MOLECULAR MODELING OF THE CONFORMATIONAL COMPLEXITY OF (-ANTI-B[A]PDE-ADDUCTED DNA USING SIMULATED ANNEALING())

Benzo[a]pyrene (B[a]P), a potent mutagen/carcinogen, reacts with DNA f ollowing metabolism to its corresponding (+)-anti-7,8-diol-9,10-epoxid e [(+)-anti-B[a]PDE], giving a major adduct(+)-trans-anti-B[a]P-N-2-dG . Evidence suggests that this adduct is responsible for most of the di fferent kinds of mutations (e.g. G-->T, G-->A, etc.) induced by (+)-an ti-B[a]PDE, raising the question of how can a single adduct cause many different kinds of mutations? One hypothesis is that different mutati ons are induced depending upon the conformation of this adduct when by passed during DNA replication. If true, then it becomes imperative to explore different reasonable conformations for this adduct, Herein a s imulated annealing protocol is employed to study the conformation of ( +)-trans-anti-B[a]P-N-2-dG with the B[a]P moiety in the minor groove a nd pointing toward the base on its 5'-side in a 5'-CGC-3' sequence con text in duplex DNA, This conformation and sequence were chosen because there is a structure derived from NMR constraints for comparison, A f our step procedure is followed: the adduct is docked in canonical B-DN A, after which the structure is subjected to an initial conjugate grad ient minimization, followed by simulated annealing and a final conjuga te gradient minimization, The quality and final energy of structures i s assessed as a function of changes in six parameters, including the l ength of the DNA helix, the initial annealing temperature (T-o), the a nnealing time (t), the molecular dynamics time step (tau) and two othe r parameters, While there is no single set of optimum parameters, reas onable low energy structures were obtained using the values t approxim ate to 40 ps (or longer), T-o approximate to 750 K and tau approximate to 1.0 fs with a helix length of 7 bp, The structures that emerge all retain the basic features of the input structure, being B-DNA-like wi th the B[a]P moiety in the minor groove pointing toward the base on th e 5'-side, However, within this broad category there are at least six subclasses of structures, of which four have lowest energy members tha t differ by <similar to 5 kcal/mol. The fact that a variety of distinc t but related structures emerge from a single starting structure as th is parameter set is varied suggests that the use of a large but manage able number of simulated annealing runs should be considered in the se arch for a cohort of related structures, This is especially important given that this breadth of potentially relevant structures of approxim ately the same energy may indeed be relevant to the hypothesis that di fferent mutations arise from a single adduct in different conformation s.