Biomedical subjects

Bernhardt L Trout

Publications and source records attributed to Bernhardt L Trout.

At least 19 recordsLinked to original sources

PubMed2006

Comparative oxidation studies of methionine residues reflect a structural effect on chemical kinetics in rhG-CSF.

The effect of protein conformation on the rate of chemical degradation is poorly understood. To address the role of structure on chemical degradation kinetics, comparative oxidation studies of methionine residues in recombinant human granulocyte colony-stimulating factor (rhG-CSF) were performed. The kinetics of oxidation of methionine residues by hydrogen peroxide (H2O2) in rhG-CSF and corresponding chemically synthesized peptides thereof was measured at different temperatures. To assess structural effects, equilibrium denaturation experiments also were conducted on rhG-CSF, yielding the free energy of unfolding as a function of temperature. A comparison of the relative rates of oxidation of methionine residues in short peptides with those of corresponding methionine residues in rhG-CSF yields an understanding of how protein tertiary structure affects oxidation reactions. For the temperature range that was studied, 4-45 degrees C, the oxidation rate constants followed an Arrhenius equation quite well, suggesting the lack of temperature-induced local structural perturbations that affect chemical degradation rates. One of the four methionine residues, Met 122, exhibited an activation energy significantly different from that of the corresponding peptide. Extrapolation of kinetic data predicts non-Arrhenius behavior around the melting temperature. Three phenomenological models based on different mechanisms are discussed, and an application to shelf life prediction of pharmaceuticals is presented.

Granulocyte Colony-Stimulating Factor↗

PubMed2006

Density functional theory study of ligand binding on CdSe (0001), (0001), and (1120) single crystal relaxed and reconstructed surfaces: implications for nanocrystalline growth.

To gain a better understanding of the influence of ligand-surface interactions on nanocrystalline growth, periodic density functional theory calculations were employed in the study of the binding of organic ligands on the relaxed nonpolar (1120) and polar Se terminated (0001) surfaces and the relaxed and vacancy and adatom reconstructed Cd terminated (0001) surface. We examined chemisorption properties of phosphine, amine, phosphine oxide, carboxylic acid, and phosphinic acid model ligands, including preferred binding sites and geometries, vibrational frequencies, and binding energetics, and compared findings to intrinsic growth via addition of CdSe molecules or Cd and Se atoms. Our results indicate that binding of the ligands is preferred in the electron-poor 1-fold sites on all surfaces, with secondary coordination of the acidic ligands through the hydroxyl hydrogen to the electron-rich surface sites. In general ligand adsorption directly obstructs binding sites for growth species on the (1120) surface and only indirectly on the two polar surfaces. The order of binding affinities on the (1120) and (0001) surfaces is PH(3) < OPH(3) approximately HCOOH < NH(3) < OPH(2)OH and that on the (0001) surface is OPH(3) approximately HCOOH < OPH(2)OH < NH(3) < PH(3). Our findings corroborate the experimental observation that incorporation of the nonbulky phosphinic acid-type ligands with high affinity and high selectivity for both the (1120) and (0001) surfaces strongly enhances unidirectional growth on the (0001) surface, while incorporation of either bulky ligands or ligands with moderate affinity does not. Higher affinity of all traditionally used ligands for the (1120) surface compared to the (0001) surface also suggests that new ligands should be engineered to achieve the synthesis of novel shapes that require preferential growth on the (1120) surface.

Journal Article↗

PubMed2006

Obtaining reaction coordinates by likelihood maximization.

We present a new approach for calculating reaction coordinates in complex systems. The new method is based on transition path sampling and likelihood maximization. It requires fewer trajectories than a single iteration of existing procedures, and it applies to both low and high friction dynamics. The new method screens a set of candidate collective variables for a good reaction coordinate that depends on a few relevant variables. The Bayesian information criterion determines whether additional variables significantly improve the reaction coordinate. Additionally, we present an advantageous transition path sampling algorithm and an algorithm to generate the most likely transition path in the space of collective variables. The method is demonstrated on two systems: a bistable model potential energy surface and nucleation in the Ising model. For the Ising model of nucleation, we quantify for the first time the role of nuclei surface area in the nucleation reaction coordinate. Surprisingly, increased surface area increases the stability of nuclei in two dimensions but decreases nuclei stability in three dimensions.

Journal Article↗

PubMed2006

Hydrogen chloride-induced surface disordering on ice.

Characterizing the interaction of hydrogen chloride (HCl) with polar stratospheric cloud ice particles is essential for understanding the processes responsible for ozone depletion. We studied the interaction of gas-phase HCl with ice between 243 and 186 K by using (i) ellipsometry to monitor the ice surface and (ii) coated-wall flow tube experiments, both with chemical ionization mass spectrometry detection of the gas phase. We show that trace amounts of HCl induce formation of a disordered region, or quasi-liquid layer, at the ice surface at stratospheric temperatures. We also show that surface disordering enhances the chlorine activation reaction of HCl with chlorine nitrate (ClONO(2)) and also enhances acetic acid (CH(3)COOH) adsorption. These results impact our understanding of the chemistry and physics of ice particles in the atmosphere.

Journal Article↗

PubMed2006

Asparagine deamidation: pH-dependent mechanism from density functional theory.

Asparagine deamidation is a decisive event in chemotherapy-induced apoptosis and a major obstacle in the formulation of monoclonal antibodies. Despite the importance of deamidation, little is known about the elementary reactions involved. B3LYP/6-31+G(d,p)/COSMO-RS calculations were used to obtain stable structures and transition states for a network of reactions. Calculated rate constants were incorporated into a kinetic model of the pH dependence and compared to a pseudo-steady-state model. At low pH, the calculations show that deamidation occurs by direct acid-catalyzed hydrolysis to aspartate. At neutral to basic pH, deamidation proceeds by the initial formation of a tetrahedral intermediate. The intermediate can be converted to succinimide by two pathways and three rate-determining steps that shift in relative importance with pH. The calculated pH-dependent rate constant qualitatively agrees with the experimental pH dependence. The rate-determining transition state structures may help to understand chemotherapy-induced apoptosis and improve protein formulations.

Amination↗

PubMed2006

Rational design of selective, sulfur-resistant oxidation emissions catalysts.

A new catalyst design strategy based on optimizing electronic structure has been proposed and then applied to a very important environmental application, the design of selective, sulfur-resistant oxidation emissions catalysts. The modified d-band center model developed by us in a previous study, together with an energy decomposition scheme, is used to correlate measures of reactivity with reaction barriers of SO2 + O --> SO3 and NO + O --> NO2 on surfaces. Our objective is to find a catalyst which is active in oxidizing NO to NO2 but relatively inactive in oxidizing SO2 to SO3. The Ir alloyed Pt(111) surface is found to have the highest selectivity for oxidation of NO over SO2 at 700 K. Unfortunately, there is a slope change in the correlation of the weighted d-band center with the adsorption of NO at the transition state, which narrows down the range of the theoretical selectivity. Our ongoing study aims at understanding the reason for this. The general importance of this study for surface catalysis is also discussed.

Journal Article↗

PubMed2006

Solvation model based on order parameters and a fast sampling method for the calculation of the solvation free energies of peptides.

An analytical solvation model is proposed as a function of an order parameter, which represents the local arrangement of water molecules in the first solvation shell of peptide atoms. The model is combined with a fast sampling method, rotational isomeric state Monte Carlo, to sample efficiently the torsional degrees of freedom on a peptide backbone. This order parameter solvation model is shown to reproduce without ad hoc fitting parameters the solvation free energies of single amino acids and tripeptides with slightly better accuracy than the generalized Born model but with several orders of magnitude improvement in efficiency. This method is a potential candidate for efficiently and accurately tackling some important issues in biophysical chemistry that are related to solvation, for example, protein folding, ligand binding, etc. Our results also present fundamental new insights into solvation. Specifically, the local water geometry, represented in this work by a properly defined order parameter, carries the majority, if not all, of the energetic information of solvation, including solute-solvent interactions and solvent reorganization in the presence of the solute.

Computer Simulation↗

PubMed2005

Properties of inhibitors of methane hydrate formation via molecular dynamics simulations.

Within the framework of a proposed two-step mechanism for hydrate inhibition, the energy of binding of four inhibitor molecules (PEO, PVP, PVCap, and VIMA) to a hydrate surface is estimated with molecular dynamic simulations. One key feature of this proposed mechanism is that the binding of an inhibitor molecule to the surface of an ensuing hydrate crystal disrupts growth and therein crystallization. It is found through the molecular dynamic simulations that inhibitor molecules that experimentally exhibit better inhibition strength also have higher free energies of binding, an indirect confirmation of our proposed mechanism. Inhibitors increasing in effectiveness, PEO < PVP < PVCap < VIMA, have increasingly negative (exothermic) binding energies of -0.2 < -20.6 < -37.5 < -45.8 kcal/mol and binding free energies of increasing favorability (+0.4 approximately = +0.5 < -9.4 < -15.1 kcal/mol). Furthermore, the effect of an inhibitor molecule on the local liquid water structure under hydrate-forming conditions was examined and correlated to the experimental effectiveness of the inhibitors. Two molecular characteristics that lead to strongly binding inhibitors were found: (1) a charge distribution on the edge of the inhibitor that mimics the charge separation in the water molecules on the surface of the hydrate and (2) the congruence of the size of the inhibitor with respect to the available space at the hydrate-surface binding site. Equipped with this molecular-level understanding of the process of hydrate inhibition via low-dosage kinetic hydrate inhibitors we can design new, more effective inhibitor molecules.

Journal Article↗

PubMed2005

First principles computational study for understanding the interactions between ssdna and gold nanoparticles: adsorption of methylamine on gold nanoparticulate surfaces.

We conducted a computational adsorption study of methylamine on various surface models of a gold nanoparticle which is facetted by multiple [111] and [100] planes. In addition to these flat surfaces, our models include the stepped surfaces (ridges) formed along the intersections of these planes. Binding on the flat surfaces was fairly weak, but substantially stronger on the ridges by an average of 4.4 kcal/mol. This finding supports the idea that ssDNA's interaction with gold nanoparticles occurs through the amines on the purine/pyrimidine rings. Also, this typically undesirable interaction between DNA and gold nanoparticles is expected to increase as the particle size decreases. Our analysis suggests that particle size is an important controlling parameter to reduce this interaction.

Adsorption↗

PubMed2005

Properties of the CdSe(0001), (0001), and (1120) single crystal surfaces: Relaxation, reconstruction, and adatom and admolecule adsorption.

Details of the chemical mechanism underlying the growth of colloidal semiconductor nanocrystals remain poorly understood. To provide insight into the subject, we have preformed a comprehensive study of the polar (0001) and (0001) and nonpolar (1120) wurtzite CdSe surfaces that are exposed during crystal growth using first-principles density functional theory (DFT-GGA) calculations. Stabilization of these surfaces by relaxation and reconstruction was considered. Two particular reconstructions of the polar surfaces were examined: vacancy formation on a 2 x 2 unit cell and addition of Se and Cd atoms on the (0001) and (0001) surfaces, respectively. Calculation results indicate that the (1120) is the most stable surface when compared to the two polar surfaces. Furthermore, reconstructions of the (0001) surface are energetically favored when compared to reconstructions of the (0001) facet. Adsorption of Cd and Se atoms and the CdSe molecule on the three relaxed surfaces and two reconstructed (0001) surfaces were also investigated. Several binding sites were considered to determine the most stable binding geometries and energetics. Atomic species preferentially bind in either 2-fold or 3-fold sites, while the CdSe molecule binds parallel to the surface on all of the considered surfaces. Vibrational frequencies of the adspecies were calculated for the most stable binding configurations and were included in the zero point energy correction. Diffusion barriers for the atomic and molecular species were estimated where possible to be between 0.2 and 0.4 eV on the three relaxed surfaces. Thermochemistry of the CdSe molecule binding and dissociation was also investigated. On all considered surfaces, dissociation is preferred to desorption with dissociation only exothermic on the (0001) surface. Comparison of the three relaxed and two reconstructed surfaces indicates that CdSe molecule binding and dissociation is thermodynamically favored on the (0001) surface. This implies that under a reaction-controlled regime, the rate of homoepitaxy would be faster on the (0001) Se terminated surface than on the (0001) and (1120) surfaces, making the (0001) surface of a nanocrystal the primary direction of growth.

Journal Article↗

PubMed2005

NO Chemisorption on Pt(111), Rh/Pt(111), and Pd/Pt(111).

The chemisorption of NO on clean Pt(111), Rh/Pt(111) alloy, and Pd/Pt(111) alloy surfaces has been studied by first principles density functional theory (DFT) computations. It was found that the surface compositions of the surface alloys have very different effects on the adsorption of NO on Rh/Pt(111) versus that on Pd/Pt(111). This is due to the different bond strength between the two metals in each alloy system. A complex d-band center weighting model developed by authors in a previous study for SO2 adsorption is demonstrated to be necessary for quantifying NO adsorption on Pd/Pt(111). A strong linear relationship between the weighted positions of the d states of the surfaces and the molecular NO adsorption energies shows the closer the weighted d-band center is shifted to the Fermi energy level, the stronger the adsorption of NO will be. The consequences of this study for the optimized design of three-way automotive catalysts, (TWC) are also discussed.

Journal Article↗

PubMed2005

Application of the cell potential method to predict phase equilibria of multicomponent gas hydrate systems.

We present the application of a mathematical method reported earlier by which the van der Waals-Platteeuw statistical mechanical model with the Lennard-Jones and Devonshire approximation can be posed as an integral equation with the unknown function being the intermolecular potential between the guest molecules and the host molecules. This method allows us to solve for the potential directly for hydrates for which the Langmuir constants are computed, either from experimental data or from ab initio data. Given the assumptions made in the van der Waals-Platteeuw model with the spherical-cell approximation, there are an infinite number of solutions; however, the only solution without cusps is a unique central-well solution in which the potential is at a finite minimum at the center to the cage. From this central-well solution, we have found the potential well depths and volumes of negative energy for 16 single-component hydrate systems: ethane (C2H6), cyclopropane (C3H6), methane (CH4), argon (Ar), and chlorodifluoromethane (R-22) in structure I; and ethane (C2H6), cyclopropane (C3H6), propane (C3H8), isobutane (C4H10), methane (CH4), argon (Ar), trichlorofluoromethane (R-11), dichlorodifluoromethane (R-12), bromotrifluoromethane (R-13B1), chloroform (CHCl3), and 1,1,1,2-tetrafluoroethane (R-134a) in structure II. This method and the calculated cell potentials were validated by predicting existing mixed hydrate phase equilibrium data without any fitting parameters and calculating mixture phase diagrams for methane, ethane, isobutane, and cyclopropane mixtures. Several structural transitions that have been determined experimentally as well as some structural transitions that have not been examined experimentally were also predicted. In the methane-cyclopropane hydrate system, a structural transition from structure I to structure II and back to structure I is predicted to occur outside of the known structure II range for the cyclopropane hydrate. Quintuple (L(w)-sI-sII-L(hc)-V) points have been predicted for the ethane-propane-water (277.3 K, 12.28 bar, and x(eth,waterfree) = 0.676) and ethane-isobutane-water (274.7 K, 7.18 bar, and x(eth,waterfree) = 0.81) systems.

Journal Article↗

PubMed2005

Electronic composition-property relationship applied to SO2 chemisorption on Pt111 surfaces, alloys, and overlayers.

We have developed a new electronic composition-property relationship between the adsorption energy of molecules binding unequally to multiple atoms on metal surfaces and the electronic properties of the surface. This relationship allows the estimation of the relative stability of adsorbates on various surfaces, assuming that the adsorbate adopts the same local configuration on each surface, and therefore also allows the estimation of the adsorption energy of molecules through large regions of parameter space in alloy systems with data from only a few explicit calculations. We have applied this relationship to the adsorption of SO(2) on Pt surfaces alloyed with Pd, Cu, Ru, and Ni. Using a new formula for weighting the metal d-band, we found a strong linear relationship between the weighted positions of the d states of surfaces and the most stable molecular adsorption energies. The consequences of our electronic composition-property relationship for catalyst design are also discussed.

Journal Article↗

PubMed2005

Role of arginine in the stabilization of proteins against aggregation.

The amino acid arginine is frequently used as a solution additive to stabilize proteins against aggregation, especially in the process of protein refolding. Despite arginine's prevalence, the mechanism by which it stabilizes proteins is not presently understood. We propose that arginine deters aggregation by slowing protein-protein association reactions, with only a small concomitant effect on protein folding. The associated rate effect was observed experimentally in association of globular proteins (insulin and a monoclonal anti-insulin) and in refolding of carbonic anhydrase. We suggest that this effect arises because arginine is preferentially excluded from protein-protein encounter complexes but not from dissociated protein molecules. Such an effect is predicted by our gap effect theory [Baynes and Trout (2004) Biophys. J. 87, 1631] for "neutral crowder" additives such as arginine which are significantly larger than water but have only a small effect on the free energies of isolated protein molecules. The effect of arginine on refolding of carbonic anhydrase was also shown to be consistent with this hypothesis.

Animals↗

PubMed2005

Effects of excipients on the hydrogen peroxide-induced oxidation of methionine residues in granulocyte colony-stimulating factor.

PURPOSE: The objective of this study was to elucidate the different mechanisms of action of different excipients on the oxidation of Met1, Met122, Met127, and Met138 in granulocyte colony-stimulating factor (G-CSF) by using hydrogen peroxide as the oxidant. METHODS: The oxidation of Met1, Met127, and Met138 was quantified by peptide mapping analysis. The oxidation of Met122 has biphasic oxidation kinetics with a faster second phase. Therefore, the oxidation of Met122 was quantified by two different methods: peptide mapping analysis for the first phase of oxidation and direct reverse-phase HPLC for the second phase of oxidation. RESULTS: The current work reveals that the preferential excluding excipients sorbitol, sucrose, and trehalose, in the concentration range 0-30% (w/v), and the preferential binding excipients urea and guanidine hydrochloride, in the concentration range 0-0.8 M, do not affect the oxidation of methionine residues in G-CSF at pH 4.5. The chelating agents citrate and EDTA have different effects on the rates of oxidation of methionine residues in G-CSF. At low concentrations, citrate decreases the rates, while at high concentrations, citrate increases the rates. EDTA decreases the rates of oxidation of methionine residues in G-CSF, such that its effect becomes more and more as its concentration is increased from 0 to 200 mM. The efficacy of EDTA on the rates of oxidation of the four methionine residues in G-CSF follows the order Met122 > Met127 > Met138 > Met1. CONCLUSIONS: Our results indicate that EDTA can protect the methionine residues in G-CSF against oxidation induced by hydrogen peroxide. The more exposed the methionine residue is, the more difficult it is to be protected by EDTA. The mechanism may be due to the specific ion binding of EDTA to proteins.

Excipients↗

PubMed2004

Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor.

The free energy barriers and a mechanism of the oxidation of the amino acid methionine in water and in granulocyte colony-stimulating factor (G-CSF) are analyzed via combined quantum mechanical and molecular mechanical (QM/MM) methods, constrained molecular dynamics, and committor probability calculations. The computed free energy barrier of free methionine amino acid is very close to the measured value (14.7 +/- 1.2 versus 15.5 +/- 0.02 kcal/mol). The reaction coordinate was found to be the difference between the O-O bond of H2O2 and the S-O bond, where the S is the sulfur atom of the methionine residue. It was confirmed by computing the committor probability distribution and the distribution of constrained forces that this coordinate is not coupled to the activation of other degrees of freedom. The computed free energies of the oxidation of methionine residues in G-CSF indicate that the protein environment has insignificant effects on the reaction barriers of oxidation. This result further validates our proposal that the access of solvent to methionine sites, as measured by the two-shell water coordination number, governs the kinetics of the oxidation reaction of methionine groups in a protein molecule. We also found that the number of hydrogen bonds between the distal oxygen of H2O2 and the water molecules near the methionine increases along the reaction coordinate as oxidation progresses, indicating that the charge separation developed during the oxidation by H2O2 is stabilized by specific interactions with water molecules, such as hydrogen bonding.

Granulocyte Colony-Stimulating Factor↗

PubMed2004

A structural and mechanistic study of the oxidation of methionine residues in hPTH(1-34) via experiments and simulations.

The relationship between the conformational properties of 1-34 human parathyroid hormone [hPTH(1-34)] and the oxidation of its methionine residues, Met8 and Met18, by hydrogen peroxide is analyzed as a function of pH by measuring the rates of oxidation and by performing MD simulations with an explicit representation of water molecules. Between pH 4 and pH 8, both Met8 and Met18 have nearly pH independent rates of oxidation, and Met18 is oxidized at a rate that is 90-100% of that of freeMet and 10-20% faster than that of Met8. We also found that average 2SWCNs calculated from MD simulations correlate well to the rates of oxidation of Met8 and Met18. The use of 2SWCNs is based on the mechanism that we proposed, the water-mediated mechanism, in which water molecules stabilize the transition state via specific interactions, but the transfer of protons (acid-catalyzed mechanism) does not play a role [Chu, J. W., and Trout, B. L. (2004) J. Am. Chem. Soc. 126 (3), 900-908]. Only at very low pH values, pH 1 for the oxidation of freeMet, does the acid-catalyzed oxidation mechanism become important. For the oxidation of Met8 and Met18 in hPTH(1-34), the acid-catalyzed mechanism becomes significant at a higher pH value, pH 2, probably due to the proximity of nearby acidic residues to Met8 (Glu4) and Met18 (Glu22). In this study, we have demonstrated that the chemistry of oxidation and the structure of polypeptides can be correlated via a detailed understanding of the reaction mechanism, appropriate sampling of configurational space, and a suitable choice of a structural property, water coordination number.

Circular Dichroism↗

PubMed2004

Molecular dynamics simulations and oxidation rates of methionine residues of granulocyte colony-stimulating factor at different pH values.

To understand the connection between the conformation of a protein molecule and the oxidation of its methionine residues, we measured the rates of oxidation of methionine residues by H(2)O(2) in granulocyte colony-stimulating factor (G-CSF) as a function of pH and also studied the structural properties of this protein as a function of pH via molecular dynamics simulations. We found that each of the four methionine groups in G-CSF have significant and different rates of oxidation as a function of pH. Moreover, Met(1), in the unstructured N-terminal region, has a rate of oxidation as low as half that of free methionine. The structural properties of G-CSF as a function of pH are evaluated in terms of properties such as hydrogen bonding, deviations from X-ray structure, helical/helical packing, and the atomic covariance fluctuation matrix of alpha-carbons. We found that dynamics (structural fluctuations) are essential in explaining oxidation and that a static picture, such as that resulting from X-ray data, fails in this regard. Moreover, the simulation results also indicate that the solvent-accessible area, traditionally used to measure solvent accessibility of a protein site, of the sulfur atom of methionine residues does not correlate well with the rate of oxidation. Instead, we identified a structural property, average two-shell water coordination number, that correlates well with measured oxidation rates.

Amino Acid Sequence↗