Browsing by Subject "protein"
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Item A structural and energetic description of protein-protein interactions in atomic detail(Texas A&M University, 2007-04-25) Fischer, Tiffany BrinkHere, we present the program QContacts, which implements Voronoi polyhedra to determine atomic and residue contacts across the interface of a protein-protein interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge interactions, we focus on QContacts?????? identification of atomic contacts in a protein interface compared against the current methods. Initially, we investigated in detail the differences between QContacts, radial cutoff and Change in Solvent Accessible Surface Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface. The results were assessed based on a set of 71 double cycle mutants. QContacts excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and the delta-SASA methods performed well at picking out direct contacts; however, QContacts was the most accurate in excluding false positives. The significance of the differences identified between QContacts and previous methods was assessed using pair-wise contact frequencies in a broader set of 592 protein interfaces. The inaccuracies introduced by commonly used radial cutoff methods were found to produce misleading bias in the residue frequencies. This bias could compromise pair-wise potentials that are based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons (Fischer et al., 2006).Item An assessment of kilocalories and protein in the diets of HIV-infected adults in Kenya(2011-05-15) Elizabeth Mary Vaughan; Victor Cardenas, MD; Harvey Bunce, PhD; Christine Arcari, PhDINTRODUCTION: The detrimental effects of HIV are well known throughout the world. This public health burden is particularly evident in Kenya, Africa, where 6.7% of adults are infected with HIV. One problem of those living with HIV in this resource-poor country is the concurrent existence of malnutrition. Previous investigators undertook many studies to bridge the link between HIV and malnutrition. However, they were unable to gather individual diet information to allow accurate estimation of kilocalorie and protein needs. These deficits hinder accurate dietary interventions for these patients. \r\nMETHODS: Over the period of April 2009 to August 2009, we designed and implemented a dietary instrument (3-day recall survey) to assess the kilocalorie and protein consumption for HIV-infected adults in Kijabe, Kenya. We used this data to compare subject consumption to predicted nutrient needs. We used Harris-Benedict (HB) and Mifflin formulas for kilocalorie need predictions and World Health Organization (WHO) equation for protein need predictions. We then characterized the relationship between dietary intake, BMI and CD4 levels.\r\nRESULTS: A total of 201 patients were surveyed, 122 (60.7% [27% males, 73% females]) met inclusion criteria. There was no statistical difference between HB and Mifflin equations for kilocalories. Males averaged 68.8% (SD 23.3) of estimated kilocalorie requirements (HB) and 100.5% (SD 45.3) of protein. Women averaged 74.4% (SD 24.4) of kilocalorie needs (HB) and 100.5% (SD 42.5) of protein. Differences between genders were not statistically significant (p=0.247 [kilocalorie], p=0.936 [protein]). There was a significant correlation between protein intake and CD4 for males (r=0.7035, p=0.0004) but not for females (r=-0.1911, p=0.1546). There was no statistical significance found between kilocalories (male r=0.104, p=0.654; female r=0.0420, p=0.765) and CD4. No relationship was found between nutrient intake and BMI (male p=0.690; female p=0.477).\r\nCONCLUSIONS: A 3-day recall dietary assessment appears to be an adequate method to obtain dietary information for adult HIV patients in East Africa. Further, we conclude that current predictive formulas for protein underestimate needs in the male HIV population. \r\nItem Diet-mixing in a Generalist Herbivore: Trade-offs Between Nutrient and Allelochemical Regulation(2014-05-07) Le Gall, MarionDespite decades of research, many key aspects related to the physiological processes and mechanisms insect herbivores use to build themselves remain poorly understood, and we especially know very little about how interactions among nutrients and allelochemicals drive insect herbivore growth processes. Understanding the physiological effects of these interactions on generalist herbivores is a critical step to a better understanding and evaluation of the different hypothesis that have been emitted regarding the benefits of polyphagy. I used both lab and field experiments to disentangle the respective effect of protein, carbohydrates and allelochemicals on a generalist herbivore, the grasshopper Melanoplus differentialis. The effect of protein and carbohydrates alone were examined using artificial diets in choice and no-choice experiments. Results were plotted using a fitness landscape approach to evaluate how protein-carbohydrate ratio and/or concentration affected performance and consumption. Growth was best near the self-selected ratio obtained from the choice experiment, most likely due to the fact that the amount of food digested was also higher on that ratio. By contrast, development time was not best near the preferred ratio most likely due to the trade-off existing between size and development time. These results illustrate how nutrient availability can shape an ecological trade-off: growing big or growing fast. When an allelochemical (gramine, an alkaloid commonly found in grass) was introduced to the artificial diets, it had an interactive effect with protein and carbohydrates on performance and consumption and performance were generally improved on diets that contained higher amount of protein. Host plants of two wild populations were determined by gut content analysis and fed in choice and no-choice experiment. First the plant material was dried and ground and its protein, carbohydrate, terpenoid and phenolic content analyzed. Both populations regulated for the same protein-carbohydrate intake. However performance was different, due to variation in plant allelochemical content. This demonstrated for the first time that nutrient regulation, not toxin dilution, is directing food selection behavior in a generalist herbivore. Finally the role of macronutrients was analyzed in a context of cost of detoxification by measuring microsomal p450 production in the presence/absence of gramine. In the presence of choice, nutrient regulation was altered when gramine was present in the protein-biased diet. In the absence of choice, insects performed better on carbohydrate biased diet. I found that gramine elevated the level of microsomal protein in the fat body.Item Dissolution Dynamic Nuclear Polarization of Polypeptides(2014-06-27) Ragavan, MukundanNuclear Magnetic Resonance (NMR) spectroscopy provides remarkable site resolution, but often requires signal averaging because of low sensitivity. Dissolution dynamic nuclear polarization (DNP), which offers large signal enhancements, has been used to follow reactions involving small molecules that typically have long spin-lattice relaxation times. This thesis presents work in the development of dissolution DNP to directly hyper-polarize and observe polypeptides, which can subsequently be used for the study of a time dependent process, such as folding. Dissolution DNP involves hyperpolarizing samples in the solid state, dissolving the samples with a stream of hot solvent and rapid transfer of the sample into an NMR tube for measurement in the solution state. Since protein samples are prone to foam under conditions for rapid sample injection, solvent systems were optimized. Solvents such as water/acetonitrile and water/methanol mixtures were utilized. An unlabeled peptide, bacitracin, was hyperpolarized on ^(1)H nuclei and enhancements of 30, 45 and 180 were obtained for amide, aliphatic and aromatic protons respectively. Although these enhancements are already significant, loss of hyperpolarization during sample injection was further alleviated by the use of isotopically enriched polypeptides. In [^(13)C, 50% ^(2)H] labeled samples of denatured L23, a 96 amino acid long ribosomal protein, signal enhancements of more than 500 times were obtained on the ^(13)C nuclei. This signal enhancement was then exploited to follow the protein folding process, using L23 as a model. Time resolved spectra of hyperpolarized L23 were measured after a pH jump and protein folding was monitored by observing changes in the carbonyl region of the spectra, which are indicative of the formation of secondary structures. Despite signal overlap in the protein spectra, using the statistical distribution of ^(13)C chemical shifts, the fractions of secondary structure elements were estimated for each scan of the DNP-NMR experiment. Additionally, individual resonances for methyl groups upfield of other protein resonances became resolved in the later transients. An option for the improvement of such site resolution by NMR experiments using coherence selection is discussed. While DNP-NMR offers the capability to observe transient species, identification of such species is difficult in cases where not all chemical shifts are known. Here, a new strategy for the analysis of DNP-NMR data is proposed based on non-negative matrix factorization (NNMF). NNMF enables identification of various sources that contribute to an observed signal. This capability is demonstrated using a series of spectra measured from an enzymatic conversion reaction of oxaloacetic acid to malic acid. Simulations were carried out to evaluate the performance of NNMF under different experimental constraints, and the strengths and limitations of the method are discussed based on the simulations.Item Effect of Increasing Protein Supplementation on Intake and Digestion of Bermudagrass Hays of Divergent Quality by Beef Cattle(2012-07-16) Payne, Catherine PomeroyBermudagrass (Cynodon dactylon (L) Pers.), one of the predominant forages in the southeastern US, varies in nutritive value in response to management and environmental factors. Beef cattle supplementation decisions are complicated by this variability. Therefore, our objective was to determine the effect of four protein supplementation levels (0, 82, 119 and 155 mg N/kg BW) on the utilization of three bermudagrass hays (5.6, 6.3, and 8.1 percent CP).Thirteen ruminally fistulated Angus x Hereford steers (BW = 330 plus/minus 19 kg) were used in a 13 x 4 incomplete Latin square design with 13 treatments. Treatments were arranged as a 3 x 4 factorial plus a control bermudagrass hay (10.8 percent CP). Hay was provided ad libitum and protein supplements were offered as range cubes once daily. Periods were 15 d with intake determinations made on d 10 through d 13 to correspond with fecal grab samples collected from d 11 through d 14. Acid detergent insoluble ash was used as an internal marker for determination of fecal output. Hay OM intake of unsupplemented steers increased linearly (P < 0.01) as hay nutritive value increased from 75 to 77, 96 and 94 g/kg BW^0.75 for 5.6, 6.3, 8.1 and 10.8 percent CP hays, respectively. A cubic increase (P = 0.03) in OM digestibility for unsupplemented hays was observed with values ranging from 46 to 65 percent. This resulted in a linear increase (P < 0.01) in total digestible OM intake in response to hay nutritive value from 35 to 45, 51, and 60 g/kg BW^0.75 for 5.6, 6.3, 8.1, and 10.8 percent CP hays, respectively. No significant effects on total digestible OM intake were observed when hays were supplemented with protein. There was a tendency for forage OM intake of the 6.3 percent CP hay to increase linearly with supplemental protein (P = 0.08). Total OM intake increased linearly (P < 0.01) when CP was supplemented to the 6.3 percent CP hay from 77 to 88, 92, and 98 g/kg BW^0.75 for 0, 82, 119, and 155 mg N/kg BW, respectively. We conclude that forage CP content was the primary driver in determining total digestible OM intake, and the effects of protein supplementation on utilization of bermudagrass hay were varied.Item Effects of Higher Carbohydrate or Higher Protein Diets with Exercise on Individual Risk Factors of Metabolic Syndrome in Women(2014-03-18) Lockard, BrittanieThe purpose of this analysis was to determine whether following a higher protein (HP) diet for 10-weeks promotes a reduction of MetS and the individual NCEP ATP III MetS risk factors better than a higher carbohydrate (HC) diet, when combined with an exercise program. 633 women (age 46.2?11.4 yrs, height 163?7 cm, weight 92.7?18 kg, BMI 34.8?6 kg/m^(2)) were assigned either a HP or HC diet in conjunction with 30 minutes of circuit-style exercise 3x/wk for 10-weeks. Participants consumed 1,425?355 kcal/day while the HP group (N=371) consumed 1.14?0.5, 1.41?0.7, and 0.63?0.3 g/kg/d CHO, PRO, fat and the HC group (N=292) consumed 0.78?0.3, 2.20?0.7, and 0.60?0.2 g/kg/d. Participants were retrospectively categorized as apparently healthy (N=377) or metabolic syndrome (?3 MetS risk factors, N=286). Body composition, anthropometrics, resting energy expenditure, lipid profiles, markers of glucose homeostasis, and fitness parameters were assessed at 0 and 10 weeks. Data were analyzed using ANOVA or MANOVA for repeated measures. The HP group experienced a greater decrease in scanned mass (HP -3.9?3.5, HC -3.0?3.5 kg, p=0.002), fat mass (HP-3.1?2.7, HC -2.4?2.8 kg, p=0.003), weight (HP -4.3?3.6, HC -3.2?3.4 kg, p<0.001), and body mass index (HP -1.6?1.3, HC -1.2?1.3 kg/m^(2), p<0.001), and tended to experience a greater decrease in waist circumference (HP -4.0?5.7, HC -3.2?5.7 cm, p=0.07). Individuals with MetS experienced greater decreases in weight (AH -3.6?3.4, MS -4.2?3.6 kg, p=0.054), body mass index (AH -1.3?1.3, MS -1.6?1.3 kg/m2, p=0.046), systolic blood pressure (AH -0.5?13.3, MS -5.9?16.0 mmHg, p<0.001), diastolic blood pressure (AH -0.4?8.9, MS -4.1?10.5 mmHg, p<0.001), triglycerides (AH -0.00?0.47, -0.23?0.73 mmol/L, p<0.001), and glucose (AH +0.01?0.73, MS -0.24?1.19 mmol/L, p=0.001) and a trend towards a greater decrease in scanned mass (AH -3.3?3.5, MS -3.8?3.5 kg, p=0.07) and lean mass (AH -0.56?2.0, MS -0.89?2.0 kg, p=0.07). Results indicate that participants following the HP diet experienced more favorable changes in body composition and triglyceride levels, and that participants with MetS have greater room for improving markers of health on a diet and exercise protocol.Item Effects of Protein Supplementation and Forage Quality on Intake and Digestion in Cattle(2012-02-14) Kunkel, JamieIn many pasture and rangeland scenarios, low-quality forages (< 6-8% CP) are the primary energy source for some portion of the year. At these times, energy is typically the first limiting nutrient to the ruminant. Low-quality forages are generally not limited in availability; however, the high cell wall content and reduced levels of CP prevent ruminants from being able to extract the harvested energy. Without provision of supplemental nutrients, the available energy may be inadequate to meet performance expectations. Protein supplementation during periods of inadequate forage quality has been observed to alleviate ruminal nitrogen deficiencies and increase forage utilization. Increased forage utilization translates into greater energy extraction allowing for increased animal performance. The first trial was conducted to evaluate the effects of utilizing non-protein nitrogen (a slow-release urea compared to urea) on intake and digestion of beef steers consuming low-quality bermudagrass hay. Steers were provided ad libitum access to a low-quality bermudagrass hay (7.3 % CP and were ruminally dosed once daily with either urea or slow-release urea (SRU) at levels to provide 0, 64, 128, or 192 mg of N/kg of initial BW per day. Additionally, steers were supplemented with glycerol at levels of 0 or 0.1% of initial BW per day. Total OMI and forage OMI (FOMI) increased quadratically (P < 0.01) with NPN supplementation. However there was not a difference in total OMI or FOMI between urea and the SRU (P = 0.24 and 0.21, respectively). The largest increases in FOMI and total OMI occurred with the first level of supplementation (64 mg N/kg BW) for both urea and SRU and intake peaked when 128 mg N/kg BW was supplemented. Total OMD was not affected by N supplementation level however N from urea tended to elicit a greater response than from the SRU (P = 0.01). Ruminal OMD increased linearly (P = 0.07) and ruminal NDF digestion increased quadratically (P = 0.09) with N supplementation. The second experiment was conducted to evaluate the effects of hay crude protein and protein supplementation on intake and digestion in beef steers. Steers received one of three bermudagrass (Cynodon Dactylon) hays of differing nutritive value (7.0, 8.4, or 13.4% CP) and either 0 or 156 mg N/kg BW supplemented as cottonseed meal once daily. No significant Hay x CSM interactions were observed for hay OMI, total OMI, TDOMI, or digestible NDF intake (P >= 0.67). Hay OMI and total OMI increased linearly (P < 0.01) with hay nutritive value. A quadratic response (P = 0.03) was observed for TDOMI with increasing hay nutritive value. This response was largely driven by a quadratic increase (P < 0.01) in OM digestion with increasing nutritive value of hays. Supplementing CSM generally did not affect HOMI (P = 0.63) although TDOMI (P = 0.03) was increased. Similarly, OM digestion (P = 0.61) and NDF digestion (P = 0.11) were not impacted by CSM supplementation.Item Effects of Sorghum Polyphenols on In Vitro Starch Digestibility and Protein Profile of Wheat Flour Tortillas(2014-04-22) Dunn, Kristen LeaAs incidences of diseases associated with dietary patterns increase in the United States, focus has been placed on improving nutritional quality of processed foods. Carbohydrates contribute the most calories in the American diet (55%), making starch-based foods a target for improvement. Tortillas are increasingly popular among American consumers, serving as a good target to address this problem. This study investigated the use of sorghum bran to increase polyphenols and dietary fiber in wheat flour tortillas and the effect on starch digestibility and protein profiles. Refined wheat flour tortillas were substituted at 10%, 15%, and 25% (Baker?s) with brans from wheat and white, brown, and black sorghum. Dough rheology, phenolic profile, starch digestibility, and protein profiles were evaluated after dough formation, hot pressing, baking, and over 14 days of storage. Bran substitution affected dough rheology, producing rougher, stiffer, less extensible dough compared to the refined control. Processing, storage, and bran source significantly affected the phenolic profile of the tortillas. Total phenols, 3- deoxyanthocyanins, and proanthocyanidins (PA) decreased with processing and storage. Dough formation drastically decreased phenol content in brown sorghum bran dough compared to other treatments. Extractable high molecular weight PA also decreased dramatically after processing by 58 ? 76% in brown sorghum bran tortillas. These tortillas had less rapidly digestible starch and more slowly digestible starch than other treatments at 25% substitution. Compared to the expected total dietary fiber (TDF), sorghum brans doubled the formation of TDF (20 ? 26%) as compared to wheat bran (11%). The largest increase was observed in brown sorghum bran tortillas. In tortillas substituted at 25%, insoluble protein (IP) increased with baking and storage as extractable protein (EP) decreased. Within the EP fraction, soluble polymeric protein (SPP) decreased by 40 ? 61% after baking. Brown sorghum bran dough contained significantly higher IP and lower SPP than other treatments; however, this effect was reduced after baking. Sorghum brans provided polyphenols that interacted with protein and starch in wheat flour tortillas. PA and SPP largely contributed to these interactions, forming insoluble complexes that decreased tortilla digestibility and may positively benefit weight management.Item Insect Herbivore Stoichiometry: The Effect of Macronutrient Quantity, Ratio, and Quality (Orthoptera: Acridae, Schistocerca americana)(2011-02-22) Boswell, Andrew William PayneThe field of ecological stoichiometry has been dominated by studies focusing on aquatic & benthic microinvertabrates with less attention given to herbivorous insects. These organisms rely on their food source(s) to supply all of the building blocks (elements) they need in order to complete their life cycle. Since insect herbivores do not have the same elemental composition as the plants they use for food the question arises; of how they go about building themselves. We investigated what happened when grasshoppers were fed diets with various macronutrient profiles, their total amounts, and when the protein quality varied. We discovered that under controlled conditions when using a high quality protein source that grasshoppers are able to maintain a strict level of elemental homeostasis, but that the elements directly related to manipulations made in the food seem to vary (carbon, which is associated with carbohydrates and nitrogen, associated with protein). We also discovered that when the quality of protein changes an immature grasshoppers elemental stoichiometry loses some of this strict homeostatic regulation.Item Intein Engineering for Protien Hydrogel Synthesis and Protein Purification(2013-11-26) Ramirez, Miguel AngelInteins are proteins encoded within a precursor gene that excise themselves after translation and ligate the surrounding proteins with a peptide bond. Since their discovery two decades ago, many inteins have been engineered for various biotechnology applications. This dissertation focuses on the use and development of intein-based technologies for applications in protein purification and immobilization. The highly efficient naturally split DnaE intein from Nostoc punctiforme (Npu DnaE) was incorporated into synthetic protein building blocks for the synthesis of protein hydrogels, and engineered to catalyze rapid C-terminal cleavage reaction and used in the rapid purification of tag-less protein. In the first application, we developed protein hydrogels as general scaffolds for protein immobilization. Immobilization has been shown to increase protein stability and facilitate enzyme recovery-and-recycle tasks. These hydrogels are composed of artificial protein building-blocks expressed in bacterial hosts. Hydrogel gelation is catalyzed by intein-mediated protein trans-splicing reactions or disulfide bond formation between different protein building blocks. The resulting artificial protein hydrogels possess high solution stability at a wide range of pHs and temperatures, undergo shear-thinning, and are compatible with organic solvents. These self-assembled protein hydrogels can protect immobilized enzymes from organic solvent denaturation during biosynthesis, be used in enzymatic biofuel cells, and are suitable for the immobilization of multiple enzymes. In the second application, we engineered the Npu DnaE intein to catalyze rapid thio-induced C-terminal cleavage reaction and subsequently developed a split intein mediated technology for recombinant protein purification (SIRP). SIRP enables efficient purification of tag-less recombinant protein from E. coli lysate in less than 1 hour ? the hitherto fastest reported intein technology for protein purification.Item Interfacial Interactions between Biomolecules and Materials(2012-10-19) Rocha-Zapata, AracelyThis research investigates the interfacial interactions between biological entities and synthetic materials at two length scales: bulk and nanometer size. At the bulk scale, biomolecule adhesion is key for synthetic material incorporation in the body. Quantifying the adhesion strength becomes necessary. For the nanometer scale, the nanoparticles are generally delivered through the blood stream and their effect on the blood flow must be studied. An experimental approach was taken to study interaction at both material length scales. The cell/protein adhesion strength to bulk-sized materials was studied. The goal was to identify the most influential factor affecting adhesion: chemistry or surface roughness. The effects of nanoparticles on the viscosity of protein and amino acid solutions were measured. A statistical thermodynamic analysis was focused on the entropy change induced by the addition of gold nanoparticles to protein/amino acid solutions. Rheological studies were applied. A rheometer with a parallel plate was used to quantify the adhesion strength of cells and proteins to synthetic surfaces at the bulk scale. The adhesion strength depends on the applied shear stress and the radius of cells or proteins that remained attached to the surface after testing. At the nanometer scale, the viscosity of the nanoparticle enhanced protein or amino acid solutions were measured with a cone and plate. The adhesion studies were conducted with the following biological entities: fibroblasts, egg-white protein, and neurons. The fibroblast adhesion to poly(carbonate) and poly(methyl methacrylate) demonstrate fibroblasts are strongly attached to highly polar materials. Protein adhesion to titanium and chromium nitride coatings showed that chemical composition is the most influential factor. The neuron adhesion to poly-D-lysine coated glass demonstrated that neuron strengthening was due to an increase in adhesion molecules at the neuron/material interface. For nanoparticulates, it was found that the charged nanoparticles affect the protein and amino acid conformation and the potential energy of the solutions. Quantifying biomolecule adhesion to surfaces and predicting the behavior of nanoparticles inside a biological system are crucial for material selection and application. The major impact of this research lies in observing the interaction mechanisms at the interfaces of material-biological entities.Item Investigation of Metalloproteins Utilizing High Resolution Mass Spectrometry(2011-08-08) Wu, ZhaoxiangCopper ions (Cu?, Cu??) play important roles in many biological processes (i.e., oxidation, dioxygen transport, and electron transfer); many of the functions in these processes result from copper ions interacting with proteins and peptides. Previous studies using matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) have shown that Cu? ions preferentially bind to electron rich groups in gas phase (i.e., N-terminal amino group, the side-chains of lysine, histidine and arginine). For peptides with more than one Cu? ligand, the interaction between Cu? ions and ligands is described in terms of competitive binding; however, Cu? coordination chemistry for multiple Cu?-containing proteins and peptides in gas phase is still not fully understood. In addition, no studies on the fragmentation chemistry for multiple Cu?-binding peptides, such as [M + 2Cu - H]? ions, have been reported. The synthesized dinuclear copper complex (alpha-cyano-4-hydroxycinnamic acid (CHCA) copper salt (CHCA)?Cu?) enhances the ion abundances for [M + xCu - (x-1)H]? (x = 1-6) ions in gas-phase when used as a MALDI matrix. Using this matrix we have investigated site-specific copper binding of several peptides using fragmentation chemistry of [M + Cu]? and [M + 2Cu - H]? ions. The fragmentation studies reveal that the binding of a single Cu? ion and two Cu? ions are different, and these differences are explained in terms of intramolecular interactions of the peptide-Cu ionic complex. The competitive Cu? binding to C-terminus (i.e., amide, carboxyl, methyl ester) versus lysine, as well as cysteine (SH/SO?H) versus arginine (guanidino), was also examined by MALDI MS and theoretical calculations (Density Functional Theory (DFT)). For example, results from theoretical and experimental (fragmentation reactions) studies on [M + Cu]? and [M + 2Cu - H]? ions suggest that cysteine side chains (SH/SO?H) are important Cu? ligands. Note that, the proton of the SH/SO?H group is mobile and can be transferred to the arginine guanidino group. For [M + 2Cu - H]? ions, deprotonation of the -SH/SO?H group is energetically more favorable than that of the carboxyl group, and the resulting thiolate/sulfonate group plays an important role in the coordination structure of [M + 2Cu - H]? ions.Item Nanocomposite Membranes for Complex Separations(2010-10-12) Yeu, Seung UkOver the past few decades there has been great interest in exploring alternatives to conventional separation methods due to their high cost and energy requirements. Membranes offer a potentially attractive alternative as they potentially address both of these points. The overarching theme of this dissertation is to design nanocomposite membranes for processes where existing separation schemes are inadequate. This dissertation focuses on three challenges: 1) designing organic-inorganic hybrid membranes for reverse-selective removal of alkanes from light gases, 2) defect-free inorganic nanocomposite membranes that have uniform pores, and 3) nanocomposite membranes for minimizing protein fouling in microfiltration applications. Reverse-selective gas separations that preferentially permeate larger/heavier molecular species based on their greater solubility have attracted considerable recent attention due to both economic and environmental concerns. In this study, dendrimer-ceramic hybrid membranes showed exceptionally high propane/nitrogen selectivities. This result was ascribed to the presence of stable residual solvent that affects the solubility of hydrocarbon species. Mesoporous silica-ceramic nanocomposite membranes have been fabricated to provide defectless mesoporous membranes. As mesoporous silica is iteratively synthesized in the ceramic macropores, the coating method and the surfactant removal step significantly affected permeance and selectivity. It was also shown that support layers can cause a lower selectivity than Knudsen limit. Membrane fouling which results from deposition and nonspecific adsorption of proteins on the membrane surface is irreversible in nature, and results in a significant decrease in the membrane performance. To address this problem, two approaches were explored: 1) control of the surface chemistry tethering alumina membranes with organic components and 2) development of a novel photocatalytic membrane that exhibits hydrophilicity and can be easily regenerated. Both approaches can offer a viable route to the synthesis of attractive membranes, in that 1) the density of protein-resistant organic groups such as PEG is controllable by changing scaffolds or synthesis conditions and 2) the photocatalytic nanocomposite membranes can open the way for a new regeneration method that is environmentally benign.Item Specific Ion Effects on Interfacial Phenomena(2012-02-14) Flores Araujo, SarahA new interdisciplinary facet of chemistry has developed, as we attempt to comprehend complex interfacial phenomena in which ions play crucial roles. Understanding the mechanisms by which ions affect water at surfaces and interact with the molecules dissolved in it, pose a ubiquitous challenge with enormous implications for biological and physical sciences. These represent steps towards unraveling mechanisms in protein folding and crystallization, protein-protein interactions, enzymatic activity, implant biocompatibility, atmospheric chemistry phenomena, and even in more inorganic processes like metal oxide dissolution and corrosion; all of them fundamental technological challenges. In this thesis, the specific ion effects on interfacial water structure adjacent to air/water and solid/water interfaces were explored using vibrational sum frequency spectroscopy. At the air/water interface, monolayers of bovine serum albumin, elastin-like peptides, and surfactants, were analyzed in presence of subphases that consisted of different sodium salts and varying pH value. The results suggested that anions interact directly with the protein?s surface, and their effects on water structure are dominated by the charge state of the interfacial layer, rather than the detailed chemical structure of the macromolecules. At the solid/liquid interface, water structure at surfaces like quartz, octadecyltrichlorosilane-covered quartz, and titanium oxide, confirmed that the propensities of anions to adsorb at an interface are favored for more polarizable anions, following the Hofmeister order, and disproving the notion that the order of the interaction can be inverted with changes in charge sign or degree of hydrophobicity of the surface. Similarly, by analyzing interfacial water structure we performed one of the very first systematic studies on the interactions of cations with metal oxide surfaces. The results showed that specific cation effects were quite prominent at low concentration and high pH value, following a direct Hofmeister series, which can be explained in terms of charge density, polarizability, and basicity of the oxide surfaces. Our findings are of interest, since they provide with essential information not only to understand protein phenomena associated with neurodegenerative conditions like Alzheimer, but also by proving the generality of ion interactions beyond biological, we can even influence the development of the next generations of microprocessors and beyond.Item The use of Surface Enhanced Raman Spectroscopy (SERS) for biomedical applications(Texas A&M University, 2007-04-25) Chowdhury, Mustafa HabibRecent advances in nanotechnology and the biotechnology revolution have created an immense opportunity for the use of noble metal nanoparticles as Surface Enhanced Raman Spectroscopy (SERS) substrates for biological sensing and diagnostics. This is because SERS enhances the intensity of the Raman scattered signal from an analyte by orders of 106 or more. This dissertation deals with the different aspects involved in the application of SERS for biosensing. It discusses initial studies performed using traditional chemically reduced silver colloidal nanoparticles for the SERS detection of a myriad of proteins and nucleic acids. It examines ways to circumvent the inherent aggregation problems associated with colloidal nanoparticles that frequently lead to poor data reproducibility. The different methods examined to create robust SERS substrates include the creation of thermally evaporated silver island films on microscope glass slides, using the technique of Nanosphere Lithography (NSL) to create hexagonally close packed periodic particle arrays of silver nanoparticles on glass substrates as well as the use of optically tunable gold nanoshell films on glass substrates. The three different types of SERS surfaces are characterized using UV-Vis absorption spectroscopy, Electron Microscopy (EM), Atomic Force Microscopy (AFM) as well as SERS using the model Raman active molecule trans-1,2-bis(4-pyridyl)ethylene (BPE). Also discussed is ongoing work in the initial stages of the development of a SERS based biosensor using gold nanoshell films for the direct detection of b-amyloid, the causative agent for Alzheimer's disease. Lastly, the use of gold nanoshells as SERS substrates for the intracellular detection of various biomolecules within mouse fibroblast cells in cell culture is discussed. The dissertation puts into perspective how this study can represent the first steps in the development of a robust gold nanoshell based SERS biosensor that can improve the ability to monitor biological processes in real time, thus providing new avenues for designing systems for the early diagnosis of diseases.Item Tubulin in vitro, in vivo and in silico(Texas A&M University, 2005-02-17) Mershin, AndreasTubulin, microtubules and associated proteins were studied theoretically, computationally and experimentally in vitro and in vivo in order to elucidate the possible role these play in cellular information processing and storage. Use of the electric dipole moment of tubulin as the basis for binary switches (biobits) in nanofabricated circuits was explored with surface plasmon resonance, refractometry and dielectric spectroscopy. The effects of burdening the microtubular cytoskeleton of olfactory associative memory neurons with excess microtubule associated protein TAU in Drosophila fruitflies were determined. To investigate whether tubulin may be used as the substrate for quantum computation as a bioqubit, suggestions for experimental detection of quantum coherence and entanglement among tubulin electric dipole moment states were developed.