DNA structures from phosphate chemical shifts

Nucleic Acids Research

Volumn 38, Issue 3, 2009, Pages 1119-1128

  Abi Ghanem, Joséphine ^a   Heddi, Brahim ^b,d   Foloppe, Nicolas ^c   Hartmann, Brigitte ^a,b  

^a INSTITUT NATIONAL DE LA TRANSFUSION SANGUINE   (France)

^b CNRS   (France)

^c Nanyang Technological University ^*  (United Kingdom)

^d NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; OLIGOMER; PROTEIN FOS; PHOSPHATE; PROTEIN C FOS; PROTEIN C JUN;

ARTICLE; CONTROLLED STUDY; DNA CONFORMATION; DNA STRUCTURE; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; NUCLEAR OVERHAUSER EFFECT; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; RELIABILITY; CHEMISTRY; CONFORMATION; NUCLEAR MAGNETIC RESONANCE;

DNA; MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; PHOSPHATES; PROTO-ONCOGENE PROTEINS C-FOS; PROTO-ONCOGENE PROTEINS C-JUN;

EID: 77951232956     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1061     Document Type: Article

References (66)

1. Bax,A. and Grishaev,A. (2005) Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr. Opin. Struct. Biol., 15, 563-570.
2. Getz,M., Sun,X., Casiano-Negroni,A., Zhang,Q. and Al-Hashimi,H.M. (2007) NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings. Biopolymers, 86, 384-402.
3. Lipsitz,R.S. and Tjandra,N. (2004) Residual dipolar couplings in NMR structure analysis. Annu. Rev. Biophys. Biomol. Struct., 33, 387-413.
4. MacDonald,D. and Lu,P. (2002) Residual dipolar couplings in nucleic acid structure determination. Curr. Opin. Struct. Biol., 12, 337-343.
5. Tjandra,N. and Bax,A. (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science, 278, 1111-1114.
6. Ikura,M., Spera,S., Barbato,G., Kay,L.E., Krinks,M. and Bax,A. (1991) Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. Biochemistry, 30, 9216-9228.
7. Wishart,D.S., Sykes,B.D. and Richards,F.M. (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol., 222, 311-333.
8. Cornilescu,G., Delaglio,F. and Bax,A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR, 13, 289-302.
9. Shen,Y., Vernon,R., Baker,D. and Bax,A. (2009) De novo protein structure generation from incomplete chemical shift assignments. J. Biomol. NMR, 43, 63-78.
10. Iwadate,M., Asakura,T. and Williamson,M.P. (1999) C alpha and C beta carbon-13 chemical shifts in proteins from an empirical database. J. Biomol. NMR, 13, 199-211.
11. Vila,J.A., Aramini,J.M., Rossi,P., Kuzin,A., Su,M., Seetharaman,J., Xiao,R., Tong,L., Montelione,G.T. and Scheraga,H.A. (2008) Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc. Natl Acad. Sci. USA, 105, 14389-14394.
12. Vila,J.A., Ripoll,D.R. and Scheraga,H.A. (2007) Use of 13Calpha chemical shifts in protein structure determination. J. Phys. Chem. B, 111, 6577-6585.
13. 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.
14. Cavalli,A., Salvatella,X., Dobson,C.M. and Vendruscolo,M. (2007) Protein structure determination from NMR chemical shifts. Proc. Natl Acad. Sci. USA, 104, 9615-9620.
15. Montalvao,R.W., Cavalli,A., Salvatella,X., Blundell,T.L. and Vendruscolo,M. (2008) Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex. J. Am. Chem. Soc., 130, 15990-15996.
16. Gong,H., Shen,Y. and Rose,G.D. (2007) Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly. Protein Sci., 16, 1515-1521.
17. Shen,Y., Lange,O., Delaglio,F., Rossi,P., Aramini,J.M., Liu,G., Eletsky,A., Wu,Y., Singarapu,K.K., Lemak,A. et al. (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc. Natl Acad. Sci. USA, 105, 4685-4690.
18. Wishart,D.S., Arndt,D., Berjanskii,M., Tang,P., Zhou,J. and Lin,G. (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res., 36, W496-W502.
19. Lankhorst,P.P., Haasnoot,C.A., Erkelens,C. and Altona,C. (1984) Carbon-13 NMR in conformational analysis of nucleic acid fragments. 3. The magnitude of torsional angle epsilon in d(TpA) from CCOP and HCOP NMR coupling constants. Nucleic Acids Res., 12, 5419-5428.
20. 13C chemical shifts. J. Am. Chem. Soc., 120, 4230-4231.
21. Ohlenschlager,O., Haumann,S., Ramachandran,R. and Gorlach,M. (2008) Conformational signatures of 13C chemical shifts in RNA ribose. J. Biomol. NMR, 42, 139-142.
22. Fares,C., Amata,I. and Carlomagno,T. (2007) 13C-detection in RNA bases: revealing structure-chemical shift relationships. J. Am. Chem. Soc., 129, 15814-15823.
23. 1H chemical shift calculations for use in structure refinement. J. Biomol. NMR, 10, 337-350.
24. Allain,F.H. and Varani,G. (1997) How accurately and precisely can RNA structure be determined by NMR? J. Mol. Biol., 267, 338-351.
25. Wu,Z., Delaglio,F., Tjandra,N., Zhurkin,V.B. and Bax,A. (2003) Overall structure and sugar dynamics of a DNA dodecamer from homo-and heteronuclear dipolar couplings and 31P chemical shift anisotropy. J. Biomol. NMR, 26, 297-315.
26. 31P chemical shift anisotropy as an aid in determining nucleic acid structure in liquid crystals. J. Am. Chem. Soc., 123, 3617-3618.
27. Chou,S.H., Cheng,J.W. and Reid,B.R. (1992) Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups. J. Mol. Biol., 228, 138-155.
28. Gorenstein,D.G. (1984) Phosphorus-31 NMR: Principles and Applications. Academic Press, New York.
29. Heddi,B., Foloppe,N., Bouchemal,N., Hantz,E. and Hartmann,B. (2006) Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition. J. Am. Chem. Soc., 128, 9170-9177.
30. Lefebvre,A., Mauffret,O., Lescot,E., Hartmann,B. and Fermandjian,S. (1996) Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG. Biochemistry, 35, 12560-12569.
31. Tisne,C., Hantz,E., Hartmann,B. and Delepierre,M. (1998) Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex. J. Mol. Biol., 279, 127-142.
32. Tisne,C., Hartmann,B. and Delepierre,M. (1999) NF-kappa B binding mechanism: a nuclear magnetic resonance and modeling study of a GGG -> CTC mutation. Biochemistry, 38, 3883-3894.
33. Fratini,A.V., Kopka,M.L., Drew,H.R. and Dickerson,R.E. (1982) Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J. Biol. Chem., 257, 14686-14707.
34. Gorenstein,D.G. (1992) 31P NMR of DNA. Methods Enzymol., 211, 254-286.
35. Gorenstein,D.G. (1994) Conformation and dynamics of DNA and protein-DNA complexes by 31P NMR. Chem. Rev., 94, 1315-1338.
36. Lankhorst,P.P., Haasnoot,C.A., Erkelens,C. and Altona,C. (1984) Carbon-13 NMR in conformational analysis of nucleic acid fragments. 2. A reparametrization of the Karplus equation for vicinal NMR coupling constants in CCOP and HCOP fragments. J. Biomol. Struct. Dyn., 1, 1387-1405.
37. Bertrand,H., Ha-Duong,T., Fermandjian,S. and Hartmann,B. (1998) Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps. Nucleic Acids Res., 26, 1261-1267.
38. Foloppe,N. and MacKerell,A. (1999) Contribution of the phosphodiester backbone and glycosyl linkage intrinsic torsional energetics to DNA structure and dynamics. J. Phys. Chem. B, 103, 10955-10964.
39. Djuranovic,D. and Hartmann,B. (2003) Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: evidence for sub-states. J. Biomol. Struct. Dyn., 20, 771-788.
40. Elsawy,K.M., Hodgson,M.K. and Caves,L.S. (2005) The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA. Nucleic Acids Res., 33, 5749-5762.
41. Tian,Y., Kayatta,M., Shultis,K., Gonzalez,A., Mueller,L.J. and Hatcher,M.E. (2009) (31)P NMR investigation of backbone dynamics in DNA binding sites (dagger). J. Phys. Chem. B, 113, 2596-2603.
42. Djuranovic,D. and Hartmann,B. (2004) DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Biopolymers, 73, 356-368.
43. Hartmann,B., Piazzola,D. and Lavery,R. (1993) BI-BII transitions in B-DNA. Nucleic Acids Res., 21, 561-568.
44. Srinivasan,A.R. and Olson,W.K. (1987) Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. J. Biomol. Struct. Dyn., 4, 895-938.
45. van Dam,L. and Levitt,M.H. (2000) BII nucleotides in the B and C forms of natural-sequence polymeric DNA: a new model for the C form of DNA. J. Mol. Biol., 304, 541-561.
46. Winger,R.H., Liedl,K.R., Pichler,A., Hallbrucker,A. and Mayer,E. (1999) Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion. J. Biomol. Struct. Dyn., 17, 223-235.
47. Heddi,B., Foloppe,N., Hantz,E. and Hartmann,B. (2007) The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J. Mol. Biol., 368, 1403-1411.
48. Heddi,B., Foloppe,N., Oguey,C. and Hartmann,B. (2008) Importance of accurate DNA structures in solution: the Jun-Fos model. J. Mol. Biol., 382, 956-970.
49. Case,D.A., Cheatham,T.E. III, Darden,T., Gohlke,H., Luo,R., Merz,K.M. Jr, Onufriev,A., Simmerling,C., Wang,B. and Woods,R.J. (2005) The Amber biomolecular simulation programs. J. Comput. Chem., 26, 1668-1688.
50. Cheatham,T.E. III, Cieplak,P. and Kollman,P.A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn., 16, 845-862.
51. Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham,T.E. III, Laughton,C.A. and Orozco,M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
52. Jorgensen,W.L., Chandrasekhar,J. and Madura,J.D. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
53. Mahoney,W. and Jorgensen,L.W. (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys., 112, 8910-8922.
54. Berendsen,H.J.C., Postma,J.P.M., van Gunsteren,W.F., DiNola,A. and Haak,J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684-3690.
55. van Gunsteren,W.F. and Berendsen,H.J.C. (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys., 34, 1311-1327.
56. Darden,T., York,D. and Pedersen,L. (1993) Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
57. Lavery,R. and Sklenar,H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, 63-91.
58. Stofer,E. and Lavery,R. (1994) Measuring the geometry of DNA grooves. Biopolymers, 34, 337-346.
59. Dickerson,R.E., Bansal,M., Calladine,C.R., Diekmann,S., Hunter,W.N., Kennard,O., von Kitzing,E., Lavery,R., Nelson,H.C.M., Olson,W.K. et al. (1989) Definition and nomenclature of nucleic acid structure parameters. EMBO J., 8, 1-4.
60. Lefebvre,A., Fermandjian,S. and Hartmann,B. (1997) Sensitivity of NMR internucleotide distances to B-DNA conformation: underlying mechanics. Nucleic Acids Res., 25, 3855-3862.
61. Beveridge,D.L., Barreiro,G., Byun,K.S., Case,D.A., Cheatham,T.E. III, Dixit,S.B., Giudice,E., Lankas,F., Lavery,R., Maddocks,J.H. et al. (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys. J., 87, 3799-3813.
62. Varnai,P., Djuranovic,D., Lavery,R. and Hartmann,B. (2002) Alpha/gamma transitions in the B-DNA backbone. Nucleic Acids Res., 30, 5398-5406.
63. Isaacs,R.J. and Spielmann,H.P. (2001) NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA. J. Mol. Biol., 311, 149-160.
64. Schmitz,U., Ulyanov,N.B., Kumar,A. and James,T.L. (1993) Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data. J. Mol. Biol., 234, 373-389.
65. Tisne,C., Delepierre,M. and Hartmann,B. (1999) How NF-kappaB can be attracted by its cognate DNA. J. Mol. Biol., 293, 139-150.
66. Djuranovic,D. and Hartmann,B. (2005) Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism. Biophys. J., 89, 2542-2551.