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Volumn 48, Issue 9, 2009, Pages 1911-1927

Noncooperative folding of subdomains in adenylate kinase

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE; BIOLOGICAL ACTIVITIES; CATALYTIC ACTIVITIES; CONFORMATIONAL CHANGES; DEUTERIUM EXCHANGES; HYDROPHOBIC CLUSTERS; HYPERTHERMOPHILIC BACTERIA; MESOPHILIC; MOLECULAR DESCRIPTIONS; NATIVE STRUCTURES; NUCLEOTIDE BINDINGS; PROTEIN ENGINEERINGS; REACTION PATHWAYS; SITE-DIRECTED MUTAGENESIS; SOLUTION STATE NMR; SPIN RELAXATIONS; STRUCTURAL BIOLOGIES; STRUCTURAL CHANGES; SUB-DOMAINS;

EID: 64549108040     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi8018042     Document Type: Article
Times cited : (47)

References (52)
  • 1
    • 33748619206 scopus 로고    scopus 로고
    • An NMR perspective on enzyme dynamics
    • Boehr, D. D., Dyson, H. J., and Wright, P. E. (2006) An NMR perspective on enzyme dynamics. Chem. Rev. 106, 3055-3079.
    • (2006) Chem. Rev , vol.106 , pp. 3055-3079
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 3
    • 21244440196 scopus 로고    scopus 로고
    • Conservation of μs-ms enzyme motions in the apo- and substrate-mimicked state
    • Beach, H., Cole, R., Gill, M. L., and Loria, J. P. (2005) Conservation of μs-ms enzyme motions in the apo- and substrate-mimicked state. J. Am. Chem. Soc. 127, 9167-9176.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 9167-9176
    • Beach, H.1    Cole, R.2    Gill, M.L.3    Loria, J.P.4
  • 4
    • 33947144085 scopus 로고    scopus 로고
    • Structure and dynamics of pin1 during catalysis by NMR
    • Labeikovsky, W., Eisenmesser, E. Z., Bosco, D. A., and Kern, D. (2007) Structure and dynamics of pin1 during catalysis by NMR. J. Mol. Biol. 367, 1370-1381.
    • (2007) J. Mol. Biol , vol.367 , pp. 1370-1381
    • Labeikovsky, W.1    Eisenmesser, E.Z.2    Bosco, D.A.3    Kern, D.4
  • 6
    • 0014429881 scopus 로고
    • Initial velocity and equilibrium kinetics of myokinase
    • Rhoads, D. G., and Lowenstein, J. M. (1968) Initial velocity and equilibrium kinetics of myokinase. J. Biol. Chem. 243, 3963-3972.
    • (1968) J. Biol. Chem , vol.243 , pp. 3963-3972
    • Rhoads, D.G.1    Lowenstein, J.M.2
  • 7
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Müller, C. W., Schlauderer, G. J., Reinstein, J., and Schulz, G. E. (1996) Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 4, 147-156.
    • (1996) Structure , vol.4 , pp. 147-156
    • Müller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 8
    • 0026544877 scopus 로고
    • Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state
    • Müller, C. W., and Schulz, G. E. (1992) Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. A model for a catalytic transition state. J. Mol. Biol. 224, 159-177.
    • (1992) J. Mol. Biol , vol.224 , pp. 159-177
    • Müller, C.W.1    Schulz, G.E.2
  • 9
    • 0029644728 scopus 로고
    • Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
    • Vonrhein, C., Schlauderer, G. J., and Schulz, G. E. (1995) Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3, 483-490.
    • (1995) Structure , vol.3 , pp. 483-490
    • Vonrhein, C.1    Schlauderer, G.J.2    Schulz, G.E.3
  • 11
    • 36148979311 scopus 로고    scopus 로고
    • NMR identification of transient complexes critical to adenylate kinase catalysis
    • Äden, J., and Wolf-Watz, M. (2007) NMR identification of transient complexes critical to adenylate kinase catalysis. J. Am. Chem. Soc. 129, 14003-14012.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 14003-14012
    • Äden, J.1    Wolf-Watz, M.2
  • 12
    • 38349092279 scopus 로고    scopus 로고
    • Conformational transitions in adenylate kinase: Allosteric communication reduces misligation
    • Whitford, P. C., Gosavi, S., and Onuchic, J. N. (2008) Conformational transitions in adenylate kinase: allosteric communication reduces misligation. J. Biol. Chem. 283, 2042-2048.
    • (2008) J. Biol. Chem , vol.283 , pp. 2042-2048
    • Whitford, P.C.1    Gosavi, S.2    Onuchic, J.N.3
  • 13
    • 12044259775 scopus 로고    scopus 로고
    • Vuister, G. W., and Bax, A. (1993) Quantitative J correlation: a new approach for measuring homonuclear 3-bond J(H(N)H(alpha) coupling-constants in N-15-enriched proteins. J. Am. Chem. Soc. 115, 7772-7777.
    • Vuister, G. W., and Bax, A. (1993) Quantitative J correlation: a new approach for measuring homonuclear 3-bond J(H(N)H(alpha) coupling-constants in N-15-enriched proteins. J. Am. Chem. Soc. 115, 7772-7777.
  • 15
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293.
    • (1995) J. Biomol. NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5    Bax, A.6
  • 16
    • 0034515845 scopus 로고    scopus 로고
    • Ansig for Windows: An interactive computer program for semiautomatic assignment of protein NMR spectra
    • Helgstrand, M., Kraulis, P., Allard, P., and Härd, T. (2000) Ansig for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra. J. Biomol. NMR 18, 329-336.
    • (2000) J. Biomol. NMR , vol.18 , pp. 329-336
    • Helgstrand, M.1    Kraulis, P.2    Allard, P.3    Härd, T.4
  • 17
    • 44049117010 scopus 로고
    • Improved 3D triple-resonance NMR techniques applied to a 31-Kda protein
    • Grzesiek, S., and Bax, A. (1992) Improved 3D triple-resonance NMR techniques applied to a 31-Kda protein. J. Magn. Reson. 96, 432-440.
    • (1992) J. Magn. Reson , vol.96 , pp. 432-440
    • Grzesiek, S.1    Bax, A.2
  • 18
    • 43949167657 scopus 로고
    • HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha-carbon and beta-carbon resonances in proteins
    • Wittekind, M., and Mueller, L. (1993) HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha-carbon and beta-carbon resonances in proteins. J. Magn. Res., Ser. B 101, 201-205.
    • (1993) J. Magn. Res., Ser. B , vol.101 , pp. 201-205
    • Wittekind, M.1    Mueller, L.2
  • 19
    • 9444245493 scopus 로고
    • Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR
    • Grzesiek, S., and Bax, A. (1992) Correlating backbone amide and side-chain resonances in larger proteins by multiple relayed triple resonance NMR. J. Am. Chem. Soc. 114, 6291-6293.
    • (1992) J. Am. Chem. Soc , vol.114 , pp. 6291-6293
    • Grzesiek, S.1    Bax, A.2
  • 20
    • 0029158840 scopus 로고
    • Assignment of side-chain C-13 resonances in perdeuterated proteins
    • Farmer, B. T., and Venters, R. A. (1995) Assignment of side-chain C-13 resonances in perdeuterated proteins. J. Am. Chem. Soc. 117, 4187-4188.
    • (1995) J. Am. Chem. Soc , vol.117 , pp. 4187-4188
    • Farmer, B.T.1    Venters, R.A.2
  • 21
    • 20444393525 scopus 로고    scopus 로고
    • Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds
    • Schanda, P., and Brutscher, B. (2005) Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. J. Am. Chem. Soc. 127, 8014-8015.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 8014-8015
    • Schanda, P.1    Brutscher, B.2
  • 23
    • 0029643523 scopus 로고
    • Protein folding intermediates: Native-state hydrogen exchange
    • Bai, Y., Sosnick, T. R., Mayne, L., and Englander, S. W. (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269, 192-197.
    • (1995) Science , vol.269 , pp. 192-197
    • Bai, Y.1    Sosnick, T.R.2    Mayne, L.3    Englander, S.W.4
  • 24
    • 0029746061 scopus 로고    scopus 로고
    • Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH
    • Chamberlain, A. K., Handel, T. M., and Marqusee, S. (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. Nat. Struct. Biol. 3, 782-787.
    • (1996) Nat. Struct. Biol , vol.3 , pp. 782-787
    • Chamberlain, A.K.1    Handel, T.M.2    Marqusee, S.3
  • 26
    • 0020855355 scopus 로고
    • Hydrogen exchange and structural dynamics of proteins and nucleic acids
    • Englander, S. W., and Kallenbach, N. R. (1984) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521-655.
    • (1984) Q. Rev. Biophys , vol.16 , pp. 521-655
    • Englander, S.W.1    Kallenbach, N.R.2
  • 27
    • 0037108164 scopus 로고    scopus 로고
    • Populating partially unfolded forms by hydrogen exchange-directed protein engineering
    • Takei, J., Pei, W., Vu, D., and Bai, Y. (2002) Populating partially unfolded forms by hydrogen exchange-directed protein engineering. Biochemistry 41, 12308-12312.
    • (2002) Biochemistry , vol.41 , pp. 12308-12312
    • Takei, J.1    Pei, W.2    Vu, D.3    Bai, Y.4
  • 30
    • 0013994339 scopus 로고
    • Hydrogen exchange in proteins
    • Hvidt, A., and Nielsen, S. O. (1966) Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287-386.
    • (1966) Adv. Protein Chem , vol.21 , pp. 287-386
    • Hvidt, A.1    Nielsen, S.O.2
  • 32
    • 31344440894 scopus 로고    scopus 로고
    • Effects of co-operative ligand binding on protein amide NH hydrogen exchange
    • Polshakov, V. I., Birdsall, B., and Feeney, J. (2006) Effects of co-operative ligand binding on protein amide NH hydrogen exchange. J. Mol. Biol. 356, 886-903.
    • (2006) J. Mol. Biol , vol.356 , pp. 886-903
    • Polshakov, V.I.1    Birdsall, B.2    Feeney, J.3
  • 33
    • 0015918941 scopus 로고
    • P 5 -Di(adenosine-5') pentaphosphate, a potent multisubstrate inhibitor of adenylate kinase
    • Lienhard, G. E., and Secemski, I. I. (1973) P 1 P 5 -Di(adenosine-5') pentaphosphate, a potent multisubstrate inhibitor of adenylate kinase. J. Biol. Chem. 248, 1121-1123.
    • (1973) J. Biol. Chem , vol.248 , pp. 1121-1123
    • Lienhard, G.E.1    Secemski, I.I.2
  • 35
    • 0037214137 scopus 로고    scopus 로고
    • Protein hydrogen exchange mechanism: Local fluctuations
    • Maity, H., Lim, W. K., Rumbley, J. N., and Englander, S. W. (2003) Protein hydrogen exchange mechanism: Local fluctuations. Protein Sci. 12, 153-160.
    • (2003) Protein Sci , vol.12 , pp. 153-160
    • Maity, H.1    Lim, W.K.2    Rumbley, J.N.3    Englander, S.W.4
  • 36
    • 0032876680 scopus 로고    scopus 로고
    • Protein conformational stabilities can be determined from hydrogen exchange rates
    • Huyghues-Despointes, B. M., Scholtz, J. M., and Pace, C. N. (1999) Protein conformational stabilities can be determined from hydrogen exchange rates. Nat. Struct. Biol. 6, 910-912.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 910-912
    • Huyghues-Despointes, B.M.1    Scholtz, J.M.2    Pace, C.N.3
  • 40
    • 0033598719 scopus 로고    scopus 로고
    • Structural distribution of stability in a thermophilic enzyme
    • Hollien, J., and Marqusee, S. (1999) Structural distribution of stability in a thermophilic enzyme. Proc. Natl. Acad. Sci. U.S.A. 96, 13674-13678.
    • (1999) Proc. Natl. Acad. Sci. U.S.A , vol.96 , pp. 13674-13678
    • Hollien, J.1    Marqusee, S.2
  • 41
    • 33144487234 scopus 로고    scopus 로고
    • Roles of static and dynamic domains in stability and catalysis of adenylate kinase
    • Bae, E., and Phillips, G. N., Jr. (2006) Roles of static and dynamic domains in stability and catalysis of adenylate kinase. Proc. Natl. Acad. Sci. U.S.A. 103, 2132-2137.
    • (2006) Proc. Natl. Acad. Sci. U.S.A , vol.103 , pp. 2132-2137
    • Bae, E.1    Phillips Jr., G.N.2
  • 42
    • 24044490917 scopus 로고    scopus 로고
    • Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase
    • Ratner, V., Amir, D., Kahana, E., and Haas, E. (2005) Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase. J. Mol. Biol. 352, 683-699.
    • (2005) J. Mol. Biol , vol.352 , pp. 683-699
    • Ratner, V.1    Amir, D.2    Kahana, E.3    Haas, E.4
  • 43
    • 0032485916 scopus 로고    scopus 로고
    • Identification of unfolding domains in large proteins by their unfolding rates
    • Deng, Y., and Smith, D. L. (1998) Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry 37, 6256-6262.
    • (1998) Biochemistry , vol.37 , pp. 6256-6262
    • Deng, Y.1    Smith, D.L.2
  • 44
    • 0033585130 scopus 로고    scopus 로고
    • Hydrogen exchange demonstrates three domains in aldolase unfold sequentially
    • Deng, Y., and Smith, D. L. (1999) Hydrogen exchange demonstrates three domains in aldolase unfold sequentially. J. Mol. Biol. 294, 247-258.
    • (1999) J. Mol. Biol , vol.294 , pp. 247-258
    • Deng, Y.1    Smith, D.L.2
  • 45
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman, K. A., Lei, M., Thai, V., Kerns, S. J., Karplus, M., and Kern, D. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 46
    • 0027528934 scopus 로고
    • Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers
    • Gerstein, M., Schulz, G., and Chothia, C. (1993) Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J. Mol. Biol. 229, 494-501.
    • (1993) J. Mol. Biol , vol.229 , pp. 494-501
    • Gerstein, M.1    Schulz, G.2    Chothia, C.3
  • 47
    • 33846847773 scopus 로고    scopus 로고
    • Conformational transitions of adenylate kinase: Switching by cracking
    • Whitford, P. C., Miyashita, O., Levy, Y., and Onuchic, J. N. (2007) Conformational transitions of adenylate kinase: switching by cracking. J. Mol. Biol. 366, 1661-1671.
    • (2007) J. Mol. Biol , vol.366 , pp. 1661-1671
    • Whitford, P.C.1    Miyashita, O.2    Levy, Y.3    Onuchic, J.N.4
  • 48
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • Miyashita, O., Onuchic, J. N., and Wolynes, P. G (2003) Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Natl. Acad. Sci. U.S.A. 100, 12570-12575.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 49
    • 61949448788 scopus 로고    scopus 로고
    • Energy landscape along an enzymatic reaction trajectory: Hinges or cracks?
    • Whitford, P. C., Onuchic, J. N., and Wolynes, P. G. (2008) Energy landscape along an enzymatic reaction trajectory: hinges or cracks? HFSP J. 2, 61-64.
    • (2008) HFSP J , vol.2 , pp. 61-64
    • Whitford, P.C.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 50
    • 0031577566 scopus 로고    scopus 로고
    • Activation of adenylate kinase by denaturants is due to the increasing conformational flexibility at its active sites
    • Zhang, H. J., Sheng, X. R., Pan, X. M., and Zhou, J. M. (1997) Activation of adenylate kinase by denaturants is due to the increasing conformational flexibility at its active sites. Biochem. Biophys. Res. Commun. 238, 382-386.
    • (1997) Biochem. Biophys. Res. Commun , vol.238 , pp. 382-386
    • Zhang, H.J.1    Sheng, X.R.2    Pan, X.M.3    Zhou, J.M.4
  • 51
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol.Graphics 14, 29-32.
    • (1996) J. Mol.Graphics , vol.14 , pp. 29-32
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3
  • 52
    • 0023697408 scopus 로고
    • Unfolding free-energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl Alpha-chymotrypsin using different denaturants
    • Santoro, M. M., and Bolen, D. W. (1988) Unfolding free-energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl Alpha-chymotrypsin using different denaturants. Biochemistry 27, 8063-8068.
    • (1988) Biochemistry , vol.27 , pp. 8063-8068
    • Santoro, M.M.1    Bolen, D.W.2


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