Molecular Dynamics Simulation Studies of DNA and Proteins: Force Field Parameter Development of Small Ligands and Convergence Analysis for Simulations of Biomolecules

In the first part of this dissertation, CHARMM force field parameters for DNA minor groove-binding polyamides were developed. The parameterization involved the subdivision of the polyamides into model compounds, which were calibrated against MP2/6-31G(d) data. To test the new parameters, fourteen 10 ns molecular dynamics crystal simulations have been carried out on a DNA/polyamide complex at low (113K) and high (300K) temperatures. Of the 18 helical parameters examined, only one (stagger) is found to be statistically significant from the crystal structure with a t-test at the 95% confidence level. For the high temperature, stagger is non-significant at the 97% confidence level, which underscores the importance of running multiple trajectories. It is observed that when the simulations are run at 300K, the DNA fragment begins to distort; however, better sampling is achieved. Competition between water and polyamides for hydrogen bonding to DNA is found to explain weak or unpredictable binding. In the second part, force field parameters for retinoids were developed. The retinoids were divided into model compounds and calibrated against MP2/6-31G(d) data. To test the parameters, five molecular dynamics crystal simulations of reported x-ray structures of protein/retinoid complexes were performed. The structural and geometric analysis of these simulations compares well to experiment, and some dynamics that could be important to ligand binding were discovered. The new parameters can now be used in simulations of retinoid-binding proteins to better understand these systems and in drug design to make new retinoids with therapeutic and anticancer potential. The last part explores the convergence of structural parameters in biomolecular systems. A simple statistical test was applied to the different parameters from a few long and many short simulations to observe which strategy is best. For the protein, both the long and short simulations gave similar results with respect to convergence. For the DNA, it was found that fraying effects penetrate four base pairs in from the ends of the helix. Structural parameters converge more quickly for the middle four bases than for all bases, and the long simulations yielded better results with respect to convergence than the short simulations

Liver tumor potency indicators for technical toxaphene and congeners simulating weathered toxaphene

<p>Technical toxaphene (TT) is a liver tumor promoter in B6C3F1 mice but not in F344 rats. To further evaluate dose-response relationships for weathered toxaphene, B6C3F1 mouse hepatocytes were treated with TT alone, five selected persistent congeners (p-26, p-50, p-62, Hx-Sed, and Hp-Sed), or two selected congener mixtures (simulating weathered toxaphene) and dose-response relationships were characterized for cytotoxicity and gap junction intercellular communication (GJIC) inhibition. Phenobarbital was included as a positive control for mouse liver tumor promotion and GJIC inhibition and dose ranges were calibrated to define benchmark dose concentrations. Each treatment group exhibited significant cytotoxicity and GJIC inhibition for at least one sex (M/F) after 3 and/or 24 h of treatment. Maximum GJIC inhibition was observed at certain noncytotoxic concentrations with sex-specific differences in relative potency estimated as the effective concentration at 20% inhibition (EC20); however, no significant EC20 differences were observed between the treatment groups. Analysis of mixture interactions at the EC20 showed that GJIC inhibition of the two weathered toxaphene mixtures was significantly less than additive compared to that for the component congeners. These findings suggest that the persistent toxaphene congener mixtures tested are not more tumorigenic than the parent insecticide mixture.</p

Assfociations of perfluoroalkyl substances (PFAS) with lower birth weight: An evaluation of potential confounding by glomerular filtration rate using a physiologically based pharmacokinetic model (PBPK)

Background: Prenatal exposure to perfluoroalkyl substances (PFAS) has been associated with lower birth weight in epidemiologic studies. This association could be attributable to glomerular filtration rate (GFR), which is related to PFAS concentration and birth weight. Objectives: We used a physiologically based pharmacokinetic (PBPK) model of pregnancy to assess how much of the PFAS–birth weight association observed in epidemiologic studies might be attributable to GFR. Methods: We modified a PBPK model to reflect the association of GFR with birth weight (estimated from three studies of GFR and birth weight) and used it to simulate PFAS concentrations in maternal and cord plasma. The model was run 250,000 times, with variation in parameters, to simulate a population. Simulated data were analyzed to evaluate the association between PFAS levels and birth weight due to GFR. We compared simulated estimates with those from a meta-analysis of epidemiologic data. Results: The reduction in birth weight for each 1-ng/mL increase in simulated cord plasma for perfluorooctane sulfonate (PFOS) was 2.72 g (95% CI: –3.40, –2.04), and for perfluorooctanoic acid (PFOA) was 7.13 g (95% CI: –8.46, –5.80); results based on maternal plasma at term were similar. Results were sensitive to variations in PFAS level distributions and the strength of the GFR–birth weight association. In comparison, our meta-analysis of epidemiologic studies suggested that each 1-ng/mL increase in prenatal PFOS and PFOA levels was associated with 5.00 g (95% CI: –21.66, –7.78) and 14.72 g (95% CI: –8.92, –1.09) reductions in birth weight, respectively. Conclusion: Results of our simulations suggest that a substantial proportion of the association between prenatal PFAS and birth weight may be attributable to confounding by GFR and that confounding by GFR may be more important in studies with sample collection later in pregnancy