Biomedical subjects

Bernhardt L Trout

Publications and source records attributed to Bernhardt L Trout.

24 records · Page 2Linked to original sources

PubMed2004

On the mechanisms of oxidation of organic sulfides by H2O2 in aqueous solutions.

The mechanism of oxidation of organic sulfides in aqueous solutions by hydrogen peroxide was investigated via ab initio calculations. Specifically, two reactions, hydrogen transfer of hydrogen peroxide to form water oxide and the oxidation of dimethyl sulfide (DMS) by hydrogen peroxide to form dimethyl sulfoxide, were studied as models of these processes in general. Solvent effects are included both via including explicitly water molecules and via the polarizable continuum model. The former was found to have a much more significant effect than the latter. When explicit water molecules are included, a mechanism different from those proposed in the literature was found. Specific interactions including hydrogen bonding with 2-3 water molecules can provide enough stabilization for the charge separation of the activation complex. The energy barrier of the oxidation of DMS by hydrogen peroxide was estimated to be 12.7 kcal/mol, within the experimental range of the oxidation of analogous compounds (10-20 kcal/mol). The major reaction coordinates of the reaction are the breaking of the O-O bond of H2O2 and the formation of the S-O bond, the transfer of hydrogen to the distal oxygen of hydrogen peroxide occurring after the system has passed the transition state. Reaction barriers of the hydrogen transfer of H2O2 are an average of 10 kcal/mol or higher than the reaction barriers of the oxidation of DMS. Therefore, a two-step oxidation mechanism in which, first, the transfer of a hydrogen atom occurs to form water oxide and, second, the transfer of oxygen to the substrate occurs is unlikely to be correct. Our proposed oxidation mechanism does not suggest a pH dependence of oxidation rate within a moderate range around neutral pH (i.e., under conditions in which hydronium and hydroxide ions do not participate directly in the reaction), and it agrees with experimental observations over moderate pH values. Also, without including a protonated solvent molecule, it has activation energies that correspond to measured activation energies.

Journal Article↗

PubMed2004

A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals.

In this article, a comprehensive picture of the oxidation of protein pharmaceuticals by peroxides is developed based on our earlier computational and experimental studies. We propose a new mechanism, the water-mediated mechanism, for the oxidation of methionine residues, and it has been shown to satisfy all available experimental data including new data reported here. Based on the water-mediated mechanism, we found a structural property, average 2-shell water coordination number, that correlates well to the relative rates of oxidation of methionine groups. We used this to study the oxidation of granulocyte colony-stimulating factor (G-CSF) and 1-34 human parathyroid hormone hPTH(1-34). We believe that this comprehensive picture should aid researchers in the pharmaceutical sciences to develop solvent formulations for therapeutic proteins in a more rational way.

Binding Sites↗

PubMed2004

Effects of antioxidants on the hydrogen peroxide-mediated oxidation of methionine residues in granulocyte colony-stimulating factor and human parathyroid hormone fragment 13-34.

PURPOSE: The effects and mechanisms of different antioxidants, methionine, glutathione, acetylcysteine, and ascorbic acid (AscH2), on the oxidation of methionine residues in granulocyte colony-stimulating factor (G-CSF) and human parathyroid hormone fragment 13-34 (hPTH 13-34) by hydrogen peroxide (H2O2) were quantified and analyzed. METHODS: The rates of oxidation of methionine residues in G-CSF were determined by peptide mapping analyses, and the oxidation of methionine residue in hPTH 13-34 was quantified by reverse-phase HPLC. RESULTS: At pH 4.5, free methionine reduces, glutathione and acetylcysteine have no obvious effect on, and AscH2 promotes the rates of oxidation of methionine residues in G-CSF. The H2O2-induced oxidation rate constants for free methionine, acetylcysteine, and glutathione at pH 4.5 were measured to be 32.07, 1.00, and 1.63 M(-1)h(-1), respectively, while the oxidation rate constant for Met1, the most readily oxidizable methionine residue in G-CSF, is 13.95 M(-1)h(-1). Therefore, the different effects of free methionine, acetylcysteine, and glutathione on the rates of oxidation of methionine residues in G-CSF are consistent with their different reactivity toward oxidation by H2O2. By using hPTH 13-34, the effect of AscH2 on the H2O2-induced oxidation of methionine residue was quantified, and the mechanisms involved were proposed. Because of the presence of trace transition metal ions in solution, at low concentrations, AscH2 is prone to be a prooxidant, increasing the hydroxyl radical (.OH) production rate via Fenton-type reactions. In addition to peroxide oxidation, these radicals lead to the degradation of hPTH 13-34 to smaller peptide fragments. At high concentrations, AscH2 tends to act as an OH scavenger. EDTA inhibits OH production and thus eliminates the degradation of hPTH 13-34 by forming complexes with transition metal ions. However, the rate of oxidation of the methionine residue in hPTH 13-34 increases as the concentration of AscH2 is increased from 0 to 200 mM, and the reason for this is still not clear. CONCLUSIONS: Our results demonstrate that free methionine is an effective antioxidant to protect G-CSF against methionine oxidation at pH 4.5. Acetylcysteine and glutathione are not effective antioxidants at pH 4.5. Their oxidation rates at different pH values imply that they would be much more effective antioxidants than free methionine at alkaline conditions. AscH2 is a powerful electron donor. It acts as a prooxidant in the conditions in this study and is unlikely to prevent oxidation by H2O2 in protein formulation, whether or not EDTA is present.

Antioxidants↗

PubMed2004

Rational design of solution additives for the prevention of protein aggregation.

We have developed a statistical-mechanical model of the effect of solution additives on protein association reactions. This model incorporates solvent radial distribution functions obtained from all-atom molecular dynamics simulations of particular proteins into simple models of protein interactions. In this way, the effects of additives can be computed along the entire association/dissociation reaction coordinate. We used the model to test our hypothesis that a class of large solution additives, which we term "neutral crowders," can slow protein association and dissociation by being preferentially excluded from protein-protein encounter complexes, in a manner analogous to osmotic stress. The magnitude of this proposed "gap effect" was probed for two simple model systems: the association of two spheres and the association of two planes. Our results suggest that for a protein of 20 A radius, an 8 A additive can increase the free energy barrier for association and dissociation by as much as 3-6 kcal/mol. Because the proposed gap effect is present only for reactions involving multiple molecules, it can be exploited to develop novel additives that affect protein association reactions although having little or no effect on unimolecular reactions such as protein folding. This idea has many potential applications in areas such as the stabilization of proteins against aggregation during folding and in pharmaceutical formulations.

Biophysical Phenomena↗

PubMed2003

Nucleation of hexagonal ice (Ih) in liquid water.

The process by which supercooled fluids form stable, crystalline solids has been found to be elusive both experimentally and via computer simulations. This is because this process, generally called nucleation, is statistical in nature and because the set of intermediate states, generally called the critical nucleus, is very short-lived. Thus, there are very large uncertainties in even the limited experimental data that exist, and computer simulations that have been performed can yield descriptive information at best. Here we present a detailed and quantitatively accurate observation of the most important nucleation process, the freezing of liquid water at ambient conditions. We have accomplished this by using a method based on choosing a suitable set of order parameters to characterize the crystallinity of the system and a non-Boltzmann sampling Monte Carlo approach to obtain a statistical average of the properties of the system during its transition from liquid to ice (Ih). We have characterized the order of the system statistically at intermediate states between liquid water and ice Ih and in so doing described the nucleation process.

Journal Article↗

PubMed2003

Nucleation of crystalline phases of water in homogeneous and inhomogeneous environments.

We employ two-body and three-body bond-orientational order-parameters, in conjunction with non-Boltzmann sampling to calculate the free energy barrier to nucleation of crystalline phases of water. We find that, as the coupling between the successive peaks of the direct correlation function increases, the free energy barrier to nucleation decreases. On this basis we explain the important parameters that govern the nucleation rate involving crystalline phases of water in different homogeneous and inhomogeneous environments, giving a "unified picture" of ice nucleation in water.

Antifreeze Proteins↗