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Volumn 62, Issue 2, 2006, Pages 501-508

Methyl dynamics for understanding hydrophobic core packing of dynamically different motifs of double-stranded RNA binding domain of protein kinase R

Author keywords

2D 13C 1H HSQC; dsRBD; Hydrophobic core packing; Methyl dynamics; NOE; PKR; Protein dynamics; Relaxation studies; T 2; T1

Indexed keywords

AMINO ACID; DOUBLE STRANDED RNA; METHYL GROUP; PROTEIN KINASE R;

EID: 30144438485     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20793     Document Type: Article
Times cited : (5)

References (42)
  • 1
    • 0034675856 scopus 로고    scopus 로고
    • A dynamically tuned double-stranded RNA binding mechanism for the activation of antiviral kinase PKR
    • Nanduri S, Rahman F, Williams BRG, Qin J. A dynamically tuned double-stranded RNA binding mechanism for the activation of antiviral kinase PKR. EMBO J 2000;19:5567-5574.
    • (2000) EMBO J , vol.19 , pp. 5567-5574
    • Nanduri, S.1    Rahman, F.2    Williams, B.R.G.3    Qin, J.4
  • 3
    • 0020855355 scopus 로고
    • Hydrogen exchange and structural dynamics of proteins and nucleic acids
    • Englander SW, Kallenbach NR. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 1983;16:521-655.
    • (1983) Q Rev Biophys , vol.16 , pp. 521-655
    • Englander, S.W.1    Kallenbach, N.R.2
  • 4
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H, Sligar SG, Wolynes PG. The energy landscapes and motions of proteins. Science 1991;254:1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 6
    • 0020698476 scopus 로고
    • Dynamics of proteins: Elements and function
    • Karplus M, McCammon JA. Dynamics of proteins: elements and function. Annu Rev Biochem 1983;52:263-300.
    • (1983) Annu Rev Biochem , vol.52 , pp. 263-300
    • Karplus, M.1    McCammon, J.A.2
  • 7
    • 0031853060 scopus 로고    scopus 로고
    • Protein dynamics from NMR
    • Kay LE. Protein dynamics from NMR. Nat Struct Biol NMR Suppl 1998;5:513-517.
    • (1998) Nat Struct Biol NMR Suppl , vol.5 , pp. 513-517
    • Kay, L.E.1
  • 8
    • 0030778008 scopus 로고    scopus 로고
    • Probing molecular motion by NMR
    • Palmer AG. Probing molecular motion by NMR. Curr Opin Struct Biol 1997;7:732-737.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 732-737
    • Palmer, A.G.1
  • 9
    • 0024429207 scopus 로고
    • NMR studies of mobility within protein structure
    • Williams RJP. NMR studies of mobility within protein structure. Eur J Biochem 1989;183:479-497.
    • (1989) Eur J Biochem , vol.183 , pp. 479-497
    • Williams, R.J.P.1
  • 10
    • 0022543092 scopus 로고
    • Backbone dynamics of a model membrane protein: Carbon-13 NMR spectroscopy of alanine methyl groups in detergent-solubilized M13 coat protein
    • Henry GD, Weiner JH, Sykes BD. Backbone dynamics of a model membrane protein: carbon-13 NMR spectroscopy of alanine methyl groups in detergent-solubilized M13 coat protein. Biochemistry 1986;25:590-598.
    • (1986) Biochemistry , vol.25 , pp. 590-598
    • Henry, G.D.1    Weiner, J.H.2    Sykes, B.D.3
  • 12
    • 0030473440 scopus 로고    scopus 로고
    • Insights into the local residual entropy of proteins provided by NMR relaxation
    • (a) Li Z, Raychaudhuri S, Wand AJ. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci 1996;5:2647-2650;
    • (1996) Protein Sci , vol.5 , pp. 2647-2650
    • Li, Z.1    Raychaudhuri, S.2    Wand, A.J.3
  • 17
    • 0035846624 scopus 로고    scopus 로고
    • Main chain and side chain dynamics of oxidized flavodoxin from Cyanobacterium anabaena
    • Liu W, Flynn PF, Fuentes EJ, Kranz JK, McCormick M, Wand AJ. Main chain and side chain dynamics of oxidized flavodoxin from Cyanobacterium anabaena. Biochemistry 2001;40:14744-14753.
    • (2001) Biochemistry , vol.40 , pp. 14744-14753
    • Liu, W.1    Flynn, P.F.2    Fuentes, E.J.3    Kranz, J.K.4    McCormick, M.5    Wand, A.J.6
  • 19
    • 0033620360 scopus 로고    scopus 로고
    • 13C NMR relaxation techniques for the study of protein methyl group dynamics in solution
    • 13C NMR relaxation techniques for the study of protein methyl group dynamics in solution. J Am Chem Soc 1999;121:2891-2902;
    • (1999) J Am Chem Soc , vol.121 , pp. 2891-2902
    • Lee, A.L.1    Flynn, P.F.2    Wand, A.J.3
  • 20
    • 0031154310 scopus 로고    scopus 로고
    • Improved labeling strategy for 13C relaxation measurements of methyl groups in proteins
    • (b) Lee AL, Urbauer JL, Wand AJ. Improved labeling strategy for 13C relaxation measurements of methyl groups in proteins. J Biomol NMR 1997;9:437-440.
    • (1997) J Biomol NMR , vol.9 , pp. 437-440
    • Lee, A.L.1    Urbauer, J.L.2    Wand, A.J.3
  • 23
    • 0034809982 scopus 로고    scopus 로고
    • Probing Slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: Application to methionine residues in a cavity mutant of T4 lysozyme
    • Skrynnikov NR, Mulder FAA, Hon B, Dahlquist FW, Kay LE. Probing Slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme. J Am Chem Soc 2001;123:4556-4566.
    • (2001) J Am Chem Soc , vol.123 , pp. 4556-4566
    • Skrynnikov, N.R.1    Mulder, F.A.A.2    Hon, B.3    Dahlquist, F.W.4    Kay, L.E.5
  • 24
    • 0037138654 scopus 로고    scopus 로고
    • Slow Internal dynamics in proteins: Application of nmr relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme
    • Mulder FAA, Hon B, Mittermaier A, Dahlquist FW, Kay LE. Slow Internal dynamics in proteins: application of nmr relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4. lysozyme. J Am Chem Soc 2002;124:1443-1451.
    • (2002) J Am Chem Soc , vol.124 , pp. 1443-1451
    • Mulder, F.A.A.1    Hon, B.2    Mittermaier, A.3    Dahlquist, F.W.4    Kay, L.E.5
  • 25
    • 0034767753 scopus 로고    scopus 로고
    • Antiviral actions of interferons
    • Samuel CE. Antiviral actions of interferons. Clin Microbiol Rev 2001;14:778-809.
    • (2001) Clin Microbiol Rev , vol.14 , pp. 778-809
    • Samuel, C.E.1
  • 26
    • 0025298202 scopus 로고
    • Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon
    • Meurs E, Chong K, Galabru J, Thomas NS, Kerr IM, Williams BRG, Hovanessian AG. Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon. Cell 1990;62:379-390.
    • (1990) Cell , vol.62 , pp. 379-390
    • Meurs, E.1    Chong, K.2    Galabru, J.3    Thomas, N.S.4    Kerr, I.M.5    Williams, B.R.G.6    Hovanessian, A.G.7
  • 29
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • (a) Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 1982;104:4546-4559;
    • (1982) J Am Chem Soc , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 30
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
    • (b) Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J Am Chem Soc 1982;104: 4559-4570.
    • (1982) J Am Chem Soc , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 31
    • 0028941877 scopus 로고
    • Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme
    • Mandel AM, Akke M, Palmer AG. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J Mol Biol 1995;246:144-163.
    • (1995) J Mol Biol , vol.246 , pp. 144-163
    • Mandel, A.M.1    Akke, M.2    Palmer, A.G.3
  • 32
    • 0029550886 scopus 로고
    • Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation
    • Tjandra N, Feller SE, Pastor RW, Bax A. Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation. J Am Chem Soc 1995;117:12562-12566.
    • (1995) J Am Chem Soc , vol.117 , pp. 12562-12566
    • Tjandra, N.1    Feller, S.E.2    Pastor, R.W.3    Bax, A.4
  • 33
    • 0026748968 scopus 로고
    • Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible
    • Barbato G, Ikura M, Kay LE, Pastor RW, Bax A. Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. Biochemistry 1992;31:5269-5278.
    • (1992) Biochemistry , vol.31 , pp. 5269-5278
    • Barbato, G.1    Ikura, M.2    Kay, L.E.3    Pastor, R.W.4    Bax, A.5
  • 34
    • 0030043573 scopus 로고    scopus 로고
    • Phosphotransfer and CheY-binding domains of the histidine autokinase CheA are joined by a flexible linker
    • Zhou H, McEvoy MM, Lowry DF, Swanson RV, Simon MI, Dahlquist FW. Phosphotransfer and CheY-binding domains of the histidine autokinase CheA are joined by a flexible linker. Biochemistry 1996;35:433-443.
    • (1996) Biochemistry , vol.35 , pp. 433-443
    • Zhou, H.1    McEvoy, M.M.2    Lowry, D.F.3    Swanson, R.V.4    Simon, M.I.5    Dahlquist, F.W.6
  • 36
    • 0031111153 scopus 로고    scopus 로고
    • Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation
    • Lee LK, Rance M, Chazin WJ, Palmer AG. Rotational diffusion anisotropy of proteins from simultaneous analysis of 15N and 13C alpha nuclear spin relaxation. J Biomol NMR 1997;9:287-298.
    • (1997) J Biomol NMR , vol.9 , pp. 287-298
    • Lee, L.K.1    Rance, M.2    Chazin, W.J.3    Palmer, A.G.4
  • 37
    • 0032134594 scopus 로고    scopus 로고
    • 1H, 13C, 15N resonance assignment of the 20 kDa double stranded RNA binding domain of PKR
    • (a) Nanduri S, Carpick B, Yang Y, Williams BRG, Qin J. 1H, 13C, 15N resonance assignment of the 20 kDa double stranded RNA binding domain of PKR. J Biomol NMR 1998;12:349-351;
    • (1998) J Biomol NMR , vol.12 , pp. 349-351
    • Nanduri, S.1    Carpick, B.2    Yang, Y.3    Brg, W.4    Qin, J.5
  • 38
    • 0032530310 scopus 로고    scopus 로고
    • Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation
    • (b) Nanduri S, Carpick BW, Yang Y, Williams BRG, Qin J. Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation. EMBOJ 1998;17:5458-5465.
    • (1998) EMBOJ , vol.17 , pp. 5458-5465
    • Nanduri, S.1    Carpick, B.W.2    Yang, Y.3    Brg, W.4    Qin, J.5
  • 39
    • 0006925492 scopus 로고
    • Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity
    • Kay LE, Keifer EP, Saarinen T. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Am Chem Soc 1992;114:10663-10665.
    • (1992) J Am Chem Soc , vol.114 , pp. 10663-10665
    • Kay, L.E.1    Keifer, E.P.2    Saarinen, T.3
  • 40
    • 44949267857 scopus 로고
    • Improved proton-detected heteronuclear correlation using gradient-enhanced z and zz filters
    • John BK, Plant D, Hurd RE. Improved proton-detected heteronuclear correlation using gradient-enhanced z and zz filters. J Mag Res A 1993;101:113-117.
    • (1993) J Mag Res A , vol.101 , pp. 113-117
    • John, B.K.1    Plant, D.2    Hurd, R.E.3
  • 42
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R, Billerter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.
    • (1996) J Mol Graph , vol.14 , pp. 51-55
    • Koradi, R.1    Billerter, M.2    Wuthrich, K.3


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