhibition through suppression of transient conformational states
    • Tzeng, S. R. & Kalodimos, C. G. Allosteric inhibition through suppression of transient conformational states. Nat. Chem. Biol. 9, 462-465 (2013).
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 462-465
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 26
    • 0021658956 scopus 로고
    • Allostery without conformational change. A plausible model
    • Cooper, A. & Dryden, D. T. Allostery without conformational change. A plausible model. Eur. Biophys. J. 11, 103-109 (1984).
    • (1984) Eur. Biophys. J. , vol.11 , pp. 103-109
    • Cooper, A.1    Dryden, D.T.2
  • 28
    • 84858234186 scopus 로고    scopus 로고
    • Agonism/antagonism switching in allosteric ensembles
    • Motlagh, H. N. & Hilser, V. J. Agonism/antagonism switching in allosteric ensembles. Proc. Natl Acad. Sci. USA 109, 4134-4139 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 4134-4139
    • Motlagh, H.N.1    Hilser, V.J.2
  • 29
    • 34347235156 scopus 로고    scopus 로고
    • Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins
    • Hilser, V. J. & Thompson, E. B. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl Acad. Sci. USA 104, 8311-8315 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 8311-8315
    • Hilser, V.J.1    Thompson, E.B.2
  • 31
    • 0034760077 scopus 로고    scopus 로고
    • Dynamic activation of protein function: A view emerging from NMR spectroscopy
    • Wand, A. J. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat. Struct. Biol. 8, 926-931 (2001).
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 926-931
    • Wand, A.J.1
  • 32
    • 0033528657 scopus 로고    scopus 로고
    • Thermodynamic stability of a cold-active alpha-amylase from the Antarctic bacterium Alteromonas haloplanctis
    • Feller, G., d'Amico, D. & Gerday, C. Thermodynamic stability of a cold-active alpha-amylase from the Antarctic bacterium Alteromonas haloplanctis. Biochemistry 38, 4613-4619 (1999).
    • (1999) Biochemistry , vol.38 , pp. 4613-4619
    • Feller, G.1    D'amico, D.2    Gerday, C.3
  • 33
    • 0030896384 scopus 로고    scopus 로고
    • Evolution of lactate dehydrogenase-A homologs of barracuda fishes (genus Sphyraena) from different thermal environments: Differences in kinetic properties and thermal stability are due to amino acid substitutions outside the active site
    • Holland, L. Z., McFall-Ngai, M. & Somero, G. N. Evolution of lactate dehydrogenase-A homologs of barracuda fishes (genus Sphyraena) from different thermal environments: differences in kinetic properties and thermal stability are due to amino acid substitutions outside the active site. Biochemistry 36, 3207-3215 (1997).
    • (1997) Biochemistry , vol.36 , pp. 3207-3215
    • Holland, L.Z.1    McFall-Ngai, M.2    Somero, G.N.3
  • 34
    • 0032530086 scopus 로고    scopus 로고
    • Hot spots in cold adaptation: Localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes
    • Fields, P. A. & Somero, G. N. Hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes. Proc. Natl Acad. Sci. USA 95, 11476-11481 (1998).
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11476-11481
    • Fields, P.A.1    Somero, G.N.2
  • 36
    • 1942438703 scopus 로고    scopus 로고
    • GALA: A designed synthetic pH-responsive amphipathic peptide with applications in drug and gene delivery
    • Li, W., Nicol, F. & Szoka, Jr. F. C. GALA: a designed synthetic pH-responsive amphipathic peptide with applications in drug and gene delivery. Adv. Drug Deliv. Rev. 56, 967-985 (2004).
    • (2004) Adv. Drug Deliv. Rev. , vol.56 , pp. 967-985
    • Li, W.1    Nicol, F.2    Szoka, F.C.3
  • 37
    • 0035875870 scopus 로고    scopus 로고
    • Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy
    • Evenas, J. et al. Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J. Mol. Biol. 309, 961-974 (2001).
    • (2001) J. Mol. Biol. , vol.309 , pp. 961-974
    • Evenas, J.1
  • 38
    • 33749007969 scopus 로고    scopus 로고
    • Backbone dynamics of TEM-1 determined by NMR: Evidence for a highly ordered protein
    • Savard, P. Y. & Gagne, S. M. Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein. Biochemistry 45, 11414-11424 (2006).
    • (2006) Biochemistry , vol.45 , pp. 11414-11424
    • Savard, P.Y.1    Gagne, S.M.2
  • 39
    • 52049112316 scopus 로고    scopus 로고
    • Increased folding stability of TEM-1 beta-lactamase by in vitro selection
    • Kather, I., Jakob, R. P., Dobbek, H. & Schmid, F. X. Increased folding stability of TEM-1 beta-lactamase by in vitro selection. J. Mol. Biol. 383, 238-251 (2008).
    • (2008) J. Mol. Biol. , vol.383 , pp. 238-251
    • Kather, I.1    Jakob, R.P.2    Dobbek, H.3    Schmid, F.X.4
  • 40
    • 0346463079 scopus 로고    scopus 로고
    • A fluorescent probe-labeled Escherichia coli aspartate transcarbamoylase that monitors the allosteric conformational state
    • West, J. M., Tsuruta, H. & Kantrowitz, E. R. A fluorescent probe-labeled Escherichia coli aspartate transcarbamoylase that monitors the allosteric conformational state. J. Biol. Chem. 279, 945-951 (2004).
    • (2004) Biol. Chem. , vol.279 , pp. 945-951
    • West, J.M.1    Tsuruta, H.2    Kantrowitz, E.R.3
  • 41
    • 0033485868 scopus 로고    scopus 로고
    • Hsp26: A temperature-regulated chaperone
    • Haslbeck, M. et al. Hsp26: a temperature-regulated chaperone. EMBO J. 18, 6744-6751 (1999).
    • (1999) EMBO J. , vol.18 , pp. 6744-6751
    • Haslbeck, M.1
  • 42
    • 21744436278 scopus 로고    scopus 로고
    • The activation mechanism of Hsp26 does not require dissociation of the oligomer
    • Franzmann, T. M., Wuhr, M., Richter, K., Walter, S. & Buchner, J. The activation mechanism of Hsp26 does not require dissociation of the oligomer. J. Mol. Biol. 350, 1083-1093 (2005).
    • (2005) J. Mol. Biol. , vol.350 , pp. 1083-1093
    • Franzmann, T.M.1    Wuhr, M.2    Richter, K.3    Walter, S.4    Buchner, J.5
  • 43
    • 22844435320 scopus 로고    scopus 로고
    • Periplasmic protein HdeA exhibits chaperone-like activity exclusively within stomach pH range by transforming into disordered conformation
    • Hong, W. et al. Periplasmic protein HdeA exhibits chaperone-like activity exclusively within stomach pH range by transforming into disordered conformation. J. Biol. Chem. 280, 27029-27034 (2005).
    • (2005) J. Biol. Chem. , vol.280 , pp. 27029-27034
    • Hong, W.1
  • 44
    • 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, 390-394 (2013).
    • (2013) Nature , vol.498 , pp. 390-394
    • Ferreon, A.C.1    Ferreon, J.C.2    Wright, P.E.3    Deniz, A.A.4
  • 45
    • 77954256912 scopus 로고    scopus 로고
    • Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity
    • Garcia-Pino, A. et al. Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Cell 142, 101-111 (2010).
    • (2010) Cell , vol.142 , pp. 101-111
    • Garcia-Pino, A.1
  • 46
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815 (1993).
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 47
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera - A visualization system for exploratory research and analysis
    • Pettersen, E. F. et al. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
    • (2004) J. Comput. Chem. , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1
  • 48
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • Krivov, G. G., Shapovalov, M. V. & Dunbrack, Jr. R. L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77, 778-795 (2009).
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack, R.L.3
  • 49
    • 27344454932 scopus 로고    scopus 로고
    • GROMACS: Fast, flexible, and free
    • Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701-1718 (2005).
    • (2005) J. Comput. Chem. , vol.26 , pp. 1701-1718
    • Van Der Spoel, D.1
  • 50
    • 25144442821 scopus 로고    scopus 로고
    • COREX/BEST server: A web browser-based program that calculates regional stability variations within protein structures
    • Vertrees, J., Barritt, P., Whitten, S. & Hilser, V. J. COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures. Bioinformatics 21, 3318-3319 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3318-3319
    • Vertrees, J.1    Barritt, P.2    Whitten, S.3    Hilser, V.J.4
  • 51
    • 0001751804 scopus 로고    scopus 로고
    • Parametrization of aliphatic CHn united atoms of GROMOS96 force field
    • Daura, X., Mark, A. E. & Van Gunsteren, W. F. Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. 19, 535-547 (1998).
    • (1998) J. Comput. Chem. , vol.19 , pp. 535-547
    • Daura, X.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 52
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg, D. & McLachlan, A. D. Solvation energy in protein folding and binding. Nature 319, 199-203 (1986).
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 55
  • 56
    • 0032622242 scopus 로고    scopus 로고
    • Sensitivity improvement of transverse relaxation-optimized spectroscopy
    • Rance, M., Loria, J. P. & Palmer, A. G. R. Sensitivity improvement of transverse relaxation-optimized spectroscopy. J. Magn. Reson. 136, 92-101 (1999).
    • (1999) J. Magn. Reson. , vol.136 , pp. 92-101
    • Rance, M.1    Loria, J.P.2    Palmer, A.G.R.3
  • 57
    • 44049118259 scopus 로고
    • Experiments for recording pureabsorption heteronuclear correlation spectra using pulsed field gradients
    • Davis, A. L., Keeler, J., Laue, E. D. & Moskau, D. Experiments for recording pureabsorption heteronuclear correlation spectra using pulsed field gradients. J. Magn. Reson. 98, 207-216 (1992).
    • (1992) J. Magn. Reson. , vol.98 , pp. 207-216
    • Davis, A.L.1    Keeler, J.2    Laue, E.D.3    Moskau, D.4


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