The molecular chaperone process of assisted protein folding, characteristic of members of the Heat Shock Protein 70 kDa (Hsp70) and Heat Shock Protein 40kDa (Hsp40) families, is essential for cytoprotection in stressful cellular conditions. Examples of such conditions are heat shock or invasion by pathogens. The Hsp70/Hsp40 process of assisted protein folding is dependent on ATP (governed by the intrinsic ATPase activity of Hsp70) and the ability of molecular chaperones to recognise and bind non-native protein conformations. Here, we analyse and attempt to characterise the molecular chaperone activity of an inducible, cytoplasmic Hsp70 (TcHsp70) from Trypanosoma cruzi and its interactions with its potential partner Hsp40s, Tcj 1, Tcj2, Tcj3 and Tcj4. A bioinformatic analyses of the primary sequences of the trypanosomal proteins revealed that they all contained the canonical domains that define other members of the Hsp70 and Hsp40 family. Tcj2 and Tcj4 showed deviations from the consensus sequence in their substrate binding regions, which may have implications for their substrate binding specificities. TcHsp70, Tcj 1, Tcj2, Tcj3 and Tcj4 were over-expressed recombinantly as 6xHis-tag fusion proteins in Escherichia coli. His-TcHsp70, Tcjl-His and His-Tcj2 were successfully purified by Nickel-affinity chromatography for functional analyses to assess the molecular chaperone activity of His-TcHsp70 in terms of its ATPase activity and substrate binding ability. The basal ATPase activity of His-TcHsp70 was determined as 40 nmol Pi/min/mg, significantly higher than that reported for other Hsp70s. This basal ATPase activity was stimulated to a maximal level of 60 nmol Pi/min/mg in the presence of His-Tcj2 and a model non-native substrate, reduced carboxymethylated αx-lactalbumin (RCMLA). Using native polyacrylamide gel electrophoresis and Western analysis, His-TcHsp70 was shown to form discrete complexes when in the presence of Tcj 1- His, His-Tcj2 and/or RCMLA. These complexes potentially represent His-TcHsp70 - RCMLA or His-TcHsp70 - Tcj interactions, that may be indicative of chaperone activity. In vivo complementation assays showed that Tcj2, but not Tcj3, was able to overcome the temperature sensitivity of the ydjJ mutant Saccharomyces cerevisiae strain JJ160, suggesting that Tcj2 may be functionally equivalent to the yeast Hsp40 Ydj1.

Orientador: Jorge Chahine / Banca: Leandro Cristante de Oliveira / Banca: Ronaldo Junio de Oliveira / Banca: Marcelo Andrés Fossey / Banca: Sidney Jurado de Carvalho / Resumo: O enovelamento de proteínas é um problema fundamental em Biofísica Molecular. Propõe8se neste trabalho um método de crescimento de estruturas proteicas utilizando uma rede denominada cubo8octaédrica. Neste processo de crescimento a partir da estrutura primária utiliza8se um potencial estatístico de interação entre pares de resíduos a fim de determinarmos a estrutura terciária da sequência. Para o ensemble estrutural analisam8se propriedades estruturais como o raio de giro das cadeias e o desvio médio quadrático das distâncias. Além deste estudo de previsão de estruturas, analisamos parâmetros energéticos termodinâmicos no estado de transição da proteína CI2 (cujo código PDB é 1 coa) bem como o cálculo dos valores de φ-values para os resíduos que fazem contatos no estado de transição / Abstract: Protein folding is a fundamental problem in Molecular Biophysics. We present a method of chain growth algorithm to lattice generation of protein structure. The interaction between pairs of residues in this process is a statistical potential proposed by THOMAS and DILL. We examine properties as radius of gyration and root mean square deviation of ensemble protein structure. Finally, we verify the themodynamics energetic parameter in the transition state of protein folding 1 coa / Doutor

The secondary structure of proteins is predicted using various binary classifiers. The data are adopted from the RS126 database. The original data consists of protein primary and secondary structure sequences. The original data is encoded using alphabetic letters. These data are encoded into unary vectors comprising ones and zeros only. Different binary classifiers, namely the naive Bayes, logistic regression and classification trees using hold-out and 5-fold cross validation are trained using the encoded data. For each of the classifiers three classification tasks are considered, namely helix against not helix (H/∼H), sheet against not sheet (S/∼S) and coil against not coil (C/∼C). The performance of these binary classifiers are compared using the overall accuracy in predicting the protein secondary structure for various window sizes. Our result indicate that hold-out cross validation achieved higher accuracy than 5-fold cross validation. The Naive Bayes classifier, using 5-fold cross validation achieved, the lowest accuracy for predicting helix against not helix. The classification tree classifiers, using 5-fold cross validation, achieved the lowest accuracies for both coil against not coil and sheet against not sheet classifications. The logistic regression classier accuracy is dependent on the window size; there is a positive relationship between the accuracy and window size. The logistic regression classier approach achieved the highest accuracy when compared to the classification tree and Naive Bayes classifiers for each classification task; predicting helix against not helix with accuracy 77.74 percent, for sheet against not sheet with accuracy 81.22 percent and for coil against not coil with accuracy 73.39 percent. It is noted that it is easier to compare classifiers if the classification process could be completely facilitated in R. Alternatively, it would be easier to assess these logistic regression classifiers if SPSS had a function to determine the accuracy of the logistic regression classifier.

Three-dimensional (3D) structure of a protein is essential as the guidance of structure-based drug dis-covery. To achieve robust homology modeling with atomic-level accuracy, reliable loop predictions are required. Here, a novel hierarchical protocol of Protein Local Optimization Program (PLOP) is designed to produce sub-2 angstrom predictions on loop regions in homology modeling. Dramatic improvements in both speed and accuracy have been realized with implementation of special-designed clustering and adaptive loop closure algorithm. Four prediction rounds are designed for homology modeling as the high-level protocol of PLOP, which allows latter rounds employ the educated guess of backbone atom positions and hydrogen bonding information inherited from the previous rounds, contributing to additional prediction accuracy. The success of PLOP has been demonstrated with four different data sets, mainly concen-trating on homology modeling of H3 loops of antibodies. GPU-accelerated sampling algorithm and deep learning models are implemented, which are able to produce promising predictions as input templates for PLOP in the context of homology modeling.

Indiana University-Purdue University Indianapolis (IUPUI) / Intrinsically disordered proteins (IDPs) are abundant in nature, being more prevalent in the proteomes of eukaryotes than those of bacteria or archaea. As introduced in Chapter I, these proteins, or portions of these proteins, lack stable equilibrium structures and instead have dynamic conformations that vary over time and population. Despite the lack of preformed structure, IDPs carry out many and varied molecular functions and participate in vital biological pathways. In particular, IDPs play important roles in cellular signaling that is, in part, enabled by the ability of IDPs to mediate molecular recognition. In Chapter II, the role of intrinsic disorder in molecular recognition is examined through two example IDPs: p53 and 14-3-3. The p53 protein uses intrinsically disordered regions at its N- and C-termini to interact with a large number of partners, often using the same residues. The 14-3-3 protein is a structured domain that uses the same binding site to recognize multiple intrinsically disordered partners. Examination of the structural details of these interactions highlights the importance of intrinsic disorder and induced fit in molecular recognition. More generally, many intrinsically disordered regions that mediate interactions share similar features that are identifiable from protein sequence. Chapter IV reviews several models of IDP mediated protein-protein interactions that use completely different parameterizations. Each model has its relative strengths in identifying novel interaction regions, and all suggest that IDP mediated interactions are common in nature. In addition to the biologic importance of IDPs, they are also practically important in the structural study of proteins. The presence of intrinsic disordered regions can inhibit crystallization and solution NMR studies of otherwise well-structured proteins. This problem is compounded in the context of high throughput structure determination. In Chapter III, the effect of IDPs on structure determination by X-ray crystallography is examined. It is found that protein crystals are intolerant of intrinsic disorder by examining existing crystal structures from the PDB. A retrospective analysis of Protein Structure Initiative data indicates that prediction of intrinsic disorder may be useful in the prioritization and improvement of targets for structure determination.

P. aerguinosa is a serious human bacterial pathogen. This thesis describes attempts to use structural biology to identify new starting points for drugs against P. aerguinosa .A number of fragment-based screening techniques were used in order to identify potential inhibitors to P. aerguinosa RmlA protein, the first enzyme in the L-Rhamnose pathway. A 500 “Rule of 3” Fragment Library (Maybridge) was investigated. The first approach was the application of Differential Scanning Fluorimetry (DSF) approach to detect ligands that bind and stabilize RmlA protein. The stabilisation of RmlA was determined by thermal unfolding in the presence of each of the 500 compounds. 21 of those compounds were found to increase the protein stability. The library was then screened by NMR spectroscopy for binding to RmlA. Two techniques were evaluated STD and WaterLOGSY. 106 compounds gave positive results in both NMR experiments. These hits were then tested by a simple STD competition binding with dTTP, a natural RmlA substrate, in order to identify those binding at the active or allosteric site. 21 out of the 106 compounds were observed to compete with dTTP. The results were compared to the results of the DSF screening. Compounds that tested positive in the dTTP competition binding STD experiment and in the DSF screening were tested for their ability to inhibit RmlA in a biological assay. A coupled enzyme assay was used to monitor RmlA activity. Only one compound, 3-pyridin-3-ylaniline, showed significant inhibition of the enzyme activity. The PA1645 protein from P. aerguinosa has been identified as essential. The protein was overexpressed, purified and crystallised. Data were collected at Diamond on beamline IO3 and phases were determined by S-SAD at a wavelength of 1.6Å. Final coordinates have been deposited in the protein data bank under entry code 2XU8. The structure has 3 molecules in the asymmetric unit. There is some ambiguity as to the validity of the proposed trimeric arrangement, with results from solution and crystal disagreeing. Fragment-based screening approach has been applied to RmlA protein, using the DSF technique, a number of ligand-based NMR experiments and a coupled enzyme biological assay. 3-pyridin-3-ylaniline was the only compound that showed significant inhibition of the enzyme activity. The structure of PA1645 from P. aerguinosa has been solved. This work will help to design new drugs to combat multi-drug resistant P. aerguinosa and MTB.

Proteins play an important role in cells, as the morphology, function and activities of the cell depend on the proteins they express. The key to understanding how different proteins function lies in an understanding of the molecular structure. The overall aim of this thesis was the determination of the structure of DWNN domains. This thesis described the preparation of samples of human DWNN suitable for structural analysis by nuclear magnetic resonance spectroscopy (NMR), as well as NMR analysis.

by Paula A. Livingston. / Thesis (M.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web. / Two protein tyrosine phosphatases, dual specificity phosphatase PVP and low molecular weight phosphatase WZB were purified and characterized. PVP was expressed as inclusion bodies and a suitable purification and refolding method was devised. Enzyme kinetics revealed that p-nitrophenylphosphate and (Sb(B-naphthyl phosphate were substrates with KM of 4.0mM and 8.1mM respectively. PVP showed no reactivity towards phosphoserine. Kinetic characterization of WZB showed that only pnitrophenylphosphate was a substrate with no affinity for Ç-naphthyl phosphate and phosphoserine. Optimal conditions for activity with PNPP were found at a pH of 5 with a KM of 1.1mM, kcat of 35.4s-1 and kcat/KM of 32.2s-1mM-1. Inhibition studies showed that phosphate, fluoride, and molybdate were competitive inhibitors with Ki of 3.2mM, 71.7mM, and 50.4(So(BM respectively and hydrogen peroxide abolished activity. Active site mutants of WZB Cys9Ser and Asp115Asn showed no activity.

Orientador: Sonia Maria Oliani / Coorientador: Cristiane Damas Gil / Banca: Eloisa Amália Vieira Ferro / Banca: Claudia Regina Bonini Domingos / Resumo: Introdução: A inflamação ocular é geralmente tratada com glicocorticoides, cujos efeitos colaterais estimulam novas estratégias terapêuticas. Nesse aspecto, destacamos a Galectina-1 (Gal-1), proteína com potencial anti- inflamatório, cuja ação em tecidos oculares foi pouco investigada. Objetivo: No presente estudo avaliamos a expressão da Gal-1 nas células epiteliais pigmentadas da retina humana (ARPE-19), após ativação pelo inflamógeno lipopolissacarídeo (LPS) e tratamentos com a Gal-1 recombinante humana (hrGal-1). Métodos: Para avaliar o efeito anti-inflamatório da Gal-1, as células ARPE-19 foram cultivadas em meio DMEM:F-12 completo (controle), ativadas pelo LPS (10 µg/mL) e tratadas com hrGal-1 (0,04; 0,4 e 4 µg/mL) ou glicocorticoide dexametasona (Dex: 1µM), nos períodos de 2, 8, 24 e 48 horas. Nessas condições, avaliamos a citotoxicidade dos tratamentos farmacológicos por ensaios de viabilidade celular e, a expressão da Gal-1 endógena nas células ativadas pelo LPS e tratadas com Dex, por meio da imunocitoquímica ultraestrutural. Nos sobrenadantes, em todos os tempos experimentais, analisamos os níveis das citocinas IL-6, IL-8, IL-10, TNF-α, IL-1β e MCP-1 pelo método de ELISA. Com a finalidade de determinar a especificidade do efeito da hrGal-1, via domínio reconhecedor de carboidrato (CRD) sobre as células ARPE-19, adicionamos nas culturas os açúcares com ou sem afinidade pelo CRD (respectivamente β-galactose ou sucrose - 100mM) e, após 8 horas, os sobrenadantes foram coletados para análise das citocinas pró-inflamatórias IL- 6 e IL-8. Ainda, investigamos a expressão da enzima ciclo-oxigenase 2 (COX- 2), um importante mediador do processo inflamatório, nos períodos de 8 e 24 horas, por imunofluorescência. Resultados: Os ensaios de viabilidade celular mostram que os diferentes tratamentos... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Introduction: Ocular inflammation has often been treated with glucocorticoids, however, collateral side effects stimulate the search for new therapeutic strategies. In view of this, we emphasis on Galectin-1 (Gal-1), a protein with anti-inflammatory potential that has been poorly investigated in ocular tissues. Aim: The aim of this paper is to evaluate the expression and mechanism of action of Gal-1 in human retinal pigment epithelial cells (ARPE-19 cells) activated by lipopolysaccharide (LPS) and treated with recombinant human Gal- 1 (hrGal-1). Methods: To assess the anti-inflammatory effect of Gal-1, ARPE- 19 cells were cultured in DMEM: complete F-12 (control), activated by LPS and treated with hrGal-1 (0,04; 0,4 e 4 µg/mL)or glucocorticoid dexamethasone (Dex: 1μM) at 2, 8, 24 and 48 hours. Under these conditions, we evaluated the cytotoxicity of pharmacological treatments by cell viability assays, and the expression of the endogenous Gal-1 in cells activated by LPS and treated with Dex by ultrastructural immunocytochemistry. In the supernatants of these cells, in all experimental periods, we analyzed the levels of IL-6, IL-8, IL-10, TNF-α, IL-1β and MCP-1 by ELISA. In order to determine the specificity of the effect of hrGal-1 via carbohydrate recognizer domain (CRD) on ARPE-19 cells, we added sugars to the culture with or without their affinity for the CRD (respectively β-galactose or sucrose - 100 mM), and these supernatants were collected after 8 hours for analysis of pro-inflammatory cytokines IL-6 and IL-8. We also analyzed the expression of the cyclooxygenase-2 (COX-2) enzyme, an important inflammatory process mediator, at 8 and 24 hours by immunofluorescence. Results: The assays of cell viability show that the different drug treatments have low cytotoxicity. The cells activated with... (Complete abstract click electronic access below) / Mestre

This thesis describes improvements to our protein loop structure prediction algorithm and use of this algorithm to inform a computational investigation of anti-HIV antibodies. First, in Section I, we outline improvements to the Protein Local Optimization Program ("Plop") that allow us to reliably restore long loops containing secondary structure elements, and predict nativelike conformations for loops whose surroundings deviate from the native crystal structure context. Shifting to focus exclusively on antibody hypervariable loop prediction, we also benchmark our results in the community-wide Second Antibody Modeling Assessment. Plop can now be reliably deployed as a tool for understanding important biological systems. In Section II, we start from a system of interest - broadly neutralizing antibodies against HIV-1 - with the long-term goal of computationally identifying more potent VRC01-class anti-HIV antibodies. We show proof of concept results for predicting relative binding affinity upon mutation using free energy perturbation (FEP) simulations for the VRC01 antibody binding to glycoprotein gp120. Using the protocols developed in Section I, we provide case studies for using Plop to understand key FEP results and guide future experiments.