메뉴 건너뛰기




Volumn 43, Issue 31, 2004, Pages 10237-10246

Cold shock domain of the human Y-box protein YB-1. Backbone dynamics and equilibrium between the native state and a partially unfolded state

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DIMERS; NUCLEAR MAGNETIC RESONANCE; STRUCTURE (COMPOSITION);

EID: 3543144798     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049524s     Document Type: Article
Times cited : (18)

References (39)
  • 1
    • 0030217514 scopus 로고    scopus 로고
    • Nuclear magnetic resonance studies of biopolymer dynamics
    • Palmer, A. G., III, Williams J., and McDermott A. (1996) Nuclear magnetic resonance studies of biopolymer dynamics, J. Phys. Chem. 100, 13293-13310.
    • (1996) J. Phys. Chem. , vol.100 , pp. 13293-13310
    • Palmer III, A.G.1    Williams, J.2    McDermott, A.3
  • 2
    • 0034984208 scopus 로고    scopus 로고
    • NMR probes of molecular dynamics: Overview and comparison with other techniques
    • Palmer, A. G., III (2001) NMR probes of molecular dynamics: overview and comparison with other techniques, Annu. Rev. Biophys. Biomol. Struct. 30, 129-155.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 129-155
    • Palmer III, A.G.1
  • 3
    • 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
  • 4
    • 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
  • 5
    • 0000660936 scopus 로고
    • Mapping of spectral density functions using heteronuclear NMR relaxation measurements
    • Peng, J. W., and Wagner, G. (1992) Mapping of spectral density functions using heteronuclear NMR relaxation measurements, J. Magn. Res. 98, 308-332.
    • (1992) J. Magn. Res. , vol.98 , pp. 308-332
    • Peng, J.W.1    Wagner, G.2
  • 7
    • 0028938022 scopus 로고
    • Protein backbone dynamics revealed by quasi-spectral density function analysis of the amide N-15 nuclei
    • Ishima, R., and Nagayama, K. (1995) Protein backbone dynamics revealed by quasi-spectral density function analysis of the amide N-15 nuclei, Biochemistry 34, 3162-3171.
    • (1995) Biochemistry , vol.34 , pp. 3162-3171
    • Ishima, R.1    Nagayama, K.2
  • 8
    • 0002530134 scopus 로고
    • α vector dynamics using dipolar relaxation rates measured at several magnetic fields
    • α vector dynamics using dipolar relaxation rates measured at several magnetic fields, J. Magn. Reson., Ser. B 111, 23-30.
    • (1995) J. Magn. Reson., Ser. B , vol.111 , pp. 23-30
    • Ishima, R.1    Nagayama, K.2
  • 9
    • 0029872895 scopus 로고    scopus 로고
    • Internal mobility in the partially folded DNA binding and dimerisation domains of GAL-4: NMR analysis of the N-H spectral density functions
    • Lefèvre, J.-F., Dayie, K. T., Peng, J. W., and Wagner, G. (1996) Internal mobility in the partially folded DNA binding and dimerisation domains of GAL-4: NMR analysis of the N-H spectral density functions, Biochemistry 35, 2674-2686.
    • (1996) Biochemistry , vol.35 , pp. 2674-2686
    • Lefèvre, J.-F.1    Dayie, K.T.2    Peng, J.W.3    Wagner, G.4
  • 10
    • 0028951040 scopus 로고
    • Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer
    • Farrow, N. A., Zhang, O., Forman-Kay, J. D., and Kay, L. E. (1995) Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer, Biochemistry 34, 868-878.
    • (1995) Biochemistry , vol.34 , pp. 868-878
    • Farrow, N.A.1    Zhang, O.2    Forman-Kay, J.D.3    Kay, L.E.4
  • 11
    • 0031027137 scopus 로고    scopus 로고
    • Characterization of the backbone dynamics of folded and denatured states of an SH3 domain
    • Farrow, N. A., Zhang, O., Forman-Kay, J. D., and Kay, L. (1997) Characterization of the backbone dynamics of folded and denatured states of an SH3 domain, Biochemistry 36, 2390-2402.
    • (1997) Biochemistry , vol.36 , pp. 2390-2402
    • Farrow, N.A.1    Zhang, O.2    Forman-Kay, J.D.3    Kay, L.4
  • 12
    • 0027988297 scopus 로고
    • Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease
    • Alexandrescu, A. T., and Shortle, D. (1994) Backbone dynamics of a highly disordered 131 residue fragment of staphylococcal nuclease, J. Mol. Biol. 242, 527-546.
    • (1994) J. Mol. Biol. , vol.242 , pp. 527-546
    • Alexandrescu, A.T.1    Shortle, D.2
  • 13
    • 0031565731 scopus 로고    scopus 로고
    • Comprehensive NOE characterization of a partially folded large fragment of Staphylococcal nuclease Δ131Δ, using NMR methods with improved resolution
    • Zhang, O., Kay, L. E., Shortle, D., and Forman-Kay, J. D. (1997) Comprehensive NOE characterization of a partially folded large fragment of Staphylococcal nuclease Δ131Δ, using NMR methods with improved resolution, J. Mol. Biol. 272, 9-20.
    • (1997) J. Mol. Biol. , vol.272 , pp. 9-20
    • Zhang, O.1    Kay, L.E.2    Shortle, D.3    Forman-Kay, J.D.4
  • 16
    • 0027479161 scopus 로고
    • OB (oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences
    • Murzin, A. G. (1993) OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences, EMBO J. 12, 861-867.
    • (1993) EMBO J. , vol.12 , pp. 861-867
    • Murzin, A.G.1
  • 18
    • 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
  • 19
    • 0000041361 scopus 로고
    • A common sense approach to peak-picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams
    • Garrett, D. S., Powers, R., Gronenborn, A. M., and Clore, G. M (1991) A common sense approach to peak-picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams, J. Magn. Reson. 95, 214-220.
    • (1991) J. Magn. Reson. , vol.95 , pp. 214-220
    • Garrett, D.S.1    Powers, R.2    Gronenborn, A.M.3    Clore, G.M.4
  • 20
    • 0001882103 scopus 로고
    • Studies of slow conformational equilibria in macromolecules by exchange of heteronuclear longitudinal 2-spin-order in a 2D difference correlation experiment
    • Wider, G., Neri, D., and Wüthrich, K. (1991) Studies of slow conformational equilibria in macromolecules by exchange of heteronuclear longitudinal 2-spin-order in a 2D difference correlation experiment, J. Biomol. NMR 1, 93-98.
    • (1991) J. Biomol. NMR , vol.1 , pp. 93-98
    • Wider, G.1    Neri, D.2    Wüthrich, K.3
  • 22
    • 34249763437 scopus 로고
    • Backbone dynamics of ribonuclease T1 and its complex with 2′GMP studied by two-dimensional heteronuclear NMR spectroscopy
    • Fushman, D., Weisemann, R., Thüringer, H., and Riiterjans, H. (1994) Backbone dynamics of ribonuclease T1 and its complex with 2′GMP studied by two-dimensional heteronuclear NMR spectroscopy, J. Biomol. NMR 4, 61-78.
    • (1994) J. Biomol. NMR , vol.4 , pp. 61-78
    • Fushman, D.1    Weisemann, R.2    Thüringer, H.3    Riiterjans, H.4
  • 24
    • 0032483047 scopus 로고    scopus 로고
    • Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: Evidence for conformational dynamics in the single-stranded RNA-binding site
    • Feng, W., Tejero, R., Zimmerman, D. E., Inouye, M., and Montelione, G. T. (1998) Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site, Biochemistry 37, 10881-10896.
    • (1998) Biochemistry , vol.37 , pp. 10881-10896
    • Feng, W.1    Tejero, R.2    Zimmerman, D.E.3    Inouye, M.4    Montelione, G.T.5
  • 25
    • 0030018401 scopus 로고    scopus 로고
    • The solution structure of the synthetic circular peptide CGVSRQGKPYC: NMR studies of the folding of a synthetic model for the DNA-binding loop of the ssDNA-binding protein encoded by gene V of phage M13
    • Rietman, B. H., Folkers, P. J. M., Folmer, R. H. A., Tesser, G. I., and Hilbers, C. W. (1996) The solution structure of the synthetic circular peptide CGVSRQGKPYC: NMR studies of the folding of a synthetic model for the DNA-binding loop of the ssDNA-binding protein encoded by gene V of phage M13, Eur. J. Biochem. 238, 706-713.
    • (1996) Eur. J. Biochem. , vol.238 , pp. 706-713
    • Rietman, B.H.1    Folkers, P.J.M.2    Folmer, R.H.A.3    Tesser, G.I.4    Hilbers, C.W.5
  • 26
    • 0142149116 scopus 로고    scopus 로고
    • Detection of nano-second internal motion and determination of overall tumbling times independent of the time scale of internal motion in proteins from NMR relaxation data
    • Larson, G., Martinez, G., Schleucher, J., and Wijmenga, S. S. (2003) Detection of nano-second internal motion and determination of overall tumbling times independent of the time scale of internal motion in proteins from NMR relaxation data, J. Biomol. NMR, 27, 291-312.
    • (2003) J. Biomol. NMR , vol.27 , pp. 291-312
    • Larson, G.1    Martinez, G.2    Schleucher, J.3    Wijmenga, S.S.4
  • 27
    • 0030759665 scopus 로고    scopus 로고
    • Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea
    • Schwalbe, H., Fiebig, K. M., Buck, M., Jones, J. A., Grimshaw, S. B., Spencer, A., Glaser, S. J., Smith, L. J., and Dobson, C. M. (1997) Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea, Biochemistry 36, 8977-8991.
    • (1997) Biochemistry , vol.36 , pp. 8977-8991
    • Schwalbe, H.1    Fiebig, K.M.2    Buck, M.3    Jones, J.A.4    Grimshaw, S.B.5    Spencer, A.6    Glaser, S.J.7    Smith, L.J.8    Dobson, C.M.9
  • 29
    • 0031937871 scopus 로고    scopus 로고
    • Stability of folding properties of a model β-sheet protein. Escherichia coli CspA
    • Reid, K. L., Rodriguez, H. M., Hillier, B. J., and Gregoret, L. M. (1998) Stability of folding properties of a model β-sheet protein, Escherichia coli CspA. Protein Sci. 7, 470-479.
    • (1998) Protein Sci. , vol.7 , pp. 470-479
    • Reid, K.L.1    Rodriguez, H.M.2    Hillier, B.J.3    Gregoret, L.M.4
  • 30
    • 0034615784 scopus 로고    scopus 로고
    • Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein
    • Mueller, U., Perl, D., Schmid, F. X., and Heinemann, U. (2000) Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein, J. Mol. Biol. 297, 295-988.
    • (2000) J. Mol. Biol. , vol.297 , pp. 295-988
    • Mueller, U.1    Perl, D.2    Schmid, F.X.3    Heinemann, U.4
  • 31
    • 0031890195 scopus 로고    scopus 로고
    • Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins
    • Perl, D., Welker, C., Schindler, T., Schröder, K., Marahiel, M. A., Jaenicke, R., and Schmid, F. X. (1998) Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins, Nat. Struct. Biol. 5, 229-235.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 229-235
    • Perl, D.1    Welker, C.2    Schindler, T.3    Schröder, K.4    Marahiel, M.A.5    Jaenicke, R.6    Schmid, F.X.7
  • 32
    • 0030450051 scopus 로고    scopus 로고
    • Thermodynamic properties of an extremely rapid protein folding reaction
    • Schindler, T., and Schmid, F. X. (1996) Thermodynamic properties of an extremely rapid protein folding reaction, Biochemistry 35, 16833-16842.
    • (1996) Biochemistry , vol.35 , pp. 16833-16842
    • Schindler, T.1    Schmid, F.X.2
  • 33
    • 0034100848 scopus 로고    scopus 로고
    • Two exposed amino acid residues confer thermostability on a cold shock protein
    • Perl, D., Mueller, U., Heinemann, U., and Schmid, F. X. (2000) Two exposed amino acid residues confer thermostability on a cold shock protein, Nat. Struct. Biol. 7, 380-383.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 380-383
    • Perl, D.1    Mueller, U.2    Heinemann, U.3    Schmid, F.X.4
  • 34
    • 0141725721 scopus 로고    scopus 로고
    • 15N relaxation study of the cold shock protein CspB at various solvent viscosities
    • 15N relaxation study of the cold shock protein CspB at various solvent viscosities, J. Biomol. NMR. 27, 221-234.
    • (2003) J. Biomol. NMR , vol.27 , pp. 221-234
    • Zeeb, M.1    Jacob, M.H.2    Schindler, T.3    Balbach, J.4
  • 37
    • 0009586942 scopus 로고    scopus 로고
    • Understanding protein folding via free-energy surfaces from theory and experiment
    • Dinner, A. R., Šali, A., Smith, L. J., Dobson, C. M., and Karplus, M. (2000) Understanding protein folding via free-energy surfaces from theory and experiment, Trends Biochem. Sci. 331-339.
    • (2000) Trends Biochem. Sci. , pp. 331-339
    • Dinner, A.R.1    Šali, A.2    Smith, L.J.3    Dobson, C.M.4    Karplus, M.5
  • 38
    • 0036183221 scopus 로고    scopus 로고
    • Im7-folding mechanism: Misfolding on a path to the native state
    • Capaldi, A. P., Kleanthous, C., and Radford, S. E. (2002) Im7-folding mechanism: misfolding on a path to the native state, Nat. Struct. Biol. 9, 209-216.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 209-216
    • Capaldi, A.P.1    Kleanthous, C.2    Radford, S.E.3
  • 39
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Konradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures, J. Mol. Graphics 14, 51-55.
    • (1996) J. Mol. Graphics , vol.14 , pp. 51-55
    • Konradi, R.1    Billeter, M.2    Wüthrich, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.