Sequence-dependent DNA deformability studied using molecular dynamics simulations

Nucleic Acids Research

Volumn 35, Issue 18, 2007, Pages 6063-6074

  Fujii, Satoshi ^a,b   Kono, Hidetoshi ^c,d   Takenaka, Shigeori ^a   Go, Nobuhiro ^c   Sarai, Akinori ^a  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

^b Advanced Technology Institute Inc (ATI)   (Japan)

^c Quantum Beam Science Directorate ^*  (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

TETRAMER;

AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; COMPUTER PROGRAM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA DETERMINATION; DNA FLANKING REGION; DNA PROTEIN COMPLEX; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION;

BASE SEQUENCE; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOSOMES;

EID: 35548987996     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm627     Document Type: Article

References (50)

1. International Human Genome Sequencing Consortium. (2004) Finishing the euchromatic sequence of the human genome. Nature, 431, 931-945.
2. Dickerson,R.E. (1983) The DNA helix and how it is read. Sci. Am., 249, 94-111.
3. Sarai,A. and Kono,H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
4. El Hassan,M.A. and Calladine,C.R. (1997) Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philos. Trans. Roy. Soc. (Ser. A), 355, 43-100.
5. Lamoureux,J.S., Stuart,D., Tsang,R., Wu,C. and Glover,J.N. (2002) Structure of the sporulation-specific transcription factor Ndt80 bound to DNA. EMBO J., 21, 5721-5732.
6. Lamoureux,J.S., Maynes,J.T. and Glover,J.N. (2004) Recognition of 5′-YpG-3′ sequences by coupled stacking/hydrogen bonding interactions with amino acid residues. J. Mol. Biol., 335, 399-408.
7. Napoli,A.A., Lawson,C.L., Ebright,R.H. and Berman,H.M. (2006) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J. Mol. Biol., 357, 173-183.
8. Chen,S., Gunasekera,A., Zhang,X., Kunkel,T.A., Ebright,R.H. and Berman,H.M. (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Alteration of DNA binding specificity through alteration of DNA kinking. J. Mol. Biol., 314, 75-82.
9. Hegde,R.S. (2002) The papillomavirus E2 proteins: Structure, function, and biology. Annu. Rev. Biophys. Biomol. Struct., 31, 343-360.
10. Huang,D.B., Phelps,C.B., Fusco,A.J. and Ghosh,G. (2005) Crystal structure of a free kappaB DNA: Insights into DNA recognition by transcription factor NF-kappaB. J. Mol. Biol., 346, 147-160.
11. Kono,H. and Sarai,A. (1999) Strucure-based prediction of DNA target sites by regulatory proteins. Proteins: Struct. Funct. Genet., 35, 114-131.
12. Gromiha,M.M., Siebers,J.G., Selvaraj,S., Kono,H. and Sarai,A. (2004) Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J. Mol. Biol., 337, 285-294.
13. Arauzo-Bravo,M., Fujii,S., Kono,H., Ahmad,S. and Sarai,A. (2005) Sequence-dependent conformational energy of dna derived from molecular dynamics simulations:tOward understanding the indirect readout mechanism in protein-DNA recognition. J. Am. Chem. Soc., 127, 16074-16089.
14. Sarai,A., Siebers,J., Selvaraj,S., Gromiha,M.M. and Kono,H. (2005) Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism. J. Bioinform. Comput. Bioi., 3, 1-15.
15. Olson,W.K., Gorin,A.A., Lu,X.J., Hock,L.M. and Zhurkin,V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA, 95, 11163-11168.
16. Go,M. and Go,N. (1976) Fluctuations of an a-helix. Biopolymers, 1119-1127.
17. Pichierri,F., Aida,M., Gromiha,M.M. and Sarai,A. (1999) Free-energy maps of base-amino acid interactions for DNA-protein recognition. J. Am. Chem. Soc., 121, 6152.
18. Sayano,K., Kono,H., Gromiha,M.M. and Sarai,A. (2000) Multicanonical monte carlo calculation of free-energy map for base-amino acid interaction. J. Comp. Chem., 21, 954-962.
19. Beveridge,D.L., Barreiro,G., Byun,K.S., Case,D.A., Cheatham,T.E.III, DixitS.B., Giudice,E., Lankas,F., Lavery,R. 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.
20. Arnott,S. and Hukins,D.W. (1973) Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J. Mol. Biol., 81, 93-105.
21. Pearlman,D.A., Case,D.A., Caldwell,J.W., Ross,W.S., Cheatham Iii,T.E., DeBolt,S., Ferguson,D., Seibel,G. and Kollman,P. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1.
22. Cheatham III,T.E. and Young,M.A. (2000) Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers, 56, 232.
23. Essmann,U., Perera,L., Berkowitz,M.L., Darden,T., Lee,H. and Pedersen,L.G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys., 103, 8577-8593.
24. 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.
25. Nose,S. (1991) Constant temperature molecular dynamics methods. Prog. Theor. Phys. Suppl., 103, 1-46.
26. Morishita,T. (2000) Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath. J. Chem. Phys., 113, 2976.
27. Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys., 23, 327-341.
28. Wang,J., Cieplak,P. and Kollman,P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049.
29. Lu,X.J. and Olson,.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
30. Olson,W.K., Colasanti,A.V., Li,Y., Ge,W., Zhang,G. and Zhurkin,V.B. (2006) DNA simulation benchmarks as revealed by X-ray structures. In Sponer,J. and Lankas,F. (eds), Computational studies of RNA and DNA. 2, 235-257.
31. Davey,C.A., Sargent,D.F., Luger,K., Maeder,A.W. and Richmond,T.J. (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9a resolution. J. Mol. Biol., 319, 1097-1113.
32. Colasanti,A.V. (2006) Ph.D. Thesis, Conformational States of Double Helical DNA, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.
33. Cheatham,T.E.III and Kollman,P.A. (1996) Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol., 259, 434-444.
34. Young,M.A., Ravishanker,G. and Beveridge,D.L. (1997) A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions, and solvation. Biophys. J., 73, 2313-2336.
35. Cornell,W.D., Cieplak,P., Bayly,C.I., Gould,I.R., MerzK.M. Jr, Ferguson,D.M., Spellmeyer,D.C., Fox,T., Caldwell,J.W. et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117 5179.
36. Arthanari,H., McConnell,K.J., Beger,R., Young,M.A., Beveridge,D.L. and Bolton,P.H. (2003) Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers, 68 3-15.
37. Becker,N.B., Wolff,L. and Everaers,R. (2006) Indirect readout: Detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials. Nucleic Acids Res., 34 5638-5649.
38. Lankas,F., Sponer,J., Langowski,J. and Cheatham,T.E.III (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J., 85, 2872-2883.
39. Matsumoto,A. and Olson,W.K. (2002) Sequence-dependent motions of DNA: A normal mode analysis at the base-pair level. Biophys. J., 83 22-41.
40. Segal,E., Fondufe-Mittendorf,Y., Chen,L., Thastrom,A., Field,Y., Moore,I.K., Wang,J.P. and Widom,J. (2006) A genomic code for nucleosome positioning. Nature, 442, 772-778.
41. Lankas,F., Lavery,R. and Maddocks,J.H. (2006) Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 14, 1527-1534.
42. Privalov,P.L., Dragan,A.I., Crane-Robinson,C., Breslauer,K.J., Remeta,D.P. and Minetti,C.A. (2007) What drives proteins into the major or minor grooves of DNA? J. Mol. Biol., 365, 1-9.
43. Dixit,S.B., Beveridge,D.L., Case,D.A., Cheatham,T.E.III, Giudice,E., Lankas,F., Lavery,R., Maddocks,J.H., Osman,R. et al. (2005) Molecular dynamics simulations of the 136 unique-tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J. 89, 3721-3740.
44. Varnai,P. and Zakrzewska,K. (2004) DNA and its counterions: A molecular dynamics study. Nucleic Acids Res., 32, 4269-4280.
45. Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham Iii,T.E,, 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.
46. Djuranovic,D. and Hartmann,B. (2004) DNA fine structure and dynamics in crystals and in-solution: The impact of BI/BII backbone conformations. Biopolymers, 13, 356-368.
47. Packer,M.J., Dauncey,M.P. and Hunter,C.A. (2000) Sequence-dependent DNA structure: Dinucleotide conformational maps. J. Mol. Biol., 295 71-83.
48. Packer,M.J., Dauncey,M.P. and Hunter,C.A. (2000) Sequence-dependent DNA structure: Tetranucleotide conformational maps. J. Mol. Biol., 295, 85-103.
49. Gardiner,E.J., Hunter,C.A., Packer,M.J., Palmer,D.S. and Willett,P. (2003) Sequence-dependent DNA structure: A database of octamer structural parameters. J. Mol. Biol., 332, 1025-1035.
50. DeLano,W.L. Pymol package. http://www.pymol.org/ (10 April 2007, date last accessed).