Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding

Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

Stabilisation of dehydrated nanoemulsions using sugar - protein matrices

There are numerous review papers discussing liquid nanoemulsions and how they compare to other emulsion systems. Little research is available on dried nanoemulsions. The objectives of this research were to (i) study the effect of varying the continuous phase of nanoemulsions with different carbohydrate/protein ratios on subsequent emulsion stability, and (ii) compare the physicochemical properties, lactose crystallisation properties, microstructure, and lipid oxidation of spray dried nanoemulsions compared to spray dried conventional emulsions having different water and sugar contents. Nanoemulsions containing sunflower oil (10% w/w), β-casein (2.5–10% w/w) and lactose or trehalose (10–17.5%) were produced following optimisation of the continuous phase by maximising and minimising viscosity and glass transition temperature (Tg’) using mixture design software. Increasing levels of β-casein from caused a significant increase in viscosity, particle size, and nanoemulsion stability, while resulting in a decrease in Tg’. Powders were made from spray drying emulsions/nanoemulsions consisting of lactose or a 70:30 mixture of lactose:sucrose (23.9%), sodium caseinate (5.1%) and sunflower oil (11.5%) in water. Nanoemulsions, produced by microfluidisation (100 MPa), had higher stability and lower viscosity than control emulsions (homogenization at 17 MPa) with lower solvent extractable free fat in the resulting powder. Partial replacement of lactose with sucrose decreased Tg and delayed Tcr. DVS and PLM showed that in powdered nanoemulsions, lactose crystallises faster than in powdered conventional emulsions. Microstructure of both powders (CLSM and cryo-SEM) showed different FGS in powders and different structure post lactose crystallisation. Powdered nanoemulsions had lower pentanal and hexanal (indicators of lipid oxidation) after 24 months storage due to their lower free fat and porosity, measured using a validated GC HS-SPME method, This research has shown the effect of altering the continuous phase of nanoemulsions on microstructure of spray dried nanoemulsions, which affects physical properties, sugar crystallisation, and lipid oxidation.

Effects of various salt purity levels on lipid oxidation and sensory characteristics of ground turkey and pork

Salt use in meat products is changing. Consumers desire sea salt which may also contain trace metals and the government is demanding a reduction in sodium. Therefore a need exists to understand how varying impurity levels in salt affect meat quality. This study evaluated the effects of various salt preparations on lipid oxidation, sensory characteristics, protein extractability, and bind strength of ground turkey and pork. This study was a completely randomized design with 5 treatment groups and 6 replications in 2 species. Ground, turkey and pork meat was formulated into one hundred and fifty gram patties with sodium chloride (1%) containing varying amounts of metal impurities (copper, iron, and manganese). Samples were randomly assigned to frozen storage periods of 0, 3, 6, and 9 weeks. After storage, samples were packaged in PVC overwrap and stored under retail display for 5 days. Samples were evaluated for proximate analysis to ensure the fat content was similar for all of the starting material.Thiobarbituric acid reactive substances (TBARS) were determined on raw and cooked samples to evaluate lipid oxidation. A trained six member sensory panel evaluated the samples at each storage period for saltiness, off flavor, and oxidized odor. Break strength was conducted using a Texture Analyzer and compared with salt soluble proteins (increasing salt concentrations) to evaluate protein extractability characteristics. Statistical analyses were conducted using the MIXED procedure of SAS within repeated measures over time where appropriate. No significant differences were observed among the salt treatments for raw and cooked TBARS when the control group was removed (P>0.05). Sensory panelists detected increased levels of off flavor and oxidized odor over the entire storage duration. Less force was required to break the patties from the control group when compared with the salt treatments (P<0.05). As salt concentration increased salt-soluble protein extraction increased, but there was no effect of salt type. Overall, no meaningful statistical differences among the various salt treatments were observed for all of the parameters evaluated for turkey and pork. Salt at a 1% inclusion rate containing varying levels of copper, iron, and manganese impurities in ground turkey thigh meat and ground pork served as a prooxidant. However, if a meat processor uses a 1% inclusion rate of salt in turkey and pork regardless of impurities included, it is unlikely that differences in shelf life or protein functionality would be observed.

On the temperature stability of extracellular hemoglobin of Glossoscolex paulistus, at different oxidation states: SAXS and DLS studies

Glossoscolex paulistus hemoglobin (HbGp) was studied by dynamic light scattering (DLS) and small angle X-ray scattering (SAXS). DLS melting curves were measured for met-HbGp at different concentrations. SAXS temperature studies were performed for oxy-, cyanomet- and met-HbGp forms, at several pH values. At pH 5.0 and 6.0, the scattering curves are identical from 20 to 60 degrees C, and R-g is 108 angstrom, independent of the oxidation form. At pH 7.0, protein denaturation and aggregation occurs above 55 degrees C and 60 degrees C, for oxy and met-HbGp, respectively. Cyanomet-HbGp, at pH 7.0, is stable up to 60 degrees C. At alkaline pH (8.0-9.0) and higher temperature, an irreversible dissociation process is observed, with a decrease of R-g, D-max and I(0). Analysis by p(r), obtained from GNOM, and OLIGOMER, was used to fit the SAXS experimental scattering curves by a combination of theoretical curves obtained for HbLt fragments from the crystal structure. Our results show clearly the increasing contribution of smaller molecular weight fragments, as a function of increasing pH and temperature, as well as, the order of thermal stabilities: cyanomet-> oxy- > met-HbGp. (C) 2012 Elsevier B.V. All rights reserved.

Ultra high-pressure homogenized emulsions stabilized by sodium caseinate: effects of protein concentration and pressure on emulsions structure and stability

Microstructure, physical properties and oxidative stability of emulsions treated by colloid mill (CM), conventional homogenization (CH, 15 MPa) and ultra-high-pressure homogenization (UHPH, 100–300 MPa) by using different concentrations of 1, 3 and 5 g/100 g of sodium caseinate (SC), were evaluated. The application of UHPH treatment at 200 and 300 MPa resulted in emulsions that were highly stable to creaming and oxidation, especially when the protein content increased from 1 to 3 and 5 g/100 g. Further, increasing the protein content to 3 and 5 g/100 g in UHPH emulsions tended to change the rheological behavior from Newtonian to shear thinning. CH emulsions containing 1 g/100 g of protein exhibited Newtonian flow behavior with lower tendencies to creaming compared to those formulated with 3 or 5 g/100 g. This study has proved that UHPH processing at pressures (200–300 MPa) and in the presence of sufficient amount of sodium caseinate (5 g/100 g), produces emulsions with oil droplets in nano-/submicron scale with a narrow size distribution and high physical and oxidative stabilities, compared to CM and CH treatments.

Time-Dependent Density Functional Molecular Orbital and Excited State Calculations on Bis(porphyrinyl)butadiynes in the Monocationic, Neutral, Monoanionic, and Dianionic Oxidation States

We report a theoretical study of the multiple oxidation states (1+, 0, 1−, and 2−) of a meso,meso-linked diporphyrin, namely bis[10,15,20-triphenylporphyrinatozinc(II)-5-yl]butadiyne (4), using Time-Dependent Density Functional Theory (TDDFT). The origin of electronic transitions of singlet excited states is discussed in comparison to experimental spectra for the corresponding oxidation states of the close analogue bis{10,15,20-tris[3‘,5‘-di-tert-butylphenyl]porphyrinatozinc(II)-5-yl}butadiyne (3). The latter were measured in previous work under in situ spectroelectrochemical conditions. Excitation energies and orbital compositions of the excited states were obtained for these large delocalized aromatic radicals, which are unique examples of organic mixed-valence systems. The radical cations and anions of butadiyne-bridged diporphyrins such as 3 display characteristic electronic absorption bands in the near-IR region, which have been successfully predicted with use of these computational methods. The radicals are clearly of the “fully delocalized” or Class III type. The key spectral features of the neutral and dianionic states were also reproduced, although due to the large size of these molecules, quantitative agreement of energies with observations is not as good in the blue end of the visible region. The TDDFT calculations are largely in accord with a previous empirical model for the spectra, which was based simplistically on one-electron transitions among the eight key frontier orbitals of the C4 (1,4-butadiyne) linked diporphyrins.