Mesodynamics in the SARS nucleocapsid measured by NMR field cycling

Journal of Biomolecular NMR

Volumn 45, Issue 1-2, 2009, Pages 217-225

  Clarkson, Michael W ^a   Lei, Ming ^a   Eisenmesser, Elan Z ^a   Labeikovsky, Wladimir ^a   Redfield, Alfred ^a   Kern, Dorothee ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

Collective motions; Dynamics; Field cycling

Indexed keywords

ARTICLE; CONTROLLED STUDY; EXPERIMENTAL MODEL; MAGNETIC FIELD; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN TRANSPORT; SARS CORONAVIRUS; SENSITIVITY ANALYSIS; SIMULATION; SPECTROMETRY; TIME; VIRUS NUCLEOCAPSID;

COMPUTER SIMULATION; MODELS, MOLECULAR; MONTE CARLO METHOD; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEOCAPSID PROTEINS; PROTEIN CONFORMATION; SARS VIRUS;

SARS CORONAVIRUS AS;

EID: 69249222495     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-009-9347-6     Document Type: Article

References (33)

1. Abragam A (1961) The principles of nuclear magnetism. Oxford, Clarendon Press
2. Brooks CL, Karplus M (1983) Deformable stochastic boundaries in molecular-dynamics. J Chem Phys 79:6312-6325
3. Brooks BR, Bruccoleri RE et al (1983) CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217
4. Brunger A, Brooks CL, Karplus M (1984) Stochastic boundary-conditions for molecular-dynamics simulations of St2 water. Chem Phys Lett 105:495-500
5. Clarkson MW, Gilmore SA, Edgell MH, Lee AL (2006) Dynamic coupling and allosteric behavior in a nonallosteric protein. Biochemistry 45:7693-7699. doi: 10.1021/Bi060652l
6. Clore GM, Szabo A et al (1990) Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins. J Am Chem Soc 112:4989-4991
7. Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-302
8. d'Auvergne EJ, Gooley PR (2003) The use of model selection in the model-free analysis of protein dynamics. J Biomol NMR 25:25-39
9. Delaglio F, Grzesiek S et al (1995) NMRPipe - a multidimensional spectral processing system based on Unix pipes. J Biomol NMR 6:277-293
10. Farrow NA, Muhandiram R et al (1994) Backbone dynamics of a free and a phosphopeptide-complexed Src homology-2 domain studied by N-15 NMR relaxation. Biochemistry 33:5984-6003
11. Fink AL (2005) Natively unfolded proteins. Curr Opin Struct Biol 15:35-41. doi: 10.1016/j.sbi.2005.01.002
12. Grubmuller H (1995) Predicting slow structural transitions in macromolecular systems - conformational flooding. Phys Rev E 52:2893-2906
13. Hsieh PK, Chang SC et al (2005) Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent. J Virol 79:13848-13855. doi: 10.1128/ Jvi.79.22.13848-13855.2005
14. Huang QL, Yu LP et al (2004) Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein. Biochemistry 43:6059-6063. doi: 10.1021/Bi036155b
15. Ichiye T, Karplus M (1991) Collective motions in proteins - a covariance analysis of atomic fluctuations in molecular-dynamics and normal mode simulations. Proteins 11:205-217
16. Johnson BA, Blevins RA (1994) NMRView - a computer-program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
17. 1 frequency dispersion in biological systems. In: Grant DM, Harris RK (eds) Encyclopedia of nuclear magnetic resonance, vol 5. Wiley, Hoboken, NJ, pp 3083-3088
18. Lee AL, Flynn PF, Wand AJ (1999) Comparison of H-2 and C-13 NMR relaxation techniques for the study of protein methyl group dynamics in solution. J Am Chem Soc 121:2891-2902
19. Lipari G, 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
20. Luchinat C, Parigi G (2007) Collective relaxation of protein protons at very low magnetic field: A new window on protein dynamics and aggregation. J Am Chem Soc 129:1055-1064. doi: 10.1021/Ja0633417
21. Luo H, Ye F et al (2004) In vitro biochemical and thermodynamic characterization of nucleocapsid protein of SARS. Biophys Chem 112:15-25. doi: 10.1016/j.bpc.2004.06.008
22. MacKerell AD, Bashford D et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
23. Mackerell AD, Feig M, Brooks CL (2004) Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25:1400-1415. doi: 10.1002/ Jcc.20065
24. Redfield AG (2003) Shuttling device for high-resolution measurements of relaxation and related phenomena in solution at low field, using a shared commercial 500 MHz NMR instrument. Magn Reson Chem 41:753-768. doi: 10.1002/Mrc.1264
25. Roberts MF, Cui QZ et al (2004) High-resolution field-cycling NMR studies of a DNA octamer as a probe of phosphodiester dynamics and comparison with computer simulation. Biochemistry 43:3637-3650. doi: 10.1021/Bi035979q
26. Saikatendu KS, Joseph JS et al (2007) Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein. J Virol 81:3913-3921. doi: 10.1128/Jvi.02236-06
27. Sivanandam VN, Cai JF, Redfield AG, Roberts MF (2009) Phosphatidylcholine "Wobble" in vesicles assessed by high-resolution C-13 field cycling NMR spectroscopy. J Am Chem Soc 131:3420-3421. doi: 10.1021/Ja808431h
28. Surjit M, Lal SK (2008) The SARS-CoV nucleocapsid protein: A protein with multifarious activities. Infect Genet Evol 8:397-405. doi: 10.1016/ j.meegid.2007.07.004
29. Surjit M, Liu BP, Chow VTK, Lal SK (2006) The nucleocapsid protein of severe acute respiratory syndrome-coronavirus inhibits the activity of cyclin-cyclin-dependent kinase complex and blocks S phase progression in mammalian cells. J Biol Chem 281:10669-10681. doi: 10.1074/jbc.M509233200
30. Tan YW, Fang SG et al (2006) Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells. Nucleic Acids Res 34:4816-4825. doi: 10.1093/Nar/Gkl650
31. Vuister GW, Wang AC, Bax A (1993) Measurement of 3-bond nitrogen carbon-J couplings in proteins uniformly Enriched in N-15 and C-13. J Am Chem Soc 115:5334-5335
32. Zhang X, Wu KL et al (2007) Nucleocapsid protein of SARS-CoV activates interleukin-6 expression through cellular transcription factor NF-kappa B. Virology 365:324-335. doi: 10.1016/j.virol.2007.04.009
33. Zuniga S, Sola I et al (2007) Coronavirus nucleocapsid protein is an RNA chaperone. Virology 357:215-227. doi: 10.1016/j.virol.2006.07.046