The mechanisms involved in enzymatic hydride transfer have been studied for years, but questions remain due, in part, to the difficulty of probing the effects of protein motion and hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and human heart lactate dehydrogenase (LDH). Calculation of the work applied to the hydride allowed for observation of the change in barrier height upon inclusion of quantum dynamics. Similar calculations were performed using deuterium as the transferring particle in order to approximate kinetic isotope effects (KIEs). The change in barrier height in YADH is indicative of a zero-point energy (ZPE) contribution and is evidence that catalysis occurs via a protein compression that mediates a near-barrierless hydride transfer. Calculation of the KIE using the difference in barrier height between the hydride and deuteride agreed well with experimental results.

Background: Perfluorooctane sulfonic acid (PFOS) is a ubiquitous environmental contaminant. Most people in developed countries have detectable serum concentrations. Lower birth weight has been associated with serum PFOS in studies world-wide, many of which have been published only recently. Methods: To facilitate a causal assessment of the birth weight and PFOS association, we updated previous meta-analyses of the association and employed a method that facilitated inclusion of all available data in one analysis. Our analysis was based on observations from 29 studies. Results: The random effects summary was −3.22 g/ng/ml (95% confidence interval [CI] = −5.11, −1.33). In a subgroup analysis stratified by when in pregnancy the PFOS concentration was measured, the summary for the early group was −1.35 (95% CI = −2.33, −0.37) and for the later group was −7.17 (95% CI = −10.93, −3.41). In a meta-regression model including a term for timing of blood draw, the intercept was slightly positive but essentially zero (0.59 g/ng/ml, 95% CI = −1.94, 3.11). In other words, the model indicated that when blood was drawn at the very beginning of pregnancy, there was essentially no relation of birth weight to PFOS. The results from the subgroup analyses differed from those from the model because the average gestational age at blood draw in the early group was 14 weeks, when bias would still be expected. A stronger inverse association in Asian studies was not completely explained by their blood draws being from later in pregnancy. Conclusions: The evidence was weakly or not supportive of a causal association.

The effect of microsolvation on the deprotonation energies of uracil was examined using DFT. The structures of uracil and its N(1) and N(3) conjugate bases were optimized with zero to six associated water molecules. Multiple configurations (upward of 93) of these hydrated clusters were located at PBE1PBE/6-311+G(d,p). Trends in these geometries are discussed, with the waters generally forming chains with small numbers of waters (one-three), rings (three-five waters), or cages (five-six waters). The difference in energy between the N1 and N3 conjugate bases is 13 kcal mol(-1) in the gas phase, and it decreases with each added water up to four. At this point the energy difference has been halved, but addition of a fifth or sixth water has little effect on the energy difference. This is understood in terms of the water structures and their ability to stabilize the negatively charged atoms in the conjugate bases.

We present new findings about how primary and secondary structure affects the role of fast protein motions in the reaction coordinates of enzymatic reactions. Using transition path sampling and committor distribution analysis, we examined the difference in the role of these fast protein motions in the reaction coordinate of lactate dehydrogenases (LDHs) of Apicomplexa organisms Plasmodium falciparum and Cryptosporidium parvum. Having evolved separately from a common malate dehydrogenase ancestor, the two enzymes exhibit several important structural differences, notably a five-amino acid insertion in the active site loop of P. falciparum LDH. We find that these active site differences between the two organisms’ LDHs likely cause a decrease in the contribution of the previously determined LDH rate-promoting vibration to the reaction coordinate of P. falciparum LDH compared to that of C. parvum LDH, specifically in the coupling of the rate-promoting vibration and the hydride transfer. This effect, while subtle, directly shows how changes in structure near the active site of LDH alter catalytically important motions. Insights provided by studying these alterations would prove to be useful in identifying LDH inhibitors that specifically target the isozymes of these parasitic organisms.

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