No description available.

<p>While a number of different proteomic, genomic, and computational approaches exist for the characterization of drug action, each of the experimental approaches developed to date has both strengths and weaknesses. Currently, there is no one "perfect" assay for drug mode-of-action studies. A protocol that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical modification- and mass spectrometry-based strategy for detecting protein-ligand interactions by monitoring the change in thermodynamic stability of proteins upon ligand binding. This is accomplished by monitoring the denaturant dependent oxidation of globally protected methionine residues. The SPROX technique has been interfaced with bottom-up proteomics methods to allow for the proteome-wide analysis of protein-ligand interactions. However, the strategy has been limited by the need to detect and quantify methionine containing peptides in the bottom-up proteomics experiment. </p><p>The work in this dissertation is focused on evaluating the current SPROX protocol, developing modifications to improve proteome coverage, and applying the SPROX platform to two different drug mode-of-action studies. Three main strategies were employed to improve protein coverage. First, a chemo-selective isolation of un-oxidized methionine containing peptides was employed to enrich for methionine containing peptides, and it was found to produce a ~2-fold improvement in proteomic coverage. Second, a pre-fractionation strategy involving the use of isoelectric focusing was employed to decrease sample complexity prior to LC-MS/MS analysis and it was found to generate a ~2-3 fold improvement in proteomic coverage, however when combined with the methionine enrichment strategy the improvement was ~6-fold as the benefits of both were additive. Third, a tryptophan modification strategy was developed that could ultimately expand the number of useful peptides in proteome-wide SPROX experiments to include those that contain tryptophan. Also, investigated was the use of several different mass spectrometer systems (including a bench-top quadrupole and orbitrap system and two different quadrupole time-of-flight systems) in the SPROX protocol. The results of these studies indicate that there is a significant advantage in proteome coverage when faster mass spectrometers are used. The use of high energy collision dissociation (HCD) in the orbitrap system was also more advantageous than the use of collision induced dissociation (CID) in the Q-ToF systems. Regardless of the mass spectrometer used, the major source of error in the SPROX experiment was found to be the random error associated with the LC-MS/MS analysis of isobaric mass tagged peptides. This random error was found to yield a false discovery rate of between 3 and 10% for "hit" peptides in the SPROX experiment. </p><p>The above improvements in the SPROX protocol were used in two protein-ligand binding experiments. One set of experiments involved studies on two small molecules with a specific anti-cancer phenotype in human colon cancer cells. These studies identified 17 proteins as potential "hits" of these two small molecules. After preliminary validation of these proteins, approximately 50% were eliminated as false positives and one protein, p80/nucleophosim, showed consistent data indicating a destabilizing interaction with both small molecules. The destabilization is indicative of an indirect interaction with the small molecules that would be mediated through a protein-protein interaction network. In another set of experiments the breast cancer drug, tamoxifen, and its main, active metabolite, 4-hydroxy tamoxifen, were assayed for binding to the proteins in a yeast cell lysate to better understand its adverse effects on yeast cells. The results of these studies identified ~80 proteins as potential "hits" of these two drugs. After preliminary validation of these proteins, approximately 30% were eliminated as false positives and one protein, SIS1, type II Hsp40, showed consistent data indicative of a direct binding interaction.</p> / Dissertation

[pt] O presente trabalho visa dois objetivos. 0 primeiro, didático, é de apresentar algumas versões da Termodinâmica dos Meios Contínuos, elucidando suas semelhanças e diferenças várias formas da segunda lei são apresentadas, questionando-se em alguns casos as suas supostas generalidades. O segundo objetivo, de pesquisa, desenvolve na versão de Serrin os conceitos de Estabilidade Termodinâmica e Exergia, aplicando-os no estudo dos ciclos de Carnot e de Rankine. Através do conceito de função de acumulação introduz-se uma nova maneira de se determinar a eficiência dos referidos ciclos. Ainda na versão de Serrin, aplica-se a teoria de processos de transição no estudo do efeito Joule-Thomson. Os fluidos de trabalho são um gás ideal, caracterizado pela convexidade do seu espaço de estados, e um fluido de Van der Halls, que não possui a mesma característica. Finalmente, no contexto da Termodinâmica de Processos Irreversíveis é feita uma comparação entre as soluções de problemas de condução de calor em meios rígidos e elásticos lineares isotrópicos. / [en] The present work has two purposes. The first one is didactic. It intend to present many versions of the Continuun Thermodynamics discussing their resemblances and diferences. Many forms of the second law are presented and in some cases their supposed generalities are questioned. The second purpose lies on the basic research. It is carried out applying the Serrin s version the concepts of Thermodynamic Stability and Availability in the studied of the Carnot s and Rankine s cycles. By meaning of the accumulation function concept a newform to determine the efficience of the above cycles is introduced. On the other hand in the Serrin s version the theory of transition processes can be applied in the study of the Joule-Thomson effect. The working fluids are an ideal gas which is characterized by the convexity of it s state space and the Van der Waals fluid which is not provided of such characteristic. Finally in the context of the Irreversible Thermodynamics is made a comparison between the solutions of heat conduction problems in rigid and linear isotropic elastic continuum.

The covalent attachment of poly(ethylene glycol) (PEG) to a protein surface (known as PEGylation), has been demonstrated to increase the serum half-life of therapeutic proteins by reducing kidney clearance and immunogenicity and by protecting against proteolysis. Theses beneficial effects could be further enhanced if PEGylation consistently increased protein conformational stability (i.e. the difference in free energy between the folded and unfolded states). However, the effects of PEGylation on protein conformational stability are unpredictable; PEGylation has been reported to increase, decrease, or have no effect on the conformational stability of medicinal proteins.This thesis details the results of two studies aimed at discovering the structural determinants which influence the thermodynamic impact of PEGylation on the WW domain, a small model protein. Chapter 1 is a brief introduction to protein therapeutics and protein PEGylation. Chapter 2 describes a study which demonstrates that the thermodynamic impact of PEGylation is strongly dependent on the site to which PEG is conjugated. The studies described in Chapter 3 elaborate on this site dependence, and demonstrate that PEG stabilizes the WW domain through interactions with the surface of the folded peptide, and that two factors – the orientation of the PEG chain (relative to the protein surface) and the identity of nearby side chains – play a critical role in determining the thermodynamic impact of PEGylation.

A laboratory scale study was carried out on a set of 6 borosilicate waste glasses made from simulated high-level nuclear waste. The test matrix was designed to explore the composition region suitable for the long-term geologic disposal of high-temperature-and high-waste-containing glasses. The glass compositions were selected to achieve maximum waste loading without a sacrifice in glass durability. The relationship between glass composition and chemical durability was examined. The qualitative effect of increasing B2O3 content on the overall waste glass leaching behavior has also been addressed. The glass composition matrix was designed by systematically varying the factors: %waste loading and (SiO2+Frit):B2O3 ratio, with (SiO2:Frit) ratio being held constant. In order to assess the chemical durability, the Product Consistency Test (ASTM C-1285) was performed. Under PCT protocol, crushed glass was allowed to react with ASTM type I water under static conditions. All leachate solutions were analyzed by the technique; Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES). A statistical regression technique was utilized to model the normalized release of the major soluble elements, Na, Si, and B, as a function of the individual as well as interactive chemical effects (B2O3, Al2O3, Fe2O3, MnO, SiO2, SrO, Na2O, B2O3*SiO2, B2O3*Al2O3, Fe2O3*Na2O, Al2O3*Na2O, and MnO*SiO2). Geochemical modeling was performed using the computer code EQ3/6 to: (1) determine the saturation states of the possible silicate minerals, a-cristobalite and chalcedony; and (2) predict the most stable mineral phase based on the mineral thermodynamic data. Mineral/water interactions were analyzed by representing the resultant glass data on a Na-Al-Si-O-H stability diagram.

Yes / The thermodynamic stability of caffeine (CA) cocrystals with dicarboxylic acids (DAs) as coformers was investigated in the presence of a range of structurally related dicarboxylic acids (SRDs). Two experimental conditions (slurry and dry-grinding) were studied for mixing the cocrystal and the SRD additive. The additives oxalic, malonic and glutaric acid led to the replacement of the acid coformer for certain cocrystals. Interestingly, a change in stoichiometry was observed for the CA:maleic acid system. A stability order among the cocrystals was established depending on their tendency to replace the coformer. To understand the factors controlling the relative stabilities, lattice energies were calculated using dispersion corrected Density Functional Theory (DFT). Gibbs free energy changes were calculated from experimental solubilities. The observed stability order corroborated well with lattice energy and Gibbs free energy computations.

<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of interactions such as binary and strong binding interactions. They also have high false-positive and false-negative rates. Described here is the development of and application of mass spectrometry-based proteomics metehods to detect and quantify the strength of protein-protein and protein-ligand interactions in the context of their interaction networks. Characterization of protein-protein and protein-ligand interactions can directly benefit diseased state analyses and drug discovery efforts. </p><p>The methodologies and protocols developed and applied in this work are all related to the Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX) and Stability of Protein from Rates of Oxidation (SPROX) techniques, which have been previously established for the thermodynamic analysis of protein folding reactions and protein-ligand binding interactions. The work in this thesis is comprised of four parts. Part I involves the development of a Histidine Slow H/D exchange protocol to facility SURPEX-like measurements on the proteomic scale. The Histidine Slow H/D exchange protocol is developed in the context of selected model protein systems and used to investigate the thermodynamic properties of proteins in a yeast cell lysate. </p><p>In Part II an isobaric mass tagging strategy is used in combination with SPROX (i.e., a so-called iTRAQ-SPROX protocol) is used to characterize the altered protein interactions networks associated with lung cancer. This work involved differential thermodynamic analyses on the proteins in two different cell lines, including ADLC-5M2 and ADLC-5M2-C2. </p><p>Parts III and IV of this thesis describe the development and application of a SPROX protocol for proteome-wide thermodynamic analyses that involves the use of Stable Isotope Labeling by Amino acid in cell Culture (SILAC) quantitation. A solution-based SILAC-SPROX protocol is described in Part III and a SILAC-SPROX protocol involving the use of cyanogen bromide and a gel-based fractionation step is described in Part IV. The SILAC-SPROX-Cyanogen bromide (SILAC-SPROX-CnBr) protocol is demonstrated to significantly improve the peptide and protein coverage in proteome-wide SPROX experiments. Both the SILAC-SPROX and SILAC-SPROX-CnBr porotocols were used to characterize the ATP binding properties of yeast proteins. Ultimately, the two protocols enabled 526 yeast proteins to be assayed for binding to AMP-PNP, an ATP mimic. A total of 140 proteins, including 37 known ATP-binding proteins, were found to have ATP binding interactions.</p> / Dissertation

This thesis is a theoretical study of configurational disorder in icosahedral boron-rich solids, in particular boron carbide, including also the development of a methodological framework for treating configurational disorder in such materials, namely superatom-special quasirandom structure (SA-SQS). In terms of its practical implementations, the SA-SQS method is demonstrated to be capable of efficiently modeling configurational disorder in icosahedral boron-rich solids, whiles the thermodynamic stability as well as the properties of the configurationally disordered icosahedral boron-rich solids, modeled from the SA-SQS method, can be directly investigated, using the density functional theory (DFT). In case of boron carbide, especially B4C and B13C2 compositions, the SA-SQS method is used for modeling configurational disorder, arising from a high concentration of low-energy B/C substitutional defects. The results, obtained from the DFT-based calculations, demonstrate that configurational disorder of B and C atoms in boron carbide is not only thermodynamically favored at high temperature, but it also plays an important role in altering the properties of boron carbide − for example, restoration of higher rhombohedral symmetry of B4C, a metal-to-nonmetal transition and a drastic increase in the elastic moduli of B13C2. The configurational disorder can also explain large discrepancies, regarding the proper- ties of boron carbide, between experiments and previous theoretical calculations, having been a long standing controversial issue in the field of icosahedral boron- rich solids, as the calculated properties of the disordered boron carbides are found to be in qualitatively good agreement with those, observed in experiments. In order to investigate the configurational evolution of B4C as a function of temperature, beyond the SA-SQS level, a brute-force cluster-expansion method in combination with Monte Carlo simulations is implemented. The results demonstrate that configurational disorder in B4C indeed essentially takes place within the icosahedra in a way that justifies the focus on lowenergy defect patterns of the superatom picture. The investigation of the thermodynamic stability of icosahedral carbon-rich boron carbides beyond the believed solubility limit of carbon (20 at.% C) demonstrates that, apart from B4C generally addressed in the literature, B2.5C represented by B10Cp2(CC) is predicted to be thermodynamically stable with respect to B4C as well as pure boron and carbon under high pressure, ranging between 40 and 67 GPa, and also at elevated temperature. B2.5C is expected to be metastable at ambient pressure, as indicated by its dynamical and mechanical stabilities at 0 GPa. A possible synthesis route of B2.5C and a fingerprint for its characterization from the simulations of x-ray powder diffraction pattern are suggested. Besides modeling configurational disorder in boron carbide, the SA-SQS method also opens up for theoretical studies of new alloys between different icosahedral boron-rich solids − for example, (B6O)1−x(B13C2)x and B12(As1−xPx)2. As for the pseudo-binary (B6O)1−x(B13C2)x alloy, it is predicted to display a miscibility gap resulting in B6O-rich and either ordered or disordered B13C2-rich domains for intermediate global compositions at all temperatures up to melting points of the materials. However, some intermixing of B6O and B13C2 to form solid solutions is also predicted at high temperature. A noticeable mutual solubility of icosahedral B12As2 and B12P2 in each other to form B12(As1−xPx)2 disordered alloy is predicted even at room temperature, and a complete closure of a pseudo-binary miscibility gap is achieved at around 900 K. Apart from B12(As1−xPx)2, the thermodynamic stability of other compounds and alloys in the ternary B-As-P system is also investigated. For the binary B-As system, zincblende BAs is found to be thermodynamically unstable with respect to icosahedral B12As2 and gray arsenic at 0 K and increasingly so at higher temperature, indicating that BAs may merely exist as a metastable phase. This is in contrast to the binary B-P system, in which zinc-blende BP and icosahedral B12P2 are both predicted to be stable. Owing to the instability of BAs with respect to B12As2 and gray arsenic, only a tiny amount of BAs is predicted to be able to dissolve in BP to form BAs1−xPx disordered alloy at elevated temperature. For example, less than 5% BAs can dissolve in BP at 1000 K. As for the binary As-P system, As1−xPx disordered alloys are predicted at elevated temperature − for example, a disordered solid solution of up to ∼75% As in black phosphorus as well as a small solubility of ∼1% P in gray arsenic at 750 K, together with the presence of miscibility gaps. The thermodynamic stability of three different compositions of α-rhombohedral boron-like boron subnitride, having been proposed so far in the literature, is investigated. Those are, B6N, B13N2, and B38N6, represented respectively by B12(N-N), B12(NBN), and [B12(N-N)]0.33[B12(NBN)]0.67. It is found that, out of these sub- nitrides, only B38N6 is thermodynamically stable from 0 GPa up to ∼7.5 GPa, depending on the temperature, and is thus concluded as a stable composition of α-rhombohedral boron-like boron subnitride.

Aggregation of the Amyloid β (Aβ) peptide to amyloid fibrils is associated with the outbreak of Alzheimer’s disease. Early aggregation intermediates in form of soluble oligomers are of special interest as they are believed to be the major toxic components in the process. These oligomers are of disordered and transient nature. Therefore, their detailed molecular structure is difficult to access experimentally and often remains unknown. In the present work extensive, fully atomistic replica exchange molecular dynamics simulations were performed to study the preaggregated, monomer states and early aggregation intermediates (dimers, trimers) of Aβ(25-35) and Aβ(10-35)-NH2 in aqueous solution. The folding and aggregation of Aβ(25-35) were studied at neutral pH and 293 K. Aβ(25-35) monomers mainly adopt β-hairpin conformations characterized by a β-turn formed by residues G29 and A30, and a β-sheet between residues N27–K28 and I31–I32 in equilibrium with coiled conformations. The β-hairpin conformations served as initial configurations to model spontaneous aggregation of Aβ(25-35). As expected, within the Aβ(25-35) dimer and trimer ensembles many different poorly populated conformations appear. Nevertheless, we were able to distinguish between disordered and fibril-like oligomers. Whereas disordered oligomers are rather compact with few intermolecular hydrogen bonds (HBs), fibril-like oligomers are characterized by the formation of large intermolecular β-sheets. In most of the fibril-like dimers and trimers individual peptides are fully extended forming in- or out-of-register antiparallel β-sheets. A small amount of fibril-like trimers contained V-shaped peptides forming parallel β-sheets. The dimensions of extended and V-shaped oligomers correspond well to the diameters of two distinct morphologies found for Aβ(25-35) fibrils. The transition from disordered to fibril-like Aβ(25-35) dimers is unfavorable but driven by energy. The lower energy of fibril-like dimers arises from favorable intermolecular HBs and other electrostatic interactions which compete with a loss in entropy. Approximately 25 % of the entropic cost correspond to configurational entropy. The rest relates to solvent entropy, presumably caused by hydrophobic and electrostatic effects. In contrast to the transition towards fibril-like dimers the first step of aggregation is driven by entropy. Here, we compared structural and thermodynamic properties of the individual monomer, dimer and trimer ensembles to gain qualitative information about the aggregation process. The β-hairpin conformation observed for monomers is successively dissolved in dimer and trimer ensembles while instead intermolecular β-sheets are formed. As expected upon aggregation the configurational entropy decreases. Additionally, the solvent accessible surface area (SASA), especially the hydrophobic SASA, decreases yielding a favorable solvation free energy which overcompensates the loss in configurational entropy. In summary, the hydrophobic effect, possibly combined with electrostatic effects, yields an increase in solvent entropy which is believed to be one major driving force towards aggregation. Spontaneous folding of the Aβ(10-35)-NH2 monomer was modeled using two force fields, GROMOS96 43a1 and OPLS/AA, and compared to primary NMR data collected at pH 5.6 and 283 K taken from the literature. Unexpectedly, the two force fields yielded significantly different main conformations. Comparison between experimental and calculated nuclear Overhauser effect (NOE) distances is not sufficient to distinguish between the different force fields. Additionally, the comparison with scalar coupling constants suggest that the chosen protonation in both simulations corresponds to a pH lower than in the experiment. Based on this analysis we were unable to determine which force field yields a better description of this system. Dimerization of Aβ(10-35)-NH2 was studied at neutral pH and 300 K. Dimer conformations arrange in many distinct, poorly populated and rather complex alignments or interlocking patterns which are rather stabilized by side chain interactions than by specific intermolecular hydrogen bonds. Similar to Aβ(25-35) dimers, transition towards β-sheet-rich, fibril-like Aβ(10-35) dimers is driven by energy competing with a loss in entropy. Here, transition is mediated by favorable peptide-solvent and solvent-solvent interactions mainly arising from electrostatic interactions. / Die Aggregation des Amyloid β (Aβ) Peptids zu Amyloidfibrillen wird mit dem Ausbruch der Alzheimer Krankheit in Verbindung gebracht. Die toxische Wirkung auf Zellen wird vor allem den zeitigen Intermediaten in Form von löslichen Oligomeren zugeschrieben. Aufgrund deren ungeordneter und flüchtiger Natur kann die molekulare Struktur solcher zeitigen Oligomere oft experimentell nicht aufgelöst werden. In der vorliegenden Arbeit wurden aufwendige atomistische Replica-Exchange-Molekulardynamik-Simulationen durchgeführt, um die molekulare Struktur von Monomeren und Oligomeren der Fragmente Aβ(25-35) und Aβ(10-35)-NH2 in Wasser zu untersuchen. Die Faltung und Aggregation von Aβ(25-35) wurde bei neutralem pH und 293 K untersucht. Monomere dieses Fragments bilden hauptsächlich β-Haarnadelkonformationen im Gleichgewicht mit Knäulstrukturen. Innerhalb der β-Haarnadelkonformationen bilden die Residuen G29 und A30 einen β-turn, während N27–K28 and I31–I32 ein β-Faltblatt bilden. Diese β-Haarnadelkonformationen bildeten den Ausgangspunkt zur Modellierung spontaner Aggregation. Wie zu erwarten, bilden sich eine Vielzahl verschiedener, gering besetzter Dimer- und Trimerkonformationen. Mit Hilfe einer gröberen Einteilung können diese in ungeordnete und fibrillähnliche Oligomere unterteilt werden. Ungeordnete Oligomere bilden kompakte Strukturen, die nur durch wenige intermolekulare Wasserstoffbrückenbindungen (HBB) stabilisiert sind. Typisch für fibrillähnliche Oligomere ist hingegen die Ausbildung großer intermolekularer β-Faltblätter. In vielen dieser Oligomere finden wir antiparallele, in- oder out-of-register β-Faltblätter gebildet durch vollständig ausgestreckte Peptide. Ein kleiner Teil der fibrillähnlichen Trimere bildet parallele, V-förmige β-Faltblätter. Die Ausdehnungen ausgestreckter und V-förmiger Oligomere entspricht in etwa den Durchmessern von zwei verschiedenen, experimentell gefundenen Fibrillmorphologien für Aβ(25-35). Die Umwandlung von ungeordneten zu fibrillähnlichen Aβ(25-35) Dimeren ist energetisch begünstigt, läuft aber nicht freiwillig ab. Fibrillähnliche Dimere haben eine geringere Energie aufgrund günstiger Peptidwechselwirkungen (HBB, Salzbrücken), welche durch den Verlust an Entropie kompensiert wird. Etwa 25 % entsprechen dem Verlust an Konfigurationsentropie. Der restliche Anteil wird einem Verlust an Lösungsmittelentropie aufgrund von hydrophoben und elektrostatischen Effekten zugesprochen. Im Gegensatz zur Umwandlung in fibrillähnliche Dimere, ist die Assoziation von Monomeren oder Oligomeren entropisch begünstigt. Beim Vergleich thermodynamischer Eigenschaften der Monomer-, Dimer- und Trimersysteme zeigt sich im Verlauf der Aggregation, wie erwartet, eine Abnahme der Konfigurationsentropie. Zusätzlich nimmt die dem Lösungsmittel zugängliche Oberfläche (SASA), insbesondere die hydrophobe SASA, ab. In Verbindung damit beobachten wir eine Abnahme der freien Solvatisierungsenergie, welche den Verlust an Konfigurationsentropie kompensiert. Mit anderen Worten, der hydrophobe Effekt in Kombination mit elektrostatischen Wechselwirkungen führt zu einem Ansteigen der Lösungsmittelentropie und begünstigt damit die Aggegation. Die spontane Faltung des Aβ(10-35)-NH2 Monomers wurde für zwei verschiedene Proteinkraftfelder, GROMOS96 43a1 und OPLS/AA, untersucht und mit primären NMR-Daten aus der Literatur, gemessen bei pH 5.6 und 283 K, verglichen. Beide Kraftfelder generieren unterschiedliche Hauptkonformationen. Der Vergleich zwischen experimentellen und berechneten Kern-Overhauser-Effekt (NOE) Abständen ist nicht ausreichend, um zwischen beiden Kraftfeldern zu unterscheiden. Der Vergleich mit Kopplungskonstanten aus Experiment und Simulation zeigt, dass beide Simulationen einem pH-Wert geringer als 5.6 ensprechen. Basierend auf den bisherigen Ergebnissen können wir nicht entscheiden, welches Kraftfeld eine bessere Beschreibung für dieses System liefert. Die Dimerisierung von Aβ(10-35)-NH2 wurde bei neutralem pH und 300 K untersucht. Wir finden eine Vielzahl verschiedener, gering besetzter Dimerstrukturen, welche eher durch Seitenkettenkontakte als durch spezifische HBB stabilisiert sind. Wie bei den Aβ(25-35) Dimeren, ist die Umwandlung zu β-Faltblattreichen, fibrillähnlichen Aβ(10-35) Dimeren energetisch begünstigt, konkurriert aber mit einem Entropieverlust. Die Umwandlung wird in diesem Fall durch elektrostatische Wechselwirkungen zwischen Peptid und Lösungsmittel und innerhalb des Lösungsmittels bestimmt.

<p>Proteins fold into well-defined three-dimensional structures to carry out their biological functions which involve non-covalent interactions with other cellular molecules. Knowledge about the thermodynamic properties of proteins and protein-ligand complexes is essential for answering fundamental biological questions and drug or biomarker discovery. Recently, chemical labeling strategies have been combined with mass spectrometry methods to generate thermodynamic information about protein folding and ligand binding interactions. The work in this thesis is focused on the development and application of two such chemical labeling protocols coupled with mass spectrometry including one termed, SUPREX (stability of unpurified proteins from rates of H/D exchange), and one termed SPROX (stability of proteins from rates of oxidation). The work described in this thesis is divided into two parts. The first part involves the application of SUPREX to the thermodynamic analysis of a protein folding chaperone, Hsp33, and its interaction with unfolded protein substrates. The second part involves the development of a new chemical labeling protocol that can be used to make protein folding and ligand binding measurements on the proteomic scale. </p><p>In the first part of this work, the SUPREX technique was used to study the binding interaction between the molecular chaperone Hsp33 and four different unfolded protein substrates including citrate synthase, lactate dehydrogenase, malate dehydrogenase, and aldolase. The results of the studies, which were performed at the intact protein level, suggest that the cooperativity of the Hsp33 folding/unfolding reaction increases upon binding with denatured protein substrates. This is consistent with the burial of significant hydrophobic surface area in Hsp33 when it interacts with its substrate proteins. The SUPREX derived Kd-values for Hsp33 complexes with four different substrates were also found to be all within a range of 3-300 nM. The interaction between Hsp33 and one of its substrates, citrate synthase (CS), was characterized at a higher structural resolution by using the SUPREX technique in combination with a protease digestion protocol. Using this protocol, the thermodynamic properties for both Hsp33 and CS were evaluated at different stages of binding, including reduced Hsp33 (inactive form), oxidized Hsp33 (active form), followed by native CS and finally of Hsp33ox -CS complexes before and after reduction with DTT. The results suggest that Hsp33 binds unfolded proteins that still have a significant amount of residual higher- order structure. Structural rearrangements of the substrate protein appear to occur upon reduction of the Hsp33-substrate complexes, which may facilitate the transfer of the substrate protein to other protein folding chaperone systems. </p><p>In the second part of this dissertation, a mass spectrometry-based covalent labeling protocol, which relies on the amidination rate of globally protected protein amine groups, was designed and applied to the thermodynamic analysis of several eight protein samples including: six purified proteins (ubiquitin, BCAII, RNaseA, 4OT, and lysozyme with, and without GlcNAc), a five-protein mixture comprised of ubiquitin, BCAII, RNaseA, Cytochome C, and lysozyme, and a yeast cell lysate. The results demonstrate that in ideal cases the folding free energies of proteins and the dissociation constants of protein-ligand complexes can be accurately evaluated using the protocol. Also demonstrated is the new method's compatibility with three different mass spectrometry-based readouts including an intact protein readout using MALDI, a gel-based proteomics readout using MALDI, and an LC-MS-based proteomics readout using isobaric mass tags. The results of the cell lysate sample analysis highlight the complementarity of the labeling protocol to other chemical modification strategies that have been recently developed to make thermodynamic measurements of protein folding and stability on the proteomic scale.</p> / Dissertation