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Volumn 411, Issue 5, 2011, Pages 1037-1048

A hydrogen bond regulates slow motions in ubiquitin by modulating a β-turn flip

Author keywords

dihedral angles; millisecond motions; slow dynamics; turn flip

Indexed keywords

AMIDE; ARGININE; ASPARTIC ACID; GLUTAMINE; HYDROGEN; ISOLEUCINE; THREONINE; UBIQUITIN;

EID: 80051666404     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.06.044     Document Type: Article
Times cited : (23)

References (49)
  • 1
    • 0033566242 scopus 로고    scopus 로고
    • Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F
    • DOI 10.1038/22357
    • Feher V.A., and Cavanagh J. Millisecond-timescale motions contribute to the function of the bacterial response regulator protein Spo0F Nature 400 1999 289 293 (Pubitemid 29334147)
    • (1999) Nature , vol.400 , Issue.6741 , pp. 289-293
    • Feher, V.A.1    Cavanagh, J.2
  • 2
    • 40549133186 scopus 로고    scopus 로고
    • Characterization of enzyme motions by solution NMR relaxation dispersion
    • Loria P.J., Berlow R.B., and Watt E.D. Characterization of enzyme motions by solution NMR relaxation dispersion Acc. Chem. Res. 41 2008 214 221
    • (2008) Acc. Chem. Res. , vol.41 , pp. 214-221
    • Loria, P.J.1    Berlow, R.B.2    Watt, E.D.3
  • 3
    • 66349134420 scopus 로고    scopus 로고
    • Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase
    • Wang Y., Berlow R.B., and Loria P.J. Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase Biochemistry 48 2009 4546 4556
    • (2009) Biochemistry , vol.48 , pp. 4546-4556
    • Wang, Y.1    Berlow, R.B.2    Loria, P.J.3
  • 4
    • 70350348011 scopus 로고    scopus 로고
    • NMR spectroscopy brings invisible protein states into focus
    • Baldwin A.J., and Kay L.E. NMR spectroscopy brings invisible protein states into focus Nat. Chem. Biol. 5 2009 808 814
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 808-814
    • Baldwin, A.J.1    Kay, L.E.2
  • 7
    • 34547935214 scopus 로고    scopus 로고
    • 2H-exchange NMR Spectroscopy
    • DOI 10.1016/j.jmb.2007.06.012, PII S0022283607007942
    • Korzhnev D.M., Religa T.L., Lundstrom P., Fersht A.R., and Kay L.E. The folding pathway of an FF domain: characterization of an on-pathway intermediate state under folding conditions by (15)N, (13)C(alpha) and (13)C-methyl relaxation dispersion and (1)H/(2)H-exchange NMR spectroscopy J. Mol. Biol. 372 2007 497 512 (Pubitemid 47267947)
    • (2007) Journal of Molecular Biology , vol.372 , Issue.2 , pp. 497-512
    • Korzhnev, D.M.1    Religa, T.L.2    Lundstrom, P.3    Fersht, A.R.4    Kay, L.E.5
  • 9
    • 33646835410 scopus 로고    scopus 로고
    • HIV-1 Tat is a natively unfolded protein: The solution conformation and dynamics of reduced HIV-1 Tat-(1-72) by NMR spectroscopy
    • DOI 10.1074/jbc.M510748200
    • Shojania S., and O'Neil J. HIV-1 Tat is a natively unfolded protein. The solution conformation and dynamics of reduced HIV-1 Tat-(1-72) by NMR spectroscopy J. Biol. Chem. 281 2006 8347 8356 (Pubitemid 43847935)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.13 , pp. 8347-8356
    • Shojania, S.1    O'Neil, J.D.2
  • 10
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr D.D., Nussinov R., and Wright P.E. The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 5 2009 789 796
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 11
    • 21244440196 scopus 로고    scopus 로고
    • Conservation of μs-ms enzyme motions in the apo- and substrate-mimicked state
    • DOI 10.1021/ja0514949
    • Beach H., Cole R., Gill M.L., and Loria J.P. Conservation of μs-ms enzyme motions in the apo- and substrate-mimicked state J. Am. Chem. Soc. 127 2005 9167 9176 (Pubitemid 40897609)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.25 , pp. 9167-9176
    • Beach, H.1    Cole, R.2    Gill, M.L.3    Loria, J.P.4
  • 14
    • 77955785905 scopus 로고    scopus 로고
    • Probing slow protein dynamics by adiabatic R (1rho) and R (2rho) NMR experiments
    • Mangia S., Traaseth N.J., Veglia G., Garwood M., and Michaeli S. Probing slow protein dynamics by adiabatic R (1rho) and R (2rho) NMR experiments J. Am. Chem. Soc. 132 2010 9979 9981
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 9979-9981
    • Mangia, S.1    Traaseth, N.J.2    Veglia, G.3    Garwood, M.4    Michaeli, S.5
  • 17
    • 34548098038 scopus 로고    scopus 로고
    • Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories
    • Pan P.W., Dickson R.J., Gordon H.L., Rothstein S.M., and Tanaka S. Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories J. Chem. Phys. 122 2005 34904 34914
    • (2005) J. Chem. Phys. , vol.122 , pp. 34904-34914
    • Pan, P.W.1    Dickson, R.J.2    Gordon, H.L.3    Rothstein, S.M.4    Tanaka, S.5
  • 19
    • 1042288192 scopus 로고    scopus 로고
    • Evidence for Slow Motion in Proteins by Multiple Refocusing of Heteronuclear Nitrogen/Proton Multiple Quantum Coherences in NMR
    • DOI 10.1021/ja0386243
    • Dittmer J., and Bodenhausen G. Evidence for slow motion in proteins by multiple refocusing of heteronuclear nitrogen/proton multiple quantum coherences in NMR J. Am. Chem. Soc. 126 2004 1314 1315 (Pubitemid 38200784)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.5 , pp. 1314-1315
    • Dittmer, J.1    Bodenhausen, G.2
  • 20
    • 70450184385 scopus 로고    scopus 로고
    • Selective characterization of microsecond motions in proteins by NMR relaxation
    • Hansen D.F., Feng H., Zhou Z., Bai Y., and Kay L.E. Selective characterization of microsecond motions in proteins by NMR relaxation J. Am. Chem. Soc. 131 2009 16257 16265
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 16257-16265
    • Hansen, D.F.1    Feng, H.2    Zhou, Z.3    Bai, Y.4    Kay, L.E.5
  • 21
    • 0034738040 scopus 로고    scopus 로고
    • Ubiquitin backbone motion studied via NH(N)-C'C(α) dipolar-dipolar and C'-C'Cα/NH(N) CSA-dipolar cross-correlated relaxation
    • DOI 10.1021/ja993845n
    • Carlomagno R., Maurer M., Hennig M., and Griesinger C. Ubiquitin backbone motion studied via NHN-C′ C-alpha dipolar-dipolar and C′-C′ C-alpha/NHN CSA-dipolar cross-correlated relaxation J. Am. Chem. Soc. 122 2000 5105 5113 (Pubitemid 30354275)
    • (2000) Journal of the American Chemical Society , vol.122 , Issue.21 , pp. 5105-5113
    • Carlomagno, T.1    Maurer, M.2    Hennig, M.3    Griesinger, C.4
  • 22
    • 1242272916 scopus 로고    scopus 로고
    • Probing slow backbone dynamics in proteins using TROSY-based experiments to detec cross-correlated time-modulation of isotropic chemicals shifts
    • DOI 10.1023/B:JNMR.0000013705.98136.99
    • Majumdar A., and Ghose R. Probing slow backbone dynamics in proteins using TROSY-based experiments to detect cross-correlated time-modulation of isotropic chemical shifts J. Biomol. NMR 28 2004 213 227 (Pubitemid 38220170)
    • (2004) Journal of Biomolecular NMR , vol.28 , Issue.3 , pp. 213-227
    • Majumdar, A.1    Ghose, R.2
  • 23
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • DOI 10.1016/0263-7855(96)00009-4
    • Koradi R., Billeter M., and Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graphics 14 1996 51 55 (Pubitemid 26152976)
    • (1996) Journal of Molecular Graphics , vol.14 , Issue.1 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 24
    • 0028122183 scopus 로고
    • Transient hydrogen bonds identified on the surface of the NMR solution structure of hirudin
    • Szyperki T., Antuch W., Schick M., Betz A., Stone S.R., and Wuthrich K. Transient hydrogen bonds identified on the surface of the NMR solution structure of hirudin Biochemistry 33 1994 9393 9410
    • (1994) Biochemistry , vol.33 , pp. 9393-9410
    • Szyperki, T.1    Antuch, W.2    Schick, M.3    Betz, A.4    Stone, S.R.5    Wuthrich, K.6
  • 25
    • 0037129945 scopus 로고    scopus 로고
    • Electrostatic interactions in ubiquitin: Stabilization of carboxylates by lysine amino groups
    • DOI 10.1021/bi025571d
    • Sundd M., Iverson M., Ibarra-Molero B., Sanchez-Ruiz J.M., and Robertson A.D. Electrostatic interactions in ubiquitin. Stabilization of carboxylates by lysine amino groups Biochemistry 41 2002 7586 7596 (Pubitemid 34627785)
    • (2002) Biochemistry , vol.41 , Issue.24 , pp. 7586-7596
    • Sundd, M.1    Iverson, N.2    Ibarra-Molero, B.3    Sanchez-Ruiz, J.M.4    Robertson, A.D.5
  • 26
    • 0041324868 scopus 로고    scopus 로고
    • Rearrangement of charge-charge interactions in variant ubiquitins as detected by double-mutant cycles and NMR
    • DOI 10.1016/S0022-2836(03)00995-1
    • Sundd M., and Robertson A.D. Rearrangement of charge-charge interactions in variant ubiquitins as detected by double mutant cycles and NMR J. Mol. Biol. 332 2003 927 936 (Pubitemid 37101378)
    • (2003) Journal of Molecular Biology , vol.332 , Issue.4 , pp. 927-936
    • Sundd, M.1    Robertson, A.D.2
  • 27
    • 0037114648 scopus 로고    scopus 로고
    • 13Cβ chemical shifts in peptides using density functional theory
    • DOI 10.1002/bip.10276
    • 13C′ chemical shifts in peptides using density functional theory Biopolymers 65 2002 408 423 (Pubitemid 35423737)
    • (2002) Biopolymers , vol.65 , Issue.6 , pp. 408-423
    • Xu, X.-P.1    Case, D.A.2
  • 28
    • 0025046144 scopus 로고
    • Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
    • DOI 10.1021/ja00168a070
    • Clore G.M., Szabo A., Bax A., Kay L.E., Driscoll P.C., and Gronenborn A.M. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic resonance of proteins J. Am. Chem. Soc. 112 1990 4989 4991 (Pubitemid 20285925)
    • (1990) Journal of the American Chemical Society , vol.112 , Issue.12 , pp. 4989-4991
    • Clore, G.M.1    Szabo, A.2    Bax, A.3    Kay, L.E.4    Driscoll, P.C.5    Gronenborn, A.M.6
  • 29
    • 0038068865 scopus 로고    scopus 로고
    • FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data
    • DOI 10.1023/A:1023808801134
    • Cole R., and Loria P.J. FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data J. Biomol. NMR 26 2003 203 213 (Pubitemid 36758441)
    • (2003) Journal of Biomolecular NMR , vol.26 , Issue.3 , pp. 203-213
    • Cole, R.1    Loria, J.P.2
  • 30
    • 33947660087 scopus 로고    scopus 로고
    • Temperature dependence of fast dynamics in proteins
    • Song X.J., Flynn P.F., Sharp K.A., and Wand J. Temperature dependence of fast dynamics in proteins Biophys. J. 92 2007 L43 L45
    • (2007) Biophys. J. , vol.92
    • Song, X.J.1    Flynn, P.F.2    Sharp, K.A.3    Wand, J.4
  • 32
    • 0028173780 scopus 로고
    • Rules for alpha-helix termination by glycine
    • Aurora R., Srinivasan R., and Rose G.D. Rules for alpha-helix termination by glycine Science 264 1994 1126 1130 (Pubitemid 2080614)
    • (1994) Science , vol.264 , Issue.5162 , pp. 1126-1130
    • Aurora, R.1    Srinivasan, R.2    Rose, G.D.3
  • 33
    • 68349093958 scopus 로고    scopus 로고
    • TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
    • Shen Y., Delaglio F., Cornilescu G., and Bax A. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts J. Biomol. NMR 44 2009 213 223
    • (2009) J. Biomol. NMR , vol.44 , pp. 213-223
    • Shen, Y.1    Delaglio, F.2    Cornilescu, G.3    Bax, A.4
  • 34
    • 34548423250 scopus 로고    scopus 로고
    • a Values, Ion Pairs, Hydrogen Bonding, and the pH-dependence of Folding the Hyperthermophile Proteins Sac7d and Sso7d
    • DOI 10.1016/j.jmb.2007.06.089, PII S0022283607008972
    • a values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d J. Mol. Biol. 372 2007 992 1008 (Pubitemid 47368346)
    • (2007) Journal of Molecular Biology , vol.372 , Issue.4 , pp. 992-1008
    • Clark, A.T.1    Smith, K.2    Muhandiram, R.3    Edmondson, S.P.4    Shriver, J.W.5
  • 35
    • 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., and McDermott A. The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch Protein Sci. 20 2011 630 639
    • (2011) Protein Sci. , vol.20 , pp. 630-639
    • Huang, K.Y.1    Amodeo, G.A.2    Tong, L.3    McDermott, A.4
  • 36
    • 34547427659 scopus 로고    scopus 로고
    • The ubiquitin protein: Chance or design?
    • Truman R. The ubiquitin protein: chance or design? J. Creat. 19 2005 116 127
    • (2005) J. Creat. , vol.19 , pp. 116-127
    • Truman, R.1
  • 37
    • 0032545165 scopus 로고    scopus 로고
    • Conformational interconversions in peptide β-turns: Analysis of turns in proteins and computational estimates of barriers
    • DOI 10.1006/jmbi.1998.2154
    • Gunasekharan K., Gomathi L., Ramakrishnan C., Chandrasekhar J., and Balaram P. Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers J. Mol. Biol. 284 1998 1505 1516 (Pubitemid 28566084)
    • (1998) Journal of Molecular Biology , vol.284 , Issue.5 , pp. 1505-1516
    • Gunasekaran, K.1    Gomathi, L.2    Ramakrishnan, C.3    Chandrasekhar, J.4    Balaram, P.5
  • 38
    • 0034769527 scopus 로고    scopus 로고
    • Peptide-plane flipping in proteins
    • DOI 10.1110/ps.23101
    • Hayward S. Peptide-plane flipping in proteins Protein Sci. 10 2001 2219 2227 (Pubitemid 32988639)
    • (2001) Protein Science , vol.10 , Issue.11 , pp. 2219-2227
    • Hayward, S.1
  • 39
    • 0038682826 scopus 로고    scopus 로고
    • Dipolar couplings in multiple alignments suggest α helical motion in ubiquitin
    • DOI 10.1021/ja029816l
    • Meiler J., Peti W., and Griesinger C. Dipolar couplings in multiple alignments suggest a helical motion in ubiquitin J. Am. Chem. Soc. 125 2003 8072 8073 (Pubitemid 36828551)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.27 , pp. 8072-8073
    • Meiler, J.1    Peti, W.2    Griesinger, C.3
  • 40
    • 72249104272 scopus 로고    scopus 로고
    • Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups
    • Vogeli B., Segawa T.F., Leitz D., Sobol A., Choutko A., and Trzesniak D. Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups J. Am. Chem. Soc. 131 2009 17215 17225
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17215-17225
    • Vogeli, B.1    Segawa, T.F.2    Leitz, D.3    Sobol, A.4    Choutko, A.5    Trzesniak, D.6
  • 41
    • 49549117842 scopus 로고    scopus 로고
    • Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies
    • Newton K., Matsumoto M.L., Wertz I.E., Kirkpatrick D.S., Lill J.R., and Tan J. Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies Cell 134 2008 668 678
    • (2008) Cell , vol.134 , pp. 668-678
    • Newton, K.1    Matsumoto, M.L.2    Wertz, I.E.3    Kirkpatrick, D.S.4    Lill, J.R.5    Tan, J.6
  • 42
    • 33646036373 scopus 로고    scopus 로고
    • Crystal structure of the ubiquitin binding domains of Rabex-5 reveals two modes of interaction with ubiquitin
    • Penengo L., Mapelli M., Murachelli A.G., Confalonieri S., Magri L., and Musacchio A. Crystal structure of the ubiquitin binding domains of Rabex-5 reveals two modes of interaction with ubiquitin Cell 124 2006 1183 1195
    • (2006) Cell , vol.124 , pp. 1183-1195
    • Penengo, L.1    Mapelli, M.2    Murachelli, A.G.3    Confalonieri, S.4    Magri, L.5    Musacchio, A.6
  • 43
    • 78649292467 scopus 로고    scopus 로고
    • Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling
    • Bosanac I., Wertz I.E., Pan B., Yu C., Kusam S., and Lam C. Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling Mol. Cell 40 2010 548 557
    • (2010) Mol. Cell , vol.40 , pp. 548-557
    • Bosanac, I.1    Wertz, I.E.2    Pan, B.3    Yu, C.4    Kusam, S.5    Lam, C.6
  • 47
    • 0004040543 scopus 로고    scopus 로고
    • University of California, San Francisco, CA
    • Goddard, T. D. & Kneller, D. G. SPARKY 3, University of California, San Francisco, CA.
    • SPARKY 3
    • Goddard, T.D.1    Kneller, D.G.2
  • 49
    • 33845561778 scopus 로고
    • Calibration of methanol and ethylene glycol nuclear magnetic resonance thermometers
    • Raiford D.S., Fisk C.L., and Becker E.D. Calibration of methanol and ethylene glycol nuclear magnetic resonance thermometers Anal. Chem. 51 1979 2050 2051
    • (1979) Anal. Chem. , vol.51 , pp. 2050-2051
    • Raiford, D.S.1    Fisk, C.L.2    Becker, E.D.3


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