Effective Computational Strategies for Determining Structures of Carcinogen-Damaged DNA

Journal of Computational Physics

Volumn 151, Issue 1, 1999, Pages 313-332

  Broyde, S ^a   Hingerty, B E ^b  

^a NEW YORK UNIVERSITY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Carcinogen DNA structures; Molecular dynamics; Molecular mechanics

Indexed keywords

BIOINFORMATICS; COMPUTATIONAL CHEMISTRY; CONFORMATIONS; DNA; ENZYMES; HYDROGEN BONDS; MOLECULAR MECHANICS; MOLECULAR MODELING; MOLECULAR ORIENTATION; NUCLEAR MAGNETIC RESONANCE; QUANTUM CHEMISTRY;

CARCINOGEN-DNA STRUCTURE; COMPUTATIONAL STRATEGY; DNA STRUCTURE; ENERGY MINIMIZATION; ENVIRONMENTAL CHEMICALS; HIGH RESOLUTION; LARGE SYSTEM SIZE; MIRROR IMAGES; NUCLEAR MAGNETIC RESONANCE STUDIES; SEARCH TECHNIQUE;

MOLECULAR DYNAMICS;

EID: 0009523933     PISSN: 00219991     EISSN: None     Source Type: Journal    
DOI: 10.1006/jcph.1998.6172     Document Type: Article

References (77)

1. Altona C., Sundaralingam G. Conformational analysis of the sugar ring in nucleosides and nucleotides: A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:1972;8205.
2. Amadei A., Linssen A. B. M., Degroot B. L., van Aalten D. M. F., Berendsen H. J. C. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dynam. 13:1996;615.
3. Auffinger P., Westhof E. Molecular dynamics: Simulations of nucleic acids. The Encyclopedia of Computational Chemistry. 3:1998;1629.
4. Babcock M., Pednault E. P. D., Olson W. K. Nucleic acid structure analysis: Mathematics for local cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237:1994;125.
5. Beard W. A., Osheroff W. P., Prasad R., Sawaya M. R., Jaju M., Wood T. G., Kraut J., Kunkel T. A., Wilson S. H. Enzyme-DNA interactions required for efficient nucleotide incorperation and discrimination in human DNA polymerase β J. Biol. Chem. 271:1996;12141.
6. Berne B. J., Straub J. Novel methods of sampling phase space in the simulation of biological systems. Curr. Op. Struct. Biol. 7:1997;181.
7. M. Billeter, Macromolecular structures determined using NMR data, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 3, 1535.
8. Brunger A. X-PLOR User Manual. 1992.
9. A. T. Brunger, L. M. Rice, Macromolecular structure calculation and refinement by simulated annealing: Methods and applications, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 3, 1525.
10. Brunger A. T., Adams P. D., Clore G. M., Delano W. L., Gros P., Grosse-Kunstleve R. W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N. S., Read R. J., Rice L. M., Simonson T., Warren G. L. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D. 54:1998;905.
11. Buening M. K., Wislocki P. G., Levin W., Yagi H., Thakker D. R., Akagi H., Koreeda M., Jerina D. M., Conney A. H. Tumorigenicity of the optical enantiomers of the diastereomeric benzo[a] pyrene 7,8-diol-9,10-epoxides in newborn mice: Exceptional activity of (+)-7b,8a-dihydroxy-9a,10a-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. Proc. Natl. Acad. Sci. USA. 75:1978;5358.
12. Case D. A., Pearlman D. A., Caldwell J. W., Cheatham T. E., Ross W. S., Simmerling C., Darden T., Merz K. M., Stanton R. V., Cheng A., Vincent J. J., Crowley M., Ferguson D. M., Radner R., Seibel G. L., Singh U. C., Weiner P., Kollman P. A. AMBER 5.0 Documentation. 1997.
13. D. A. Case, NMR refinement, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 3, 1866.
14. P. Cieplak, Nucleic acid force fields, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 3, 1922.
15. Cheng S. C., Hilton B. D., Roman J. M., Dipple A. DNA adducts from carcinogenic and noncarcinogenic enantiomers of benzo[a]pyrene dihydrodiol epoxide. Chem. Res. Tox. 2:1989;334.
16. Conney A. H. Induction of microsomal enzymes by foreign chemicals and carcinogenesis by polycyclic aromatic hydrocarbons. Cancer Res. 42:1982;4875.
17. Cornell W. D., Cieplak 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. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179.
18. Cosman M., de los Santos C., Fiala R., Hingerty B. E., Ibanez V., Margulis L. A., Live D., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the major adduct between the carcinogen (+)-anti. Proc. Natl. Acad. Sci. USA. 89:1992;1914.
19. Cosman M., de los Santos C., Fiala R., Hingerty B. E., Ibanez V., Luna E., Harvey R. G., Geacintov N. E., Broyde S., Patel D. Solution conformation of the (+)-cis-anti. Biochemistry. 32:1993;4145.
20. Cosman M., Fiala R., Hingerty B., Laryea A., Lee H., Harvey R. G., Amin S., Geacintov N. E., Broyde S., Patel D. Solution conformation of the (+)-trans-anti. Biochemistry. 32:1993;12488.
21. Cosman M., Fiala R., Hingerty B. E., Amin S., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the (+)-trans-anti. Biochemistry. 33:1994;11507.
22. Cosman M., Fiala R., Hingerty B. E., Amin S., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the (+)-cis-anti. Biochemistry. 33:1994;11518.
23. Cosman M., Xu R., Hingerty B. E., Amin S., Harvey R. G., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the (-)-trans-anti. Biochemistry. 34:1995;6247.
24. Cosman M., Laryea A., Fiala R., Hingerty B. E., Amin S., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the (-)-trans-antitrans-anti. Biochem. 34:1995;1295.
25. Cosman M., Hingerty B. E., Luneva N., Amin S., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the (-)-cis-anti. Biochemistry. 35:1996;9850.
26. Darden T., York D., Pedersen L. G. Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:1993;10089.
27. de los Santos C., Cosman M., Hingerty B. E., Ibanez V., Margulis L. A., Geacintov N. E., Broyde S., Patel D. J. Influence of benzo[a]pyrene diol epoxide chirality on solution conformations of DNA covalent adducts: The (-)-trans-antitrans-anti. Biochemistry. 31:1992;5245.
28. Denissenko M. F., Pao A., Tang M.-S., Pfeifer G. P. Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots inP53. Science. 274:1996;430.
29. 1. Biochemistry. 34:1996;14021.
30. 1. Biochemistry. 34:1996;14037.
31. Feng B., Gorin A., Kolbanovskiy A., Hingerty B. E., Geacintov N. E., Broyde S., Patel D. J. Solution conformation of the (-)-trans-anti. Biochemistry. 45:1997;13780.
32. Fenley M. O., Manning G. S., Olson W. K. Approach to the limit of counterion condensation. Biopolymers. 30:1990;1191.
33. Fenley M. O., Olson W. K., Chua K., Boschitsch A. H. Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA. J. Comp. Chem. 17:1996;976.
34. Fountain M. A., Krugh T. R. Structural characterization of a (+)-trans-anti. Biochemistry. 34:1995;3152.
35. Geacintov N. E., Cosman M., Hingerty B. E., Amin S., Broyde S., Patel D. J. NMR solution structures of stereoisomeric covalent polycyclic aromatic carcinogen-DNA adducts: Principles, patterns and diversity. Chem. Res. in Toxicology. 10:1997;111.
36. G. Grimmer, Relevance of polycyclic aromatic hydrocarbons as environmental carcinogens, Proc. 13th Int. Symp. Polynuclear Aromatic Hydrocarbons, P. GarriguesM. Lamotte, Gordon and Breach, Langhorne, PA, 1993, 31.
37. Harvey R. G. Polycyclic Aromatic Hydrocarbons: Chemistry and Carcinogenicity. 1991.
38. M.-H. Hao, H. A. Scheraga, Conformational sampling, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 1, 552.
39. Hingerty B. E., Broyde S. Carcinogen-base stacking and base-base stacking in dCpdG modified by (+) and (-)anti. Biopolymers. 24:1985;2279.
40. Hingerty B. E., Ritchie R. H., Ferrell T. L., Turner J. E. Dielectric effects in biopolymers: The theory of ionic saturation revisited. Biopolymers. 24:1985;427.
41. Hingerty B. E., Figueroa S., Hayden T., Broyde S. Prediction of DNA structure from sequence: A build-up technique. Biopolymers. 28:1989;1195.
42. R. L. Jernigan, I. Bahar, Conformational search: Proteins, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 1, 563.
43. I. Kolossvary, W. C. Guida, Conformational analysis, 1, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 1, 513.
44. Kozack R., Loechler E. L. Molecular modeling of the conformational complexity of (+)-anti. Carcinogenesis. 18:1997;1585.
45. 2. Carcinogenesis. 20:1999;85.
46. R. Lavery, Nucleic acid conformation and flexibility: Modeling using molecular mechanics, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 3, 1913.
47. 6.
48. 6. Proc. Am. Assoc. Cancer Res. 37:1996;118.
49. Meehan T., Straub K. Double-stranded DNA stereoselectively binds benzo[a]pyrene diol epoxides. Nature. 277:1979;410.
50. Olson W. Spatial conformation of ordered polynucleotide chains. V. Conformational energy estimates of helical structure. Biopolymers. 17:1978;1015.
51. Olson W. K., Sussman J. L. How flexible is the furanose ring? A comparison of experimental and theoretical studies. J. Am. Chem. Soc. 104:1982;270.
52. W. K. Olson, A. R. Srinivasan, Classical energy calculations of DNA, RNA and their constituents, Landolt-Bornstein Numerical Data and Functional Relationships in Science and Technology, Group VII. Biophysics Volume 1D, W. Saenger, Springer-Verlag, Berlin, 1990, 415.
53. Ornstein R., Rein R. Energetics of intercalation specificity. I. Backbone unwinding. Biopolymers. 18:1979;1277.
54. Page J. E., Zajc B., Oh-hara T., Lakshman M. K., Sayer J. M., Jerina D. M., Dipple A. Sequence context profoundly influences the mutagenic potency oftrans. Biochemistry. 37:1998;9127.
55. Pearlman D., Case D., Caldwell J., Seibel G., Singh U. C., Weiner P., Kollman P. A. AMBER 4.0 Documentation. 1986, 1991.
56. Pelletier H., Sawaya M. R., Wolfle W., Wilson S. H., Kraut J. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science. 264:1994;1891.
57. Perera F. P. Environment and cancer: Who are susceptible? Science. 278:1997;1068.
58. J. L. Perrin, N. Poirot, P. Liska, C. Hanras, A. Theinpont, G. Felix, Trace enrichment and HPLC analysis of PAHs in edible oils and fat products, using liquid chromatography on electron acceptor stationary phases in connection with reverse phase and fluorescence detection, Proc. 13th Int. Symp. Polynuclear Aromatic Hydrocarbons, P. GarriguesM. Lamotte, Gordon and Breach, Langhorne, PA, 1993, 337.
59. Rice L. M., Brunger A. T. Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement. Proteins Struc. Func. Gen. 19:1994;277.
60. Saenger W. Principles of Nucleic Acid Structure. 1984.
61. T. Schlick, B. E. Hingerty, C. Peskin, M. Overton, S. Broyde, Search strategies, minimization algorithms and molecular dynamics simulations for exploring conformational spaces of nucleic acids, Theoretical Biochemistry and Molecular Biophysics, D. BeveridgeR. Lavery, Adenine Press, Schenectady, NY, 1990, 39.
62. Schlick T., Skeel R. D., Brunger A. T., Kale L. V., Board J. A. Jr., Hermans J., Schulten K. Algorithmic challenges in computational molecular biophysics. J. Comput. Phys. 151:1999;9.
63. 6. Biochemistry. 34:1995;1364.
64. 6. Biochemistry. 34:1995;9009.
65. Simmerling C., Miller J. L., Kollman P. A. Combined locally enhanced sampling and particle mesh ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid. J. Am. Chem. Soc. 120:1998;7149.
66. 2. Cancer Res. 51:1991;3482.
67. Singh S. B., Beard W. A., Hingerty B. E., Wilson S. H., Broyde S. Interactions between DNA polymerase β and the major covalent adduct of the carcinogen (+)-anti. Biochemistry. 37:1998;878.
68. Slaga T. J., Bracken W. J., Gleason G., Levin W., Yagi H., Jerina D. M., Conney A. H. Marked differences in the skin tumor-initiating activities of the optical enantiomers of the diastereomeric benzo[a]pyrene 7,8-diol-9,10-epoxides. Cancer Res. 39:1979;67.
69. Srinivasan A. R., Yathindra N., Rao V. S. R., Trakash S. Preferred phosphodiester conformations in nucleic acids: A virtual bond torsion potential to estimate lone-pair interactions in a phosphodiester. Biopolymers. 19:1980;165.
70. S. Vajda, Conformational Analysis; 2, The Encyclopedia of Computational Chemistry, P. v. R. SchleyerN. L. AllingerT. ClarkJ. GasteigerP. A. KollmanH. F. Schaefer, IIIP. R. Schreiner, Wiley, Chichester, 1998, 1, 521.
71. Vousden K. H., Bos J. L., Marshall C. J., Philips D. H. Mutations activating human C-Ha-rasI protooncogene (HRASI) induced by chemical carcinogens and depurination. Proc. Natl. Acad. Sci. USA. 83:1986;1222.
72. Wu X., Wang S. Self guided molecular dynamics simulation for efficient conformational search. J. Phys. Chem. B. 102:1998;7238.
73. Xie X., Geacintov N. E., Broyde S. Origin of opposite orientations in stereoisomeric DNA adducts derived from benzo[a]pyrene diol epoxide enantiomers with different tumorigenic potentials. Biochem. 38:1999;2956.
74. 6syn. Biochemistry. 34:1995;13570.
75. 21. Biochemistry. 35:1996;4334.
76. 61, Biochemistry, 35, 6212, 6224.
77. Zhou R. H., Berne B. J. Smart walking - A new method for boltzmann sampling of protein conformations. J. Comp. Phys. 107:1997;9185.