Electrostatic energy analysis of 8-oxoguanine DNA lesion - Molecular dynamics study

Computational Biology and Chemistry

Volumn 27, Issue 3, 2003, Pages 431-441

  Pinak, Miroslav ^a  

^a JAPAN ATOMIC ENERGY AGENCY   (Japan)

Author keywords

8 Oxoguanine; DNA; Electrostatic energy; Flipped out base; MD

Indexed keywords

ELECTROSTATICS; ENZYMES; MOLECULAR DYNAMICS;

ELECTROSTATIC ENERGY;

DNA;

8 HYDROXYGUANINE; 8-HYDROXYGUANINE; DNA; DRUG DERIVATIVE; GUANINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DNA DAMAGE; DNA REPAIR; ELECTRICITY; HYDROGEN BOND; METABOLISM; THERMODYNAMICS; TIME;

DNA; DNA DAMAGE; DNA REPAIR; ELECTROSTATICS; GUANINE; HYDROGEN BONDING; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; THERMODYNAMICS; TIME FACTORS;

EID: 0043231319     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1476-9271(02)00104-4     Document Type: Article

References (24)

1. Abascal J.-L.-F., Montoro J.-C.-G. J. Chem. Phys. 9:2001;4277.
2. Barnet R.-N., Cleveland C.-L., Joy A., Landman U., Schuster G.-B. Science. 294:2001;567.
3. Bayly C.-I., Cieplak P., Cornell W.-D., Kollman P.-A. J. Phys. Chem. 97:1993;10269.
4. Beachy M.-D., Chasman D., Murphy R.-B., Halgren T.-A., Friesner R.-A. J. Am. Chem. Soc. 119:1997;5908.
5. Beato M. Cell. 56:1989;335.
6. Case, D.-A., Pearlman, D.-A., Caldwell, J.-W., Cheathman III, T.-E., Ross, W.-S., Simmerling, C.-L., Darden, T.-A., Merz, K.-M., Stanton, R.-V., Cheng, A.-L., Vincent, J.-J., Crowley, M., Ferguson, D.-M., Radmer, R.-J., Seibel, G.-L., Weiner, P.-K., Kollman, P.-A., 1997. AMBER 5.0, University of California San Francisco.
7. Cornell W.-D., Ciepelak P., Bayly C.-I., Gould I.-R., Merz K.-M. Jr., Ferguson D.-M., Spellmeyer D.-C., Fox T., Caldwell J.-W., Kollman P.-A. J. Am. Chem. Soc. 117:1995;5179.
8. Darden T., York D., Pedersen L. J. Chem. Phys. 98:1993;10089.
9. Delphi, Molecular Simulations, Inc., 2000.
10. Dianov G., Bischoff C., Sunesen M., Bohr W.-A. Nucleic Acids Res. 27:(5):1999;1365.
11. Gilson M.-K., Honig B.-H. Nature. 330:1987;84.
12. Ham J., Thompson A., Needham M., Webb P., Parker M. Nucleic Acids Res. 16:(12):1988;5263.
13. Harrison S.-C., Aggarwal A.-K. Annu. Rev. Biochem. 59:1990;933.
14. Hazra T.-K., Muller J.-G., Manuel R.-C., Burrows C.-J., Lloyd R.-S., Mitra S. Nucleic Acids Res. 29:(9):2001;1967.
15. Hollestein M., Shomer B., Greenblatt M., Soussi T., Hovig E., Montesano R., Harris C.-C. Nucleic Acids Res. 24:1996;141.
16. Honig B., Nicholls A. Science. 268:1995;1144.
17. Insight II 97.0, Molecular Simulations, Inc. 1977, San Diego, CA, USA.
18. Naray-Szabo G., Ferenczy G.-G. Chem. Rev. 95:1995;829.
19. Nash H.-M., Lu R., Lane W.-S., Verdine G.-L. Chem. Biol. 4:1997;693.
20. Pinak M. Mol. Sim. 23:1999;307.
21. Politzer P., Muray J.-S. Lipkowitz K.B., Boyd D.B. Reviews in Computational Chemistry. 2:1991;273 VCH, New York. Chapter 7.
22. Shortle D.Q. Rev. Biophys. 25:1992;205.
23. Wilkinson, A., Weiner, P., van Gunsteren, W., 1997. In: Wilfred, F., van Gunsteren, W., Weiner, P.-K. (Eds.), Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, vol. 1.
24. Yang A.-S., Honig B. Curr. Opin. Struct. Biol. 2:1992;40.