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Volumn 52, Issue 11, 2013, Pages 1874-1885

Solution structure of the Q41N variant of ubiquitin as a model for the alternatively folded N2 state of ubiquitin

Author keywords

[No Author keywords available]

Indexed keywords

AMBIENT PRESSURES; CONFORMATIONAL CHANGE; CONFORMATIONAL FLUCTUATIONS; HYDRODYNAMIC PRESSURE; NUCLEAR MAGNETIC RESONANCE(NMR); SOLUTION STRUCTURES; STRUCTURE AND DYNAMICS; UBIQUITIN-INTERACTING MOTIFS;

EID: 84875476681     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi301420m     Document Type: Article
Times cited : (26)

References (59)
  • 1
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr, D. D., McElheny, D., Dyson, H. J., and Wright, P. E. (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
  • 4
    • 34250821717 scopus 로고    scopus 로고
    • Mechanism of coupled folding and binding of an intrinsically disordered protein
    • Sugase, K., Dyson, H. J., and Wright, P. E. (2007) Mechanism of coupled folding and binding of an intrinsically disordered protein Nature 447, 1021-1025
    • (2007) Nature , vol.447 , pp. 1021-1025
    • Sugase, K.1    Dyson, H.J.2    Wright, P.E.3
  • 5
    • 77956501272 scopus 로고    scopus 로고
    • A transient and low-populated protein-folding intermediate at atomic resolution
    • Korzhnev, D. M., Religa, T. L., Banachewicz, W., Fersht, A. R., and Kay, L. E. (2010) A transient and low-populated protein-folding intermediate at atomic resolution Science 329, 1312-1316
    • (2010) Science , vol.329 , pp. 1312-1316
    • Korzhnev, D.M.1    Religa, T.L.2    Banachewicz, W.3    Fersht, A.R.4    Kay, L.E.5
  • 6
    • 70450191983 scopus 로고    scopus 로고
    • Dynamic activation of an allosteric regulatory protein
    • Tzeng, S. R. and Kalodimos, C. G. (2009) Dynamic activation of an allosteric regulatory protein Nature 462, 368-372
    • (2009) Nature , vol.462 , pp. 368-372
    • Tzeng, S.R.1    Kalodimos, C.G.2
  • 8
    • 0038682826 scopus 로고    scopus 로고
    • Dipolar couplings in multiple alignments suggest α helical motion in ubiquitin
    • Meiler, J., Peti, W., and Griesinger, C. (2003) Dipolar couplings in multiple alignments suggest α helical motion in ubiquitin J. Am. Chem. Soc. 125, 8072-8073
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 8072-8073
    • Meiler, J.1    Peti, W.2    Griesinger, C.3
  • 12
    • 3342936435 scopus 로고    scopus 로고
    • High-pressure NMR spectroscopy for characterizing folding intermediates and denatured states of proteins
    • Kamatari, Y., Kitahara, R., Yamada, H., Yokoyama, S., and Akasaka, K. (2004) High-pressure NMR spectroscopy for characterizing folding intermediates and denatured states of proteins Methods 34, 133-143
    • (2004) Methods , vol.34 , pp. 133-143
    • Kamatari, Y.1    Kitahara, R.2    Yamada, H.3    Yokoyama, S.4    Akasaka, K.5
  • 13
    • 33645981275 scopus 로고    scopus 로고
    • Conformational fluctuations of proteins revealed by variable pressure NMR
    • Li, H. and Akasaka, K. (2006) Conformational fluctuations of proteins revealed by variable pressure NMR Biochim. Biophys. Acta 1764, 331-345
    • (2006) Biochim. Biophys. Acta , vol.1764 , pp. 331-345
    • Li, H.1    Akasaka, K.2
  • 16
    • 0035856546 scopus 로고    scopus 로고
    • Two folded conformers of ubiquitin revealed by high-pressure NMR
    • Kitahara, R., Yamada, H., and Akasaka, K. (2001) Two folded conformers of ubiquitin revealed by high-pressure NMR Biochemistry 40, 13556-13563
    • (2001) Biochemistry , vol.40 , pp. 13556-13563
    • Kitahara, R.1    Yamada, H.2    Akasaka, K.3
  • 17
    • 0037452877 scopus 로고    scopus 로고
    • Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding
    • Kitahara, R. and Akasaka, K. (2003) Close identity of a pressure-stabilized intermediate with a kinetic intermediate in protein folding Proc. Natl. Acad. Sci. U.S.A. 100, 3167-3172
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 3167-3172
    • Kitahara, R.1    Akasaka, K.2
  • 18
    • 14644424521 scopus 로고    scopus 로고
    • NMR snapshots of a fluctuating protein structure: Ubiquitin at 30 bar-3 kbar
    • Kitahara, R., Yokoyama, S., and Akasaka, K. (2005) NMR snapshots of a fluctuating protein structure: Ubiquitin at 30 bar-3 kbar J. Mol. Biol. 347, 277-285
    • (2005) J. Mol. Biol. , vol.347 , pp. 277-285
    • Kitahara, R.1    Yokoyama, S.2    Akasaka, K.3
  • 21
    • 37849000182 scopus 로고    scopus 로고
    • Basic folded and low-populated locally disordered conformers of SUMO-2 characterized by NMR spectroscopy at varying pressures
    • Kitahara, R., Zhao, C., Saito, K., Koshiba, S., Ioune, M., Kigawa, T., Yokoyama, S., and Akasaka, K. (2008) Basic folded and low-populated locally disordered conformers of SUMO-2 characterized by NMR spectroscopy at varying pressures Biochemistry 47, 30-39
    • (2008) Biochemistry , vol.47 , pp. 30-39
    • Kitahara, R.1    Zhao, C.2    Saito, K.3    Koshiba, S.4    Ioune, M.5    Kigawa, T.6    Yokoyama, S.7    Akasaka, K.8
  • 22
    • 77649105245 scopus 로고    scopus 로고
    • Dynamic correlation between pressure-induced protein structural transition and water penetration
    • Imai, T. and Sugita, Y. (2010) Dynamic correlation between pressure-induced protein structural transition and water penetration J. Phys. Chem. B 114, 2281-2286
    • (2010) J. Phys. Chem. B , vol.114 , pp. 2281-2286
    • Imai, T.1    Sugita, Y.2
  • 23
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 Å resolution
    • Vijay-Kumar, S., Bugg, C. E., and Cook, W. J. (1987) Structure of ubiquitin refined at 1.8 Å resolution J. Mol. Biol. 194, 531-544
    • (1987) J. Mol. Biol. , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 24
    • 80051591247 scopus 로고    scopus 로고
    • Mapping the hydration dynamics of ubiquitin
    • Nucci, N. V., Pometun, M. S., and Wand, A. J. (2011) Mapping the hydration dynamics of ubiquitin J. Am. Chem. Soc. 133, 12326-12329
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 12326-12329
    • Nucci, N.V.1    Pometun, M.S.2    Wand, A.J.3
  • 26
    • 84856707634 scopus 로고    scopus 로고
    • Time scales of slow motions in ubiquitin explored by heteronuclear double resonance
    • Salvi, N., Ulzega, S., Ferrage, F., and Bodenhausen, G. (2012) Time scales of slow motions in ubiquitin explored by heteronuclear double resonance J. Am. Chem. Soc. 134, 2481-2484
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 2481-2484
    • Salvi, N.1    Ulzega, S.2    Ferrage, F.3    Bodenhausen, G.4
  • 27
    • 79952143817 scopus 로고    scopus 로고
    • The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch
    • Huang, K. Y., Amodeo, G. A., Tong, L. A., and McDermott, A. (2011) The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch Protein Sci. 20, 630-639
    • (2011) Protein Sci. , vol.20 , pp. 630-639
    • Huang, K.Y.1    Amodeo, G.A.2    Tong, L.A.3    McDermott, A.4
  • 28
    • 80051666404 scopus 로고    scopus 로고
    • A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip
    • Sidhu, A., Surolia, A., Robertson, A. D., and Sundd, M. (2011) A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip J. Mol. Biol. 411, 1037-1048
    • (2011) J. Mol. Biol. , vol.411 , pp. 1037-1048
    • Sidhu, A.1    Surolia, A.2    Robertson, A.D.3    Sundd, M.4
  • 29
    • 29144518532 scopus 로고    scopus 로고
    • The ubiquitin domain superfold: Structure-based sequence alignments and characterization of binding epitopes
    • Kiel, C. and Serrano, L. (2006) The ubiquitin domain superfold: Structure-based sequence alignments and characterization of binding epitopes J. Mol. Biol. 355, 821-844
    • (2006) J. Mol. Biol. , vol.355 , pp. 821-844
    • Kiel, C.1    Serrano, L.2
  • 31
    • 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
  • 32
    • 34249765651 scopus 로고
    • Nmr View: A computer program for the visualization and analysis of NMR data
    • Johnson, B. A. and Blevins, R. A. (1994) Nmr View: A computer program for the visualization and analysis of NMR data J. Biomol. NMR 4, 603-614
    • (1994) J. Biomol. NMR , vol.4 , pp. 603-614
    • Johnson, B.A.1    Blevins, R.A.2
  • 33
    • 34547923673 scopus 로고    scopus 로고
    • KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
    • Kobayashi, N., Iwahara, J., Koshiba, S., Tomizawa, T., Tochio, N., Güntert, P., Kigawa, T., and Yokoyama, S. (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies J. Biomol. NMR 39, 31-52
    • (2007) J. Biomol. NMR , vol.39 , pp. 31-52
    • Kobayashi, N.1    Iwahara, J.2    Koshiba, S.3    Tomizawa, T.4    Tochio, N.5    Güntert, P.6    Kigawa, T.7    Yokoyama, S.8
  • 34
    • 0034912667 scopus 로고    scopus 로고
    • On-line cell high-pressure nuclear magnetic resonance technique: Application to protein studies
    • Akasaka, K. and Yamada, H. (2001) On-line cell high-pressure nuclear magnetic resonance technique: Application to protein studies Methods Enzymol. 338, 134-158
    • (2001) Methods Enzymol. , vol.338 , pp. 134-158
    • Akasaka, K.1    Yamada, H.2
  • 35
    • 84855376610 scopus 로고    scopus 로고
    • Modification of encapsulation pressure of reverse micelles in liquid ethane
    • Peterson, R. W., Nucci, N. V., and Wand, A. J. (2011) Modification of encapsulation pressure of reverse micelles in liquid ethane J. Magn. Reson. 212, 229-233
    • (2011) J. Magn. Reson. , vol.212 , pp. 229-233
    • Peterson, R.W.1    Nucci, N.V.2    Wand, A.J.3
  • 36
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann, T., Güntert, P., and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA J. Mol. Biol. 319, 209-227
    • (2002) J. Mol. Biol. , vol.319 , pp. 209-227
    • Herrmann, T.1    Güntert, P.2    Wüthrich, K.3
  • 37
    • 0032185144 scopus 로고    scopus 로고
    • Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination
    • Ottiger, M., Delaglio, F., Marquardt, J. L., Tjandra, N., and Bax, A. (1998) Measurement of dipolar couplings for methylene and methyl sites in weakly oriented macromolecules and their use in structure determination J. Magn. Reson. 134, 365-369
    • (1998) J. Magn. Reson. , vol.134 , pp. 365-369
    • Ottiger, M.1    Delaglio, F.2    Marquardt, J.L.3    Tjandra, N.4    Bax, A.5
  • 38
    • 68349093958 scopus 로고    scopus 로고
    • TALOS plus: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
    • Shen, Y., Delaglio, F., Cornilescu, G., and Bax, A. (2009) TALOS plus: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44, 213-223
    • (2009) J. Biomol. NMR , vol.44 , pp. 213-223
    • Shen, Y.1    Delaglio, F.2    Cornilescu, G.3    Bax, A.4
  • 39
    • 0034852135 scopus 로고    scopus 로고
    • Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage
    • Zweckstetter, M. and Bax, A. (2001) Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage J. Biomol. NMR 20, 365-377
    • (2001) J. Biomol. NMR , vol.20 , pp. 365-377
    • Zweckstetter, M.1    Bax, A.2
  • 42
    • 0028941877 scopus 로고
    • Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme
    • Mandel, A. M., Akke, M., and Palmer, A. G. (1995) Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme J. Mol. Biol. 246, 144-163
    • (1995) J. Mol. Biol. , vol.246 , pp. 144-163
    • Mandel, A.M.1    Akke, M.2    Palmer, A.G.3
  • 43
    • 0038068865 scopus 로고    scopus 로고
    • FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data
    • Cole, R. and Loria, J. P. (2003) FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data J. Biomol. NMR 26, 203-213
    • (2003) J. Biomol. NMR , vol.26 , pp. 203-213
    • Cole, R.1    Loria, J.P.2
  • 45
    • 0031989849 scopus 로고    scopus 로고
    • Accurate quantitation of water-amide proton exchange rates using the Phase-Modulated CLEAN chemical EXchange (CLEANEX-PM) approach with a Fast-HSQC (FHSQC) detection scheme
    • Hwang, T. L., van Zijl, P. C. M., and Mori, S. (1998) Accurate quantitation of water-amide proton exchange rates using the Phase-Modulated CLEAN chemical EXchange (CLEANEX-PM) approach with a Fast-HSQC (FHSQC) detection scheme J. Biomol. NMR 11, 221-226
    • (1998) J. Biomol. NMR , vol.11 , pp. 221-226
    • Hwang, T.L.1    Van Zijl, P.C.M.2    Mori, S.3
  • 46
    • 42449128777 scopus 로고    scopus 로고
    • Pressure-induced changes in the solution structure of the GB1 domain of protein G
    • Wilton, D. J., Tunnicliffe, R. B., Kamatari, Y. O., Akasaka, K., and Williamson, M. P. (2008) Pressure-induced changes in the solution structure of the GB1 domain of protein G Proteins 71, 1432-1440
    • (2008) Proteins , vol.71 , pp. 1432-1440
    • Wilton, D.J.1    Tunnicliffe, R.B.2    Kamatari, Y.O.3    Akasaka, K.4    Williamson, M.P.5
  • 48
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly improved protein chemical shift prediction
    • Han, B., Liu, Y., Ginzinger, S. W., and Wishart, D. S. (2011) SHIFTX2: Significantly improved protein chemical shift prediction J. Biomol. NMR 50, 43-57
    • (2011) J. Biomol. NMR , vol.50 , pp. 43-57
    • Han, B.1    Liu, Y.2    Ginzinger, S.W.3    Wishart, D.S.4
  • 49
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of Nuclear Magnetic Resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari, G. and Szabo, A. (1982) Model-free approach to the interpretation of Nuclear Magnetic Resonance relaxation in macromolecules. 1. Theory and range of validity J. Am. Chem. Soc. 104, 4546-4559
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 50
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
    • Lipari, G. and Szabo, A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results J. Am. Chem. Soc. 104, 4559-4570
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 51
    • 0141625302 scopus 로고    scopus 로고
    • Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation
    • Swanson, K. A., Kang, R. S., Stamenova, S. D., Hicke, L., and Radhakrishnan, I. (2003) Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation EMBO J. 22, 4597-4606
    • (2003) EMBO J. , vol.22 , pp. 4597-4606
    • Swanson, K.A.1    Kang, R.S.2    Stamenova, S.D.3    Hicke, L.4    Radhakrishnan, I.5
  • 52
    • 0027250665 scopus 로고
    • Primary structure effects on peptide group hydrogen exchange
    • Bai, Y. W., Milne, J. S., Mayne, L., and Englander, S. W. (1993) Primary structure effects on peptide group hydrogen exchange Proteins 17, 75-86
    • (1993) Proteins , vol.17 , pp. 75-86
    • Bai, Y.W.1    Milne, J.S.2    Mayne, L.3    Englander, S.W.4
  • 53
    • 0026460815 scopus 로고
    • Hydrogen exchange in native and alcohol forms of ubiquitin
    • Pan, Y. Q. and Briggs, M. S. (1992) Hydrogen exchange in native and alcohol forms of ubiquitin Biochemistry 31, 11405-11412
    • (1992) Biochemistry , vol.31 , pp. 11405-11412
    • Pan, Y.Q.1    Briggs, M.S.2
  • 54
    • 65249173891 scopus 로고    scopus 로고
    • The multiple layers of ubiquitin-dependent cell cycle control
    • Wickliffe, K., Williamson, A., Jin, L. Y., and Rape, M. (2009) The multiple layers of ubiquitin-dependent cell cycle control Chem. Rev. 109, 1537-1548
    • (2009) Chem. Rev. , vol.109 , pp. 1537-1548
    • Wickliffe, K.1    Williamson, A.2    Jin, L.Y.3    Rape, M.4
  • 55
    • 77953108542 scopus 로고    scopus 로고
    • The diversity of ubiquitin recognition: Hot spots and varied specificity
    • Winget, J. M. and Mayor, T. (2010) The diversity of ubiquitin recognition: Hot spots and varied specificity Mol. Cell 38, 627-635
    • (2010) Mol. Cell , vol.38 , pp. 627-635
    • Winget, J.M.1    Mayor, T.2
  • 56
    • 73449088337 scopus 로고    scopus 로고
    • Crystal structure of UbcH5b-ubiquitin intermediate: Insight into the formation of the self-assembled E2∼Ub conjugates
    • Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Tanaka, K., Wakatsuki, S., and Kato, K. (2010) Crystal structure of UbcH5b-ubiquitin intermediate: Insight into the formation of the self-assembled E2∼Ub conjugates Structure 18, 138-147
    • (2010) Structure , vol.18 , pp. 138-147
    • Sakata, E.1    Satoh, T.2    Yamamoto, S.3    Yamaguchi, Y.4    Yagi-Utsumi, M.5    Kurimoto, E.6    Tanaka, K.7    Wakatsuki, S.8    Kato, K.9
  • 58
    • 77649272589 scopus 로고    scopus 로고
    • Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain
    • Sgourakis, N. G., Patel, M. M., Garcia, A. E., Makhatadze, G. I., and McCallum, S. A. (2010) Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain J. Mol. Biol. 396, 1128-1144
    • (2010) J. Mol. Biol. , vol.396 , pp. 1128-1144
    • Sgourakis, N.G.1    Patel, M.M.2    Garcia, A.E.3    Makhatadze, G.I.4    McCallum, S.A.5
  • 59
    • 84861392508 scopus 로고    scopus 로고
    • Structural insights into the conformation and oligomerization of E2-ubiquitin conjugates
    • Page, R. C., Pruneda, J. N., Amick, J., Klevit, R. E., and Misra, S. (2012) Structural insights into the conformation and oligomerization of E2-ubiquitin conjugates Biochemistry 51, 4175-4187
    • (2012) Biochemistry , vol.51 , pp. 4175-4187
    • Page, R.C.1    Pruneda, J.N.2    Amick, J.3    Klevit, R.E.4    Misra, S.5


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