Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme. Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.

The kidney regulates the excretion of water and electrolytes, which maintains homeostasis and enables control of arterial blood pressure. Hyaluronan, a large negatively charged interstitial glucosaminoglycan, is heterogeneously distributed within the kidney, primarily found in the medulla. Medullary hyaluronan content changes depending on the state of body hydration and plays a part in fluid regulation through its water binding and viscoelastic properties. The aim of this thesis was to provide new insight into the regulation of intrarenal hyaluronan during different states of body hydration, during completion of kidney development, and during diabetes mellitus. Dehydration reduces medullary interstitial hyaluronan in parallel with reduced hyaluronan synthase 2 gene expression and increased urinary hyaluronidase activity. Acute hydration results in an increase in medullary hyaluronan, an increase that requires nitric oxide and prostaglandins. Urinary hyaluronidase activity decreases during hydration. The elevation of hyaluronan is important for reducing water permeability of the interstitium i.e. favoring diuresis. Changes in hyaluronan concentration constitute a morphoregulatory pathway that plays a key role in nephrogenesis. The reduction in neonatal hyaluronan depended on an angiotensin II mediated process that does not appear dependent on lymph vessel formation. If angiotensin II is blocked with an ACE inhibitor, hyaluronan accumulates, which results in structural and functional abnormalities in the kidney. Renomedullary hyaluronan is elevated during uncontrolled diabetes, which coincides with induction of hyaluronan synthase 2 mRNA, hyperglycemia, glucosuria, proteinuria and overt diuresis. The levels of hyaluronan are probably at a terminus ad quem as no further response was seen during hydration. The higher interstitial expression of hyaluronan during diabetes may be involved in the progression of diabetic nephropathy. This thesis in physiology provides new mechanistic insights into the regulation of renal hyaluronan during various aspects of fluid handling.

This Thesis presents studies of molecular association in aqueous solution and at the liquid/solid interface. The investigated molecular systems range from self-aggregating surfactants to hydration water in contact with micelles or individual molecules. In most studies, combinations of various NMR methods were applied. These vary from simple chemical shift and intensity measurements to more elaborate self-diffusion and intermolecular cross-relaxation experiments. Non-ideal mixed micelles of fluorinated and hydrogenated surfactants were studied by an experimental procedure that allows an analysis in terms of micellar structure, using a minimal number of initial assumptions. Quantitative conclusions about micro-phase separation within mixed micelles were obtained within the framework of the regular solution theory. Additionally, NMR was introduced and developed as a powerful method for studying adsorption of surfactants at solid interfaces. Adsorption isotherms for pure and mixed surfactant systems and non-ideal mixing behavior of fluorinated and hydrogenated surfactants at solid surfaces were quantified. Fluorosurfactant-protein association was investigated using the methods described. Intermolecular cross-relaxation rates between solute and solvent molecules were recorded at several different magnetic fields. The results reveal strong frequency dependence for both small molecules and micelles. This finding demonstrates that intermolecular cross-relaxation is not solely controlled by fast local motions, but also by long-range translational dynamics. Data analysis in terms of recently developed relaxation models provides information about the hydrophobic hydration and micellar structure. / QC 20100914

The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed.   In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods.   For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers.   For the two tungstoenzymes, several different mechanistic scenarios have been considered to identify the energetically most feasible one. For both enzymes, new mechanisms are proposed.   Finally, the mechanism of mycolic acid cyclopropane synthase has been shown to be a direct methyl transfer to the substrate double bond, followed by proton transfer to the bicarbonate.   From the studies of these enzymes, we demonstrate that density functional calculations are able to solve mechanistic problems related to enzymatic reactions, and a wealth of new insight can be obtained.

No description available.

Membrane proteins are vital for cellular homeostasis. They maintain the electrochemical gradients that are essential for signaling and control the fine balance of trace elements. In order to fulfill these tasks, they need to undergo controlled conformational transitions within the lipid bilayer of a cell membrane. It is well-recognized that membrane protein structure and function depends on the lipid membrane. However, much less is known about the role of water re-partitioning at the protein–lipid interface and particularly within a membrane protein during functional transitions. Intra-membrane protein hydration is expected to be particularly important for ion transport processes, where the hydration shell of a solvated ion needs to be rearranged and partially removed in order to bind the ion within the transporter before it is re-solvated upon exiting the membrane protein. These processes are spatially and temporally organized in metal-transporting ATPases of the PIB-subtype of P-type ATPases. Here, the functional role of water entry into the transmembrane region of the copper-transporting PIB-type ATPase CopA from Legionella pneumophila (LpCopA) has been investigated. The recombinant protein was affinity-purified and functionally reconstituted into nanodiscs prepared with the extended scaffolding protein MSP1E3D1. Nanodiscs provide a planar native-like lipid bilayer in a water-soluble nanoparticle with advantageous optical properties for spectroscopy. The small polarity-sensitive fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) was used as a probe for the molecular environment of the conserved copper-binding cysteine-proline-cysteine (CPC) motif which is located close to a wide “entry platform” for Cu+ to the transmembrane (TM) channel. The systematic study of proteins with mutated metal-binding motifs using steady-state and time-resolved fluorescence spectroscopy indicates that strong gradients of hydration and protein flexibility can exist across the narrow range of the CPC motif. The data suggest that Cu+ passes a “hydrophobic gate” at the more cytoplasmic C384 provided by rather stable TM helix packing before entering a more flexible and readily hydratable site in the interior of LpCopA around C382 where the polarity is strongly regulated by protein–lipid interactions. This flexibility could also be partly mediated by rearrangements of an adjacent amphipathic protein stretch that runs parallel to the membrane surface as a part of the cytoplasmic entry site. Using tryptophan fluorescence, circular dichroism, and Fourier-transform infrared absorption spectroscopy of a synthetic peptide derived from this segment, its lipid-dependent structural variability could be revealed. Depending on lipid-mediated helix packing interactions, the CPC motif has the potential to support a strong dielectric gradient with about ten units difference in permittivity across the CPC distance. This property may be crucial in establishing the directionality of ion transport by a non-symmetric re-solvation potential in the ion release channel of LpCopA. The experimental elucidation of these molecular details emphasizes not only the importance of intra-membrane protein water which has been hypothesized particularly for PIB-type ATPases. Moreover it is shown here, that the lateral pressure of a cell membrane may provide a force that restores a low hydration state from a transiently formed state of high internal water content at the distal side of the CPC motif. ATP-driven conformational changes that induce intra-membrane protein hydration of a conformational intermediate of the Post-Albers cycle could thus be set back efficiently by lateral pressure of the cell membrane at a later step of the cycle.

Extensive research has already been performed on Aloe vera therefore it is important that researchers include other aloe species, such as Aloe marlothii and Aloe ferox, in studies involving aloe plant materials (Loots et al., 2007:6891). The use of natural products has regained popularity and in recent years the demand for alternative medication has risen considerably (Walji & Wiktorowicz, 2013:86). The hydration state of the human skin is fundamental for its normal functioning (Verdier-Sévrain & Bonté, 2007:75), with healthy skin possessing a water content higher than 10% (w/v) (Blank, 1952:439). This demonstrates the importance of the topical application of skin moisturisers as part of basic skin care regime (Verdier-Sévrain & Bonté, 2007:75). The first part of this project focused on the in vivo skin hydration effects of the precipitated polysaccharide components of A. vera, A. ferox and A. marlothii leaf gel materials (3% (w/v)) after single (30, 90 and 150 min after application) and multiple applications (twice daily application over a period of four weeks) on healthy volunteers, respectively. The anti-erythema effects of these aloe materials on sodium lauryl sulphate irritated skin were also examined. The skin hydration effects of the aloe materials were determined with the Corneometer® CM 825 and Visioscan® VC 98 during the short term study (single application) and longer term study (multiple applications). In addition, as an indirect measurement of skin hydration, the Cutometer® dual MPA 580 was used to measure skin elasticity during the longer term study. To determine the anti-erythema effects of the aloe materials when applied to irritated skin areas, the haemoglobin content of the skin was measured with a Mexameter® MX 18. The results from the in vivo study indicated that A. ferox gel material dehydrated the skin, whereas A. vera and A. marlothii gel materials hydrated the skin during the short term study. Results from the longer term study showed that all the aloe leaf materials have skin dehydration effects, probably due to the aloe absorbing moisture from the skin into the applied gel layer upon drying. From the anti-erythema study, it was seen that A. vera and A. ferox materials had the potential to reduce erythema on the skin similar to that of the positive control group (i.e. hydrocortisone gel) after six days of treatment. The skin possesses exceptional barrier properties which can mostly be ascribed to the outermost layer of the skin, the stratum corneum (SC). Due to the physical barrier the skin has against drug permeation, the delivery of drug molecules into and across the skin continues to be challenging (Lane, 2013:13) and to overcome this barrier, penetration enhancers can be used to efficiently deliver drugs across the skin (Barry, 2002:522). The aim of the second part of this project was to determine the skin penetration enhancing effects of the gel and whole leaf materials of A. vera, A. marlothii and A. ferox. Ketoprofen was used as the marker compound and a high performance liquid chromatography (HPLC) method was developed and validated to determine the amount of ketoprofen present in the samples. Prior to the skin diffusion studies, membrane release studies were performed to test whether the solutions containing different concentrations of the aloe leaf materials (i.e. 3.00%, 1.50% and 0.75% (w/v)) released ketoprofen from their gel-like structures. From these studies, it was evident the 0.75% (w/v) concentration had the highest average percentage ketoprofen release, which was subsequently chosen as the concentration for the aloe leaf materials tested in the transdermal skin diffusion studies. The in vitro permeation study was conducted across dermatomed (400 μm thick) skin in Franz diffusion cells. Tape stripping was performed after completion of the diffusion studies to determine the concentration ketoprofen present in the SC-epidermis and epidermis-dermis layers of the skin. Results from the in vitro permeation study showed that A. vera gel enhanced the flux of ketoprofen to the highest extent (20.464 μg/cm2.h) when compared to the control group (8.020 μg/cm2.h). Aloe marlothii gel (12.756 μg/cm2.h) and A. ferox whole leaf material (12.187 μg/cm2.h) also enhanced the permeation of ketoprofen across the skin compared to the control group. A. vera gel material was the most efficient transdermal drug penetration enhancer of the selected aloe species investigated. In order to determine by which mechanism the aloe leaf materials enhanced the skin permeation of ketoprofen (Hadgraft et al., 2003:141), the permeation profiles were analysed using a non-linear curve-fitting procedure (Díez-Sales et al., 1991:3) to obtain α, β and kp values. A change in the α-value indicated the aloe leaf material influenced the partition coefficient (K), whereas a change in β indicated the aloe leaf material influenced the diffusivity (D) (with the assumption that h, the diffusional path length is constant) (Otto et al., 2010:278). The calculated α-values indicated the drug permeation enhancing effect of A. vera gel can be ascribed to an increased partitioning of the drug into the skin. The calculated β-values showed A. ferox whole leaf altered the diffusion characteristics of the skin for ketoprofen. The tape stripping results showed A. marlothii whole leaf delivered the highest concentration of the ketoprofen into the SC-epidermis and epidermis-dermis layers of the skin. / PhD (Pharmaceutics), North-West University, Potchefstroom Campus, 2014

Extensive research has already been performed on Aloe vera therefore it is important that researchers include other aloe species, such as Aloe marlothii and Aloe ferox, in studies involving aloe plant materials (Loots et al., 2007:6891). The use of natural products has regained popularity and in recent years the demand for alternative medication has risen considerably (Walji & Wiktorowicz, 2013:86). The hydration state of the human skin is fundamental for its normal functioning (Verdier-Sévrain & Bonté, 2007:75), with healthy skin possessing a water content higher than 10% (w/v) (Blank, 1952:439). This demonstrates the importance of the topical application of skin moisturisers as part of basic skin care regime (Verdier-Sévrain & Bonté, 2007:75). The first part of this project focused on the in vivo skin hydration effects of the precipitated polysaccharide components of A. vera, A. ferox and A. marlothii leaf gel materials (3% (w/v)) after single (30, 90 and 150 min after application) and multiple applications (twice daily application over a period of four weeks) on healthy volunteers, respectively. The anti-erythema effects of these aloe materials on sodium lauryl sulphate irritated skin were also examined. The skin hydration effects of the aloe materials were determined with the Corneometer® CM 825 and Visioscan® VC 98 during the short term study (single application) and longer term study (multiple applications). In addition, as an indirect measurement of skin hydration, the Cutometer® dual MPA 580 was used to measure skin elasticity during the longer term study. To determine the anti-erythema effects of the aloe materials when applied to irritated skin areas, the haemoglobin content of the skin was measured with a Mexameter® MX 18. The results from the in vivo study indicated that A. ferox gel material dehydrated the skin, whereas A. vera and A. marlothii gel materials hydrated the skin during the short term study. Results from the longer term study showed that all the aloe leaf materials have skin dehydration effects, probably due to the aloe absorbing moisture from the skin into the applied gel layer upon drying. From the anti-erythema study, it was seen that A. vera and A. ferox materials had the potential to reduce erythema on the skin similar to that of the positive control group (i.e. hydrocortisone gel) after six days of treatment. The skin possesses exceptional barrier properties which can mostly be ascribed to the outermost layer of the skin, the stratum corneum (SC). Due to the physical barrier the skin has against drug permeation, the delivery of drug molecules into and across the skin continues to be challenging (Lane, 2013:13) and to overcome this barrier, penetration enhancers can be used to efficiently deliver drugs across the skin (Barry, 2002:522). The aim of the second part of this project was to determine the skin penetration enhancing effects of the gel and whole leaf materials of A. vera, A. marlothii and A. ferox. Ketoprofen was used as the marker compound and a high performance liquid chromatography (HPLC) method was developed and validated to determine the amount of ketoprofen present in the samples. Prior to the skin diffusion studies, membrane release studies were performed to test whether the solutions containing different concentrations of the aloe leaf materials (i.e. 3.00%, 1.50% and 0.75% (w/v)) released ketoprofen from their gel-like structures. From these studies, it was evident the 0.75% (w/v) concentration had the highest average percentage ketoprofen release, which was subsequently chosen as the concentration for the aloe leaf materials tested in the transdermal skin diffusion studies. The in vitro permeation study was conducted across dermatomed (400 μm thick) skin in Franz diffusion cells. Tape stripping was performed after completion of the diffusion studies to determine the concentration ketoprofen present in the SC-epidermis and epidermis-dermis layers of the skin. Results from the in vitro permeation study showed that A. vera gel enhanced the flux of ketoprofen to the highest extent (20.464 μg/cm2.h) when compared to the control group (8.020 μg/cm2.h). Aloe marlothii gel (12.756 μg/cm2.h) and A. ferox whole leaf material (12.187 μg/cm2.h) also enhanced the permeation of ketoprofen across the skin compared to the control group. A. vera gel material was the most efficient transdermal drug penetration enhancer of the selected aloe species investigated. In order to determine by which mechanism the aloe leaf materials enhanced the skin permeation of ketoprofen (Hadgraft et al., 2003:141), the permeation profiles were analysed using a non-linear curve-fitting procedure (Díez-Sales et al., 1991:3) to obtain α, β and kp values. A change in the α-value indicated the aloe leaf material influenced the partition coefficient (K), whereas a change in β indicated the aloe leaf material influenced the diffusivity (D) (with the assumption that h, the diffusional path length is constant) (Otto et al., 2010:278). The calculated α-values indicated the drug permeation enhancing effect of A. vera gel can be ascribed to an increased partitioning of the drug into the skin. The calculated β-values showed A. ferox whole leaf altered the diffusion characteristics of the skin for ketoprofen. The tape stripping results showed A. marlothii whole leaf delivered the highest concentration of the ketoprofen into the SC-epidermis and epidermis-dermis layers of the skin. / PhD (Pharmaceutics), North-West University, Potchefstroom Campus, 2014

Numerous recurrent situations following mixing and pumping of mortars and concretes cause degradation of fluidity and hardening characteristics. Which, in turn, lead to adverse effects on the quality of workmanship and structural defects. Nonetheless, relatively little research on the mixing and pumping energies used for the onsite transport and preparation of mortar or concrete has been directed at the core reasons or mechanisms for changes in technological properties. This dissertation describes and explains the effects of various mixing and pumping parameters on the mortar characteristics in a field trial and on a laboratory scale. Observations using a rheograph revealed that shearing action does exhibit the most pronounced influence on the characteristics of mortars during the pumping. The performed investigations indicate that higher shearing actions, for example, excessive mixing duration and long-distance pumping lead to reduced flowability, accelerated and increased hydration rate, increased early compressive strength and early-age shrinkage. From these findings, the underlying mechanism responsible for acceleration and increase of hydration rate is pinpointed as: the increased dissolution from the active surface area due to the destruction of the protective superficial layers of cement grains, as well as a transition from flocculation to dispersion. The creation of new surfaces leads to further consumption of active super plasticizer in solution phase and to subsequent degrading changes in fluidity (decreasing flowability). The degradation of fluidity and densification of microstructure provoked by the hydration changes do increase the early age shrinkage of mortar.

Most metals and alloys in the presence of oxygen and moisture will instantaneously react and form a thin (2-5 nm) surface oxide layer. For further reaction to occur, oxygen ions and/or metal cations often diffuse through the already formed oxide layer. The corrosion resistance of a metal in aggressive environments at high temperatures depends on the properties of the surface oxide scale. Zirconium-based alloys represent the main structural materials used in water-cooled nuclear reactors. For these materials, the formation of a thin, adherent oxide scale with long-term stability in high temperature water/steam under irradiation conditions, is crucial. In this thesis, the transport of oxygen and hydrogen through Zr-based oxide scales at relevant temperatures for the nuclear industry is investigated using isotopic gas mixtures and isotope-monitoring techniques such as Gas Phase Analysis and Secondary Ion Mass Spectrometry. Porosity development in the oxide scales generates easy diffusion pathways for molecules across the oxide layer during oxidation. A considerable contribution of molecular oxygen to total oxygen transport in zirconia has been observed at temperatures up to 800°C. A novel method for evaluation of the gas diffusion, gas concentration and effective pore size of oxide scales is presented in this thesis. Effective pore sizes in the nanometer range were found for pretransition oxides on Zircaloy-2. A mechanism for densification of oxide scales by obtaining a better balance between inward oxygen and outward metal transport is suggested. Outward Zr transport can be influenced by the presence of hydrogen in the oxide and/or metal substrate. Inward oxygen transport can be promoted by oxygen dissociating elements such as Fe-containing second phase particles. The results suggest furthermore that a proper choice of the second-phase particles composition and size distribution can lead to the formation of dense oxides, which are characterized by low oxygen and hydrogen uptake rates during oxidation. Hydrogen uptake in Zr-based materials during oxidation in high temperature water/steam can generate degradation due to the formation of brittle hydrides in the metal substrate. A promising method for the suppression of hydrogen uptake has been developed and is presented in this thesis. / QC 20100629