ABSTRACT Equilibrium unfolding, single- and double-jump kinetic studies were conducted to determine the unfolding and refolding pathway of glutaredoxin 2. Structural changes for wild-type glutaredoxin 2 were monitored by far-ultraviolet circular dichroism and intrinsic tryptophan fluorescence for equilibrium unfolding and intrinsic tryptophan fluorescence for single- and double-jump kinetics studies. Glutaredoxin 2 possesses two tryptophan residues in domain 2. In order to monitor changes in domain 1, cysteine 9 at the active site cysteines, situated in domain 1, was labelled with an extrinsic fluorophore, AEDANS, and a mutant was created (Y58W glutaredoxin 2). The AEDANS labelled protein displayed decreased alpha-helical secondary structure and conformational stability. A high degree of cooperativity and similar conformational stability was observed during the two-state transition of the urea-induced equilibrium unfolding of both the wild-type and Y58W glutaredoxin 2 proteins therefore Y58W glutaredoxin 2 could be used to assess structural changes in the local environment of domain 1 during unfolding and refolding. Two phases of unfolding, the fast and slow phase, occurred for both the wild-type and Y58W proteins. The slow phase involves structural rearrangements that expose small amounts of surface area while the fast phase represents gross structural unfolding exposing large amounts of surface area. The isomerization of the Val48-Pro49 peptide bond to the trans conformation occurs during the slow phase and this isomerization is coupled to conformational unfolding of the protein. The structural separation of these phases could be represented by two structural units (unit x and unit y), these units do not represent domain 1 and 2. The units could also result in parallel refolding pathways with the folding of the x unit involving the fast and slow refolding phases and the folding of the y unit of structure is represented by the medium phase of refolding. The fast and slow phases are further separated as the fast phase represents the gross structural folding of glutaredoxin 2 for species with the Val48-Pro49 peptide bond in the native cis conformation. The development of the slow phase after extended unfolding delay periods during double-jump refolding studies, as well as the acceleration of the rate of the phase by the peptidyl prolyl isomerase hFKBP-12 proved that the phase involves a proline peptide bond iv isomerization. This phase represents a slow isomerization coupled with conformational folding similar to the slow unfolding phase. Complex unfolding and refolding kinetics indicated the involvement of kinetic intermediates during (un)folding.

Proteínas são heteropolímeros lineares essenciais à vida, responsáveis pela estruturação dos organismos e pela maioria dos processos bioquímicos que os mantêm vivos e permitem sua reprodução. Essa variedade de funções é refletida na diversidade estrutural encontrada no universo das proteínas, já que sua função é intrinsecamente ligada à sua rigorosa conformação espacial. A partir dos experimentos de Anfinsen (1973), ficou demonstrado que o enovelamento dessas moléculas (folding) se dá essencialmente por meio de um processo físico-químico guiado pela interação entre os aminoácidos da cadeia protéica e entre estes e o meio solvente, quando sob condições fisiológicas (temperatura, pressão, pH). O completo entendimento do mecanismo de folding tem também importância médica, pois várias doenças como mal de Alzheimer, diabetes tipo II, encefalite bovina espongiforme e várias formas de câncer estão relacionadas com falhas estruturais das proteínas. Neste trabalho, por meio de experimentação computacional por dinâmica molecular (DM) em diferentes condições térmicas, estudamos inicialmente o papel das pontes dissulfeto (S-S) e das ligações de hidrogênio (LH) na estabilidade da proteína. Em seguida, adotando exclusivamente o regime de alta temperatura (T = 448K) em combinação com simulações de longa duração (até ~100ns), no intuito de expandir a exploração do espaço configuracional, verificamos a premissa de que as forças entrópicas, geradas pelo efeito hidrofóbico, seriam dominantes no processo de busca pela estrutura nativa. Neste trabalho foi utilizada como um protótipo de proteína pequena e com pontes S-S, a toxina Ts Kappa (MM=3,8 Kda; pdb id: 1tsk), que é dotada de três pontes S-S. A estabilidade conformacional foi analisada por meio de uma série de simulações de DM em temperaturas crescentes e em duas situações: com e sem os cross-links S-S. Nossos resultados indicam que para incrementos nas temperaturas significativamente elevadas, como 50K acima da temperatura em que a estrutura nativa foi determinada por NMR (283K), a remoção das S-S não compromete a estabilidade conformacional da proteína. De fato, a ausência dos cross-links elimina certas restrições geométricas permitindo agora que diferentes combinações de LH sejam feitas, inclusive entre resíduos adjacentes à cisteína, os quais de certa forma substituem as pontes S-S em seus papeis conformacionais pois a estrutura nativa é essencialmente mantida. No segundo experimento o espaço configuracional foi varrido extensamente durante 100ns e à temperatura de 398K. No caso da Ts Kappa com suas pontes dissulfeto intactas, a desestruturação da proteína é limitada pelas fortes pontes covalentes S-S, mas com a remoção delas, a proteína se desnaturou completamente ao longo dos primeiros 50ns. Contudo, a partir deste ponto a cadeia desnaturada passou a seguir, de forma espontânea e sistemática, uma rota de re-estruturação em direção à nativa, com o reestabelecimento de todas suas estruturas secundárias. Ao redor de 100ns a cadeia atingiu um estado de grande identidade estrutural com sua correspondente estrutura nativa. Em conclusão, os presentes resultados corroboram as premissas de que o folding de proteínas ocorre por meio de um processo em duas etapas, temporalmente separadas: no início, as forças entrópicas são dominantes e são as que induzem a cadeia para a conformação nativa. Então, uma vez na vizinhança da estrutura nativa, as pontes de hidrogênio (agora protegidas da competição com o meio solvente), juntamente com um mais eficiente empacotamento estrutural das cadeias laterais devido às complementaridade estéricas das mesmas (e assim otimizando as interações de van der Waals), iniciam a etapa de estabilização energética da proteína. / Proteins are linear heteropolymers essential for life; they are responsible for many distinct functions as the structural components of organism, and for most of the biochemical processes to maintain a reproductive life. Such diversity of functions is correlated with the extremely large accessible conformational space, since function and spatial structure are interdependent. After Anfinsen experiments (1973), it becomes clear that the protein folding is essentially a physical-chemical process guided by interactions among the chain constituents (amino acid sequence) and interactions between the chain and the solvent, under physiological conditions (temperature, pressure, pH). Because miss-folded proteins are related with diseases (Alzheimer, type II diabetes, several forms of cancer, etc.) the full understanding of the folding mechanism has also significant medical interest. In this work, by means of molecular dynamics (MD) simulations under distinct thermal conditions, we first consider the role of disulfide cross-links (S-S) and hydrogen bonds (HB) with respect to the protein thermal stability. Then, using exclusively high temperature regime (T = 448K) combined with extended time simulations (up to ~100ns), in order to fully span of configurational space, we analyzed the hypothesis that the entropic forces, generated by the hydrophobic effect, are dominant in the search process for the native structure. The protein Ts Kappa was used a prototype for small proteins having S-S bridges (MM=3,8Kda; 3 S-S - pdb id: 1tsk). The thermal conformational stability was analyzed from a series of MD simulations under growing temperatures, using two distinct cases: with and without cross-links S-S. Our results suggest that for significant temperature increments, such as 50K above the temperature used in the Ts Kappa structure determination (by NMR at 283K), the thermal conformational stability of the proteins is not affected if the S-S bridges are removed. Indeed, cutting of the cross-links eliminates certain geometrical constraints, what permits the formation of new combinations of HB, which in some way take the place of the S-S bridges on its conformational role since the native structure is essentially maintained. In the second computational experiment, the configurational space was extensively swapped during 100ns at a fixed temperature T=398K. In the case with preserved S-S bridges, the structural unpacking is limited by the three covalent cross-links, but without the S-S bridges the protein denaturation was complete after 50ns. However, after this point the chain started spontaneous and systematically a configurational rote that finally, after about 100ns, reached a conformation very similar with the native (RMSD » 0.5nm), reestablishing all its secondary structure. Concluding, the present results corroborate the hypothesis that the protein folding is a process in two stages temporally separated: first, entropic forces are dominant and guide the chain into the native structure, and then, once in the native neighborhood, the HB (now protected from competition with the solvent), altogether with a more efficient structural specificity of the side chains (optimizing the van de Walls interactions), start the energetic stabilization of the protein.

Este estudo tem como finalidade principal a análise termodinâmica e estatística de proteínas através de modelos mínimos. Uma proteína é um polímero de aminoácidos, cuja função está essencialmente relacionada às conformações espaciais que ela adota em solução aquosa. Na forma funcional (dita nativa), essas conformações flutuam levemente em torno de um mínimo de energia-livre. O processo pelo qual uma cadeia protéica transita de estados não-nativos para a estrutura nativa é chamado de enovelamento, ou dobramento. Uma questão em aberto no campo de estudo de proteínas consiste justamente em entender a fundo o processo de enovelamento, cujo avanço tem um vasto potencial de aplicação, desde a predição de estruturas a partir de sequências de aminoácidos até o planejamento de fármacos e moléculas bioativas. Nossa investigação teórica procura abordar aspectos do enovelamento expressos através de grandezas termodinâmicas (energia média, calor específico, número de ligações de hidrogênio, entre outras) derivadas de modelos estatísticos na rede. Assim, num primeiro momento, analisamos o chamado modelo HP, ora por meio de enumeração exata, para cadeias curtas, ora por simulações de Monte Carlo, para cadeias maiores. No primeiro caso, propusemos a existência de uma relação entre a ocorrência de um segundo pico no calor específico associado na literatura à transição de congelamento com uma drástica redução no número de configurações entre os primeiros estados excitados e aqueles de menor energia. Observamos, também, que esse pico pode aparecer tanto para homopolímeros quanto para heteropolímeros, em ambas as redes quadrada e triangular. Num segundo momento, nosso enfoque se voltou para a inclusão de um solvente aquoso (dado pelo modelo de Bell-Lavis) ao sistema inicial. Isso nos possibilitou verificar, usando exclusivamente simulações de Monte Carlo e o algoritmo de Metropolis, o comportamento e a competição das ligações de hidrogênio água-água, água-proteína, proteína-proteína e na primeira camada de solvatação. O modelo acoplado exibiu algumas características do enovelamento, como o colapso hidrofóbico e a separação de monômeros (apolares no núcleo e polares na superfície), embora não capture a desnaturação fria. No apêndice, adicionamos algumas propostas para realização do cálculo numérico da pressão no ensemble canônico, desenvolvidas em paralelo ao projeto principal desta dissertação, mas que, numa primeira análise, verificamos serem consistentes e passíveis de futuros desdobramentos. / The finality of this study is to analyse proteins thermodynamics and statistics through minimal models. A protein is a polymer of amino acids, whose spatial conformations in aqueous solution determine its function. In the functional form (said native), those conformations fluctuates slightly around a free-energy minimum. The process by which a protein chain passes from non-native states to a stable native structure is called protein folding. An open question in the field of protein studies is to understand more deeply the folding process, whose advance can find a wide range of potential applications, since ab initio structure prediction from the amino acids sequence to biomolecules design. The theoretical approaches used here focus on aspects of protein folding given by some thermodynamic quantities (as mean energy, specific heat, number of hydrogen bonds and so on) obtained from statistical lattice models. Initially, we analyse the so-called HP model, at first using exact enumeration for short chains, then by Monte Carlo simulations for longer chains. In the first case, we propose a correlation between the occurrence of a second peak in the specific heat associated in the literature with a freezing transition and a sharp reduction on the number of configurations from the first excited states to the lowest energy states. In addition, we observe that this peak may appear to both homopolymers and heteropolymers on square and triangular lattices. At a second moment, our focus turned to the introduction of a water-like solvent (Bell-Lavis model) to the initial system. This allowed us to verify, exclusively by means of Monte Carlo simulations with Metropolis algorithm, the behavior and competition of hydrogen bonds between water-water molecules, water-protein, and protein-protein monomers and at the first hydration layer. The combined model showed some classical folding properties, as hydrophobic collapse and monomers segregation (apolar residues at the core and polar residues at the surface), although it did not capture cold denaturation. We have included in the appendix some proposals to perform numerical calculations of the canonical pressure, which were developed alongside the main subject of this thesis and a first analysis has proved to be consistent and susceptible to further developments.

The mitochondrion is the powerhouse of the cell. Therefore, it is critical to the homeostasis of the cell that populations of mitochondria that are damaged or in excess are degraded. The process of targeted elimination of damaged or excess mitochondria by autophagy is called mitophagy. In this report, analysis of the mitophagy regulators PINK1/PARKIN and BNIP3L and their roles are assessed in the lens. PARKIN, an E3 ubiquitin ligase, has been shown to play a role in directing damaged mitochondria for degradation. While BNIP3L, an outer mitochondrial membrane protein, increases in expression in response to excess mitochondria and organelle degradation during cellular differentiation. We have shown that PARKIN is both induced and translocates from the cytoplasm to the mitochondria in human epithelial lens cells upon oxidative stress exposure. In addition, our findings also show that overexpression of BNIP3L causes premature clearance of mitochondria and other organelles, while loss of BNIP3L results in lack of clearance. Prior to this work, PARKIN mediated mitophagy had not been shown to act as a protective cellular response to oxidative stress in the lens. This project also resulted in the novel finding that BNIP3L-mediated mitophagy mechanisms are required for targeted organelle degradation in the lens. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2015 / FAU Electronic Theses and Dissertations Collection

Proteínas são heteropolímeros lineares essenciais à vida, responsáveis pela estruturação dos organismos e pela maioria dos processos bioquímicos que os mantêm vivos e permitem sua reprodução. Essa variedade de funções é refletida na diversidade estrutural encontrada no universo das proteínas, já que sua função é intrinsecamente ligada à sua rigorosa conformação espacial. A partir dos experimentos de Anfinsen (1973), ficou demonstrado que o enovelamento dessas moléculas (folding) se dá essencialmente por meio de um processo físico-químico guiado pela interação entre os aminoácidos da cadeia protéica e entre estes e o meio solvente, quando sob condições fisiológicas (temperatura, pressão, pH). O completo entendimento do mecanismo de folding tem também importância médica, pois várias doenças como mal de Alzheimer, diabetes tipo II, encefalite bovina espongiforme e várias formas de câncer estão relacionadas com falhas estruturais das proteínas. Neste trabalho, por meio de experimentação computacional por dinâmica molecular (DM) em diferentes condições térmicas, estudamos inicialmente o papel das pontes dissulfeto (S-S) e das ligações de hidrogênio (LH) na estabilidade da proteína. Em seguida, adotando exclusivamente o regime de alta temperatura (T = 448K) em combinação com simulações de longa duração (até ~100ns), no intuito de expandir a exploração do espaço configuracional, verificamos a premissa de que as forças entrópicas, geradas pelo efeito hidrofóbico, seriam dominantes no processo de busca pela estrutura nativa. Neste trabalho foi utilizada como um protótipo de proteína pequena e com pontes S-S, a toxina Ts Kappa (MM=3,8 Kda; pdb id: 1tsk), que é dotada de três pontes S-S. A estabilidade conformacional foi analisada por meio de uma série de simulações de DM em temperaturas crescentes e em duas situações: com e sem os cross-links S-S. Nossos resultados indicam que para incrementos nas temperaturas significativamente elevadas, como 50K acima da temperatura em que a estrutura nativa foi determinada por NMR (283K), a remoção das S-S não compromete a estabilidade conformacional da proteína. De fato, a ausência dos cross-links elimina certas restrições geométricas permitindo agora que diferentes combinações de LH sejam feitas, inclusive entre resíduos adjacentes à cisteína, os quais de certa forma substituem as pontes S-S em seus papeis conformacionais pois a estrutura nativa é essencialmente mantida. No segundo experimento o espaço configuracional foi varrido extensamente durante 100ns e à temperatura de 398K. No caso da Ts Kappa com suas pontes dissulfeto intactas, a desestruturação da proteína é limitada pelas fortes pontes covalentes S-S, mas com a remoção delas, a proteína se desnaturou completamente ao longo dos primeiros 50ns. Contudo, a partir deste ponto a cadeia desnaturada passou a seguir, de forma espontânea e sistemática, uma rota de re-estruturação em direção à nativa, com o reestabelecimento de todas suas estruturas secundárias. Ao redor de 100ns a cadeia atingiu um estado de grande identidade estrutural com sua correspondente estrutura nativa. Em conclusão, os presentes resultados corroboram as premissas de que o folding de proteínas ocorre por meio de um processo em duas etapas, temporalmente separadas: no início, as forças entrópicas são dominantes e são as que induzem a cadeia para a conformação nativa. Então, uma vez na vizinhança da estrutura nativa, as pontes de hidrogênio (agora protegidas da competição com o meio solvente), juntamente com um mais eficiente empacotamento estrutural das cadeias laterais devido às complementaridade estéricas das mesmas (e assim otimizando as interações de van der Waals), iniciam a etapa de estabilização energética da proteína. / Proteins are linear heteropolymers essential for life; they are responsible for many distinct functions as the structural components of organism, and for most of the biochemical processes to maintain a reproductive life. Such diversity of functions is correlated with the extremely large accessible conformational space, since function and spatial structure are interdependent. After Anfinsen experiments (1973), it becomes clear that the protein folding is essentially a physical-chemical process guided by interactions among the chain constituents (amino acid sequence) and interactions between the chain and the solvent, under physiological conditions (temperature, pressure, pH). Because miss-folded proteins are related with diseases (Alzheimer, type II diabetes, several forms of cancer, etc.) the full understanding of the folding mechanism has also significant medical interest. In this work, by means of molecular dynamics (MD) simulations under distinct thermal conditions, we first consider the role of disulfide cross-links (S-S) and hydrogen bonds (HB) with respect to the protein thermal stability. Then, using exclusively high temperature regime (T = 448K) combined with extended time simulations (up to ~100ns), in order to fully span of configurational space, we analyzed the hypothesis that the entropic forces, generated by the hydrophobic effect, are dominant in the search process for the native structure. The protein Ts Kappa was used a prototype for small proteins having S-S bridges (MM=3,8Kda; 3 S-S - pdb id: 1tsk). The thermal conformational stability was analyzed from a series of MD simulations under growing temperatures, using two distinct cases: with and without cross-links S-S. Our results suggest that for significant temperature increments, such as 50K above the temperature used in the Ts Kappa structure determination (by NMR at 283K), the thermal conformational stability of the proteins is not affected if the S-S bridges are removed. Indeed, cutting of the cross-links eliminates certain geometrical constraints, what permits the formation of new combinations of HB, which in some way take the place of the S-S bridges on its conformational role since the native structure is essentially maintained. In the second computational experiment, the configurational space was extensively swapped during 100ns at a fixed temperature T=398K. In the case with preserved S-S bridges, the structural unpacking is limited by the three covalent cross-links, but without the S-S bridges the protein denaturation was complete after 50ns. However, after this point the chain started spontaneous and systematically a configurational rote that finally, after about 100ns, reached a conformation very similar with the native (RMSD » 0.5nm), reestablishing all its secondary structure. Concluding, the present results corroborate the hypothesis that the protein folding is a process in two stages temporally separated: first, entropic forces are dominant and guide the chain into the native structure, and then, once in the native neighborhood, the HB (now protected from competition with the solvent), altogether with a more efficient structural specificity of the side chains (optimizing the van de Walls interactions), start the energetic stabilization of the protein.

Abstract not available

<p>This thesis is based on studies, described in four papers, in which the folding energy landscape of MerP was investigated by various techniques. MerP is a water-soluble 72 amino acid protein with a secondary structure consisting of four anti-parallel β-strands and two α-helices on one side of the sheet in the order β1α1β2β3α2β4. </p><p>The first paper describes the use of CD and fluorescence analysis to examine the folding/unfolding process of MerP. From these experiments it was found that the protein folds according to a two-state model in which only the native and unfolded forms are populated without any visible intermediates. With a rate constant of 1.2 s^-1, the folding rate was found to be unusually slow for a protein of this size.</p><p>The studies presented in the second and third papers were based on measurements of native-state amide proton exchange at different temperatures (Paper II) and GuHCl concentrations (Paper III) in the pre-transitional region. In these studies partially unfolded forms were found for MerP which are essentially unrelated to each other. Thus, in the folding energy landscape of MerP, several intermediates seem to occur on different folding trajectories that are parallel to each other. The slow folding rate of MerP might be coupled to extensive visitation of these conformations. Hydrogen exchange in MerP did also reveal structure-dependent differences in compactness between the denatured states in GuHCl and H₂O.</p><p>In the last paper multivariate data analysis was applied to 2-dimensional NMR data to detect conformational changes in the structure of MerP induced by GuHCl. From this analysis it was suggested that regions involved in the most flexible part of the protein structure are disrupted at rather low denaturant concentrations (< 2.1 M GuHCl) while the native structures of the most stable parts are still not completely ruptured at 2.9 M GuHCl.</p><p>Finally, the stability, kinetics, contact order and folding nuclei of six proteins with similar topology (MerP, U1A, S6, ADA2h, AcP and HPr) were compared. In this analysis it was found that their folding properties are quite diverse, despite their topological similarities, and no general rules that have been formulated yet can adequately predict their folding behaviour.</p>

<p>Protein folding and export to the membrane are crucial events in the cell. Both processes may be initiated already at the ribosome, assisted by factors that bind to the polypeptide as it emerges from the ribosome. The signal recognition particle (SRP) scans the ribosome for nascent peptides destined for membrane insertion and targets these ribosomes to the site for translocation in the membrane. Trigger factor (TF) is a folding chaperone that interacts with nascent chains to promote their correct folding, prevent misfolding and aggregation. </p><p>In this thesis, we first investigated membrane targeting and insertion of two heterologous membrane proteins in E. coli by using in vitro translation, membrane targeting and cross-linking. We found that these proteins are dependent on SRP for targeting and that they initially interact with translocon components in the same way as native nascent membrane proteins. </p><p>Moreover we have characterised the SRP and TF interactions with the ribosome both with cross-linking experiments and with quantitative binding experiments. Both SRP and TF bind to ribosomal L23 close to the nascent peptide exit site where they are strategically placed for binding to the nascent polypeptide. </p><p>Quantitative analysis of TF and SRP binding determined their respective KD values for binding to non translating ribosomes and reveals that they bind simultaneously to the ribosome, thus having separate binding sites on L23. </p><p>Finally, binding studies on ribosome nascent chain adds clues as to how TF functions as a chaperone.</p>

Graduation date: 2005

OmniMerge performs a systematic search to enumerate all conformations of a molecule (at a given level of torsion-angle resolution) that satisfy a set of local geometric constraints. Constraints would typically come from NMR experiments, but applications such as docking or homology modeling could also give rise to similar constraints. The molecule to be searched is partitioned into small subchains so that the set of possible conformations for the whole molecule may be constructed by merging the feasible conformations for the subchain parts. However, instead of using a binary tree for straightforward divide-and-conquer, OmniMerge defines a sub-problem for every possible subchain of the molecule. Searching every subchain provides a counter-intuitive advantage: with every possible subdivision available for merging, one may choose the most favorable merge for each subchain, particularly for the bottleneck chain(s). Improving the bottleneck step may therefore cause the whole search to be completed more quickly. Finally, to discard infeasible conformations more rapidly, OmniMerge filters the solution set of each subchain based on compatibility with the solutions sets of all overlapping subchains. These two innovations—choosing the most favorable merges and enforcing consistency between overlapping subchains—yield significant improvements in run time. By determining the extent of structural variability permitted by a set of constraints, OmniMerge offers the potential to aid error analysis and improve confidence for NMR results on peptides and moderate-sized molecules. / Singapore-MIT Alliance (SMA)