Research Objectives
In this project, we study carcinogen-damaged DNA in order to model replication in the presence of an enzyme.
Computational Approach
Molecular dynamics calculations using the program AMBER were performed for carcinogen-damaged DNA in the presence of a replicating enzyme. Calculations employing a number of computers were performed, with the Cray C90 at NERSC playing a key role in these computations.
Accomplishments
Recently we reported on a molecular-dynamics simulation (with the program AMBER) for the major adduct of the tumorigenic member of the pair in a base-sequence context that models an arm of a DNA replication fork. The simulation included aqueous solvent and a mammalian replication enzyme. Very intensive molecular-dynamics calculations were performed for a total of 12,000 atoms (including about 2,000 water molecules) -- the first dynamics simulation done for carcinogen-damaged DNA modeling replication in the presence of an enzyme.
In this simulation, a structure evolved in which the activated tumorigenic benzo[a]pyrene adduct formed hydrogen bonds with a key amino acid residue of a polymerase enzyme shown to be essential for faithful and efficient replication. When this residue, argenine 283, is replaced by other amino acids, the enzyme makes replication errors and is markedly slowed down. These are the same effects that are induced by the activated benzo[a]pyrene adduct, suggesting that the adverse biological effects of the adduct may stem at least in part from its compromising the central role of a key amino acid residue associated with the polymerase required for faithful and efficient replication. |
Significance
Many polycylic aromatic hydrocarbons (PAH), environmental pollutants that are mutagenic and tumorigenic, are activated to mirror image pairs of diol epoxides. Each member of the pair can react with DNA to form a covalent reaction product known as an adduct. Such adducts can cause mutations when the DNA replicates, which may finally lead to tumors. However, a fascinating observation has puzzled researchers for decades: even though both members of the pair can react with DNA to the same site, the tumorigenicity of one member is always much greater than that of the other. A structural distinction has long been sought as the underlying origin to the biological difference. Benzo[a]pyrene, present in automobile exhaust and tobacco smoke, is the prototype PAH which manifests this intriguing phenomenon.
Publications
N. E. Geacintov, M. Cosman, B. E. Hingerty, S. Amin, S. Broyde, and D. J. Patel, "NMR solution structures of stereoisomeric polycyclic aromatic carcinogen-DNA adducts: Principles, patterns, and diversity," Chemical Research in Toxicology 10, 111-146 (1997).
B. Feng, A. Gorin, B. E. Hingerty, N. E. Geacintov, S. Broyde, and D. Patel, "Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template-primer junction," J. Biochemistry 36, 13769-13779 (1997).
S. B. Singh, W. Beard, B. E. Hingerty, S. H. Wilson, and S. Broyde, "Interactions between DNA polymerase beta and the major covalent adduct of the carcinogen (+)-anti-benzo[a]pyrene diol epoxide with DNA at a primer-template junction," J. Biochemistry 37, 867-877 (1998). |
