As células-tronco mesenquimais (MSCs) são células multipotentes que tem o potencial de se diferenciarem em várias linhagens celulares in vitro e in vivo. Estas são encontradas em nichos específicos em muitos órgãos e tecidos adultos, tais como medula óssea, tecido adiposo, músculo, dente, cordão umbilical, pele, cartilagem articular, sendo facilmente isoladas, expandidas e com alta capacidade proliferativa in vitro. Assim, estas características têm despertado grande interesse na sua utilização como uma potencial fonte de células para o reparo e regeneração tecidual de diversos órgãos e tecidos. Pouco se conhece sobre as moléculas que são secretadas pelas MSCs para a matriz extracelular (MEC) e que estão na interface célula-matriz e estão presentes em vias de transdução de sinais intracelulares. Desta forma, o objetivo deste trabalho foi avaliar o perfil de expressão gênica de enzimas que remodelam a MEC (metaloproteinases de matriz MMPs: 15 membros) e seus inibidores (inibidores teciduais das metaloproteinases de matriz TIMPs: 4 membros e RECK) e proteína da membrana plasmática (Caveolina-1) durante a diferenciação osteogenica in vitro a partir de células-tronco mesenquimais da polpa dentária humana (DPSCs). Para tanto, utilizamos polpas dentárias humanas provenientes de terceiros molares de indivíduos adultos (18-32 anos n=3) e as DPSCs isoladas foram imunofenotipadas por citometria de fluxo, avaliada a taxa de proliferação, induzidas as diferenciações osteogênica (1, 7, 14, 21 e 28 dias) e adipogênica (28 dias) e os transcritos avaliados por PCR em tempo real. Estas células foram positivas para o marcadores CD29, CD105, STRO-1, CD44, CD90 negativas os marcadores para CD31, CD45, CD34 e CD14 e são capazes de se diferenciarem em osteoblastos e adipócitos. Verificamos que as MMP-2, MMP-3, MMP-13, MMP-14, MMP-25, TIMP-3, TIMP-4 e Caveolina-1 foram diferencialmente expressas durante a diferenciação osteogênica, sendo reguladas positivamente apenas no período de 28 dias pós indução e a TIMP-1 regulada positivamente desde o primeiro dia de indução. A MMP-11 e MMP-16 não foram detectadas nas DPSCs e nem durante a diferenciação osteogênica. Desta forma, concluímos que MMPs encontradas bem como a Caveolina-1 e as TIMP-3 e TIMP-4 podem estar participando dos dos eventos de diferenciação óssea em DPSCs, a TIMP-1 pode estar participando de eventos biológicos relacionados as propriedades do estado indiferenciado das DPSCs e da diferenciação óssea e que as MMP-11 e MMP-16 não são expressas pelas DPSCs e também não estão envolvidas na diferenciação osteogênica. / Mesenchymal stem cells (MSCs) are multipotent cells that have the potential to differentiate into various cell lineages in vitro and in vivo. These are found in specific niches in many adult organs and tissues, such as bone marrow, adipose tissue, muscle, tooth, umbilical cord, skin, cartilage, being easily isolated, expanded and high proliferative capacity in vitro. Thereby, these features have attracted great interest in its use as a potential source of cells for tissue repair and regeneration of various organs and tissues. Little is known about the molecules secreted by MSCs into the extracellular matrix (ECM), present at cell-matrix interface and present on intracellular signal transduction. Thus, the aim of this study was to evaluate gene expression profile of ECM remodeling enzymes (matrix metalloproteinases MMPs: 15 members) and their inhibitors (tissue inhibitors of matrix metalloproteinases TIMPs: 4 members and RECK) and plasma membrane proteins (Caveolin-1) that participate in signaling pathways during osteogenic differentiation in vitro from human dental pulp stem cells (DPSCs). Normal human impacted third molars were collected from adults (18-32 years-old n=3) and DPSCs isolated were immunophenotyping by flow cytometry, evaluated the proliferation ratio, induced to osteogenic (1, 7, 14, 21 and 28-days) and adipogenic differentiation (28-days) and the transcript levels evaluated by Real Time PCR. These cells are positive for CD29, CD105, STRO -1, CD44, and CD90 markers and negative for CD31, CD45, CD34, and CD14 markers and are capable of differentiating into osteoblasts and adipocytes. We found that MMP- 2, MMP -3, MMP -13, MMP -14, MMP -25, TIMP-3, TIMP-4 and Caveolin-1 were differentially expressed during osteogenic differentiation, being upregulated only at 28 days post-induction and TIMP-1 upregulated from the first day of induction. MMP-11 and MMP-16 were not detected in DPSCs neither during differentiation. Thus, we conclude that MMPs, Caveolin-1 found as well as TIMP-3 and TIMP-4 may be participating in the event of bone differentiation in DPSCs, TIMP-1 may participate in biological events related to the properties of the undifferentiated state DPSCs and osteogenic differentiation, MMP-11 and MMP-16 are not also expressed by DPSCs and are not involved in osteogenic differentiation.

Nile tilapia, Oreochromis niloticus, is one of the most important farmed fish globally. One of the most serious bacterial diseases constraining global tilapia production is Francisellosis caused by Francisella noatunensis subsp. orientalis (Fno). Although outbreaks of Fno are increasing worldwide, there are no licenced commercial vaccines to prevent the disease for use on tilapia farms. Thus, the current treatment of choice is the use of antibiotics combined with increasing water temperature up to 30°C. Studies investigating the diversity of circulating Fno isolates and the immune response of tilapia elicited by vaccination against piscine francisellosis are lacking. In addition, the current conventional and molecular tools used for detection of Fno have many drawbacks, making detection of Fno a challenging process. In this study, five clinical isolates of Fno from diverse geographical locations (UK, Costa Rica, Mexico, Japan and Austria), previously characterised by morphology, genotype, antimicrobial susceptibility and virulence, were used in a proteomic study. The whole proteomic cell profile of the five isolates were homogenous by one-dimension sodium dodecyl polyacrylamide gel electrophoresis (1D-SDS-PAGE), while minor differences in the intensity of 15 proteins between the strains were observed by two-dimension SDS-PAGE (2DE), including some important virulence related proteins. The UK isolate was the most significantly different isolate when compared to the other Fno isolates in the current study. The Fno UK isolate had significantly higher abundance of 10/15 of the significantly expressed proteins including four of the essential pathogenicity and virulence related proteins (IglC, GroEL, DnaK, ClpB) compared to the other used Fno isolates. The antigenic profiles of the five Fno isolates were studied by 1D western blotting using tilapia hyper immune sera which recognised an immunodominant band of a molecular weight of ~ 17-28 kDa in all tested Fno isolates. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI/MS/MS) identified 47 proteins in this antigenic band. Some of the identified proteins are associated with Fno pathogenicity. 2D western blot analysis of the vaccine isolate (Fno UK) revealed differential antigen recognition between sera from vaccinated and non-vaccinated fish following experimental challenge (26 antigenic spots recognised by sera from vaccinated fish; 31 antigenic spots recognised by sera from vaccinated and challenged fish and 30 antigenic spots recognised by non-vaccinated and challenged fish). The identity of these proteins was determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and some of them are known Francisella virulence related proteins. Bioinformatics analyses revealed diverse categories of proteins with high biological functions, however the vast majority of these proteins are involved in energy production and metabolic pathways of the bacteria. This detailed analysis will facilitate the development of cross-strain protective subunit Fno vaccines and antigen-targeted Fno diagnostics. The outer membrane proteins (OMPs) of the same five Fno isolates were extracted using the ionic detergent sarkosyl. The OMP fraction of the different isolates were separated via 1D-SDS PAGE and the digested peptides of the UK isolate were analysed by LC/ESI/MS/MS. High degree of similarity was observed in the OMP profile of the five Fno isolates with an abundant protein band at 17-28 kDa, which was found to be antigenic by 1D western blot using convalescent tilapia sera. LC/ESI/MS/MS analysis of the OMPs of the Fno UK isolate identified 239 proteins, including 44 proteins in the antigenic band (17-28 kDa). Comparison between the proteins identified in the immunogenic band of whole cell lysate and OMP fraction of the Fno UK isolate showed 30 common proteins between the two preparations, 17 proteins were identified only in the whole cell extract and 14 were identified only in OMP fraction. Outer membrane proteins (e.g. Omp-A), virulence related proteins such (e.g. IglC) and other stress related proteins (e.g. AhpC/TSA family peroxiredoxin) were more abundant in the OMP fraction than the whole cell lysate. In silico analysis enabled prediction of the function and location of the OMPs identified by Mass-spectrometry. The findings of this study provide preliminary data on bacterial surface proteins that exist in direct contact with the host immune defence during infection and offering an insight into their potential role as novel targets for Fno diagnostics and vaccine development. The efficacy of an injectable whole cell oil-adjuvanted vaccine was evaluated against challenge with heterologous Fno isolates in Nile tilapia, Oreochromis niloticus. Three duplicate groups of 130 healthy Nile tilapia (~15 g) were intraperitoneally (i.p.) injected with the vaccine, adjuvant-alone or PBS followed by an i.p. challenge with three Fno isolates from geographically distinct locations. The vaccine provided significant protection to all immunised tilapia groups with a significantly higher relative percent survival (RPS) of 82.3% against homologous challenge, compared to 69.8% and 65.9% after heterologous challenge. Protection correlated with significantly elevated specific antibody responses and western blot analysis demonstrated cross-isolate antigenicity with sera from fish post-vaccination and post-challenge. Moreover, a significantly lower bacterial burden was detected by quantitative real-time polymerase chain reaction (qPCR) in conjunction with significantly greater expression of IgM, IL-1β, TNF-a and MHCII 72 hours post-vaccination (hpv) in spleen samples from vaccinated tilapia compared to those of adjuvant-alone and control fish. The latter results suggested stimulation of protective immune responses following vaccination. In addition, a whole cell formalin killed autogenous immersion vaccine against Fno was developed using the same isolate used for the injectable vaccine. Duplicate tanks of 35 tilapia fry were immersed in the vaccine or in sterile Modified Muller Hinton broth (MMHB) diluted in tank water (1:10 dilution) for 30 s and at 30 days post-vaccination (dpv), all fish groups were immersion challenged with the homologous Fno isolate and monitored for 21 days. A moderate RPS of 43.7% was provided by the vaccine. Serum IgM levels were below the threshold in 30 % of the vaccinated fry 30 dpv. Also, the IgM levels of the vaccinated fry were not significantly different from control fry 21 days-post challenge. A recombinase polymerase amplification (RPA) assay was developed and validated for rapid detection of Fno. The RPA reaction was performed at a constant temperature of 42°C for 20 min. The RPA assay was performed using a quantitative plasmid standard containing a unique Fno gene sequence. Validation of the assay was performed not only by using DNA from Fno, closely related Francisella species and other common bacterial pathogens in fish farms, but also by screening 78 Nile tilapia and 5 water samples collected from UK and Thailand. All results were compared with those obtained by previously established real-time qPCR. The developed RPA showed high specificity in detection of Fno with no cross-detection of either the closely related Francisella spp. or the other species of bacteria tested. The Fno-RPA performance was highly comparable to the published qPCR with detection limits at 15 and 11 DNA molecules detected, respectively. The Fno-RPA was rapid, giving results in approximately 6 min in contrast to the qPCR that required approximately 90 min to reach the same detection limits. Moreover, the RPA was more tolerant to reaction inhibitors than qPCR when tested with field samples. The fast reaction, simplicity, cost-effectiveness, sensitivity and specificity make the RPA an attractive diagnostic tool that will contribute to control the infection through prompt on-site detection of Fno. The overall results of this study indicated that Fno isolates from different origins share a high degree of homology in their proteomic and antigenic profile. Proteomic characterisation data of Fno isolates has contributed to understanding the diversity of Fno isolates and assisted in identifying suitable candidates for developing an effective Fno vaccine. / Moreover, this study has proven the efficacy of a cross protective Fno injection vaccine in tilapia fingerlings, with further optimisation needed for immersion vaccination of fry, and given insights into the immune response of tilapia to vaccination against francisellosis. In addition, it provided a rapid, sensitive, specific and robust molecular tool for detection of Fno that can assist surveillance and control of piscine francisellosis on tilapia farms.

As células-tronco mesenquimais (MSCs) são células multipotentes que tem o potencial de se diferenciarem em várias linhagens celulares in vitro e in vivo. Estas são encontradas em nichos específicos em muitos órgãos e tecidos adultos, tais como medula óssea, tecido adiposo, músculo, dente, cordão umbilical, pele, cartilagem articular, sendo facilmente isoladas, expandidas e com alta capacidade proliferativa in vitro. Assim, estas características têm despertado grande interesse na sua utilização como uma potencial fonte de células para o reparo e regeneração tecidual de diversos órgãos e tecidos. Pouco se conhece sobre as moléculas que são secretadas pelas MSCs para a matriz extracelular (MEC) e que estão na interface célula-matriz e estão presentes em vias de transdução de sinais intracelulares. Desta forma, o objetivo deste trabalho foi avaliar o perfil de expressão gênica de enzimas que remodelam a MEC (metaloproteinases de matriz MMPs: 15 membros) e seus inibidores (inibidores teciduais das metaloproteinases de matriz TIMPs: 4 membros e RECK) e proteína da membrana plasmática (Caveolina-1) durante a diferenciação osteogenica in vitro a partir de células-tronco mesenquimais da polpa dentária humana (DPSCs). Para tanto, utilizamos polpas dentárias humanas provenientes de terceiros molares de indivíduos adultos (18-32 anos n=3) e as DPSCs isoladas foram imunofenotipadas por citometria de fluxo, avaliada a taxa de proliferação, induzidas as diferenciações osteogênica (1, 7, 14, 21 e 28 dias) e adipogênica (28 dias) e os transcritos avaliados por PCR em tempo real. Estas células foram positivas para o marcadores CD29, CD105, STRO-1, CD44, CD90 negativas os marcadores para CD31, CD45, CD34 e CD14 e são capazes de se diferenciarem em osteoblastos e adipócitos. Verificamos que as MMP-2, MMP-3, MMP-13, MMP-14, MMP-25, TIMP-3, TIMP-4 e Caveolina-1 foram diferencialmente expressas durante a diferenciação osteogênica, sendo reguladas positivamente apenas no período de 28 dias pós indução e a TIMP-1 regulada positivamente desde o primeiro dia de indução. A MMP-11 e MMP-16 não foram detectadas nas DPSCs e nem durante a diferenciação osteogênica. Desta forma, concluímos que MMPs encontradas bem como a Caveolina-1 e as TIMP-3 e TIMP-4 podem estar participando dos dos eventos de diferenciação óssea em DPSCs, a TIMP-1 pode estar participando de eventos biológicos relacionados as propriedades do estado indiferenciado das DPSCs e da diferenciação óssea e que as MMP-11 e MMP-16 não são expressas pelas DPSCs e também não estão envolvidas na diferenciação osteogênica. / Mesenchymal stem cells (MSCs) are multipotent cells that have the potential to differentiate into various cell lineages in vitro and in vivo. These are found in specific niches in many adult organs and tissues, such as bone marrow, adipose tissue, muscle, tooth, umbilical cord, skin, cartilage, being easily isolated, expanded and high proliferative capacity in vitro. Thereby, these features have attracted great interest in its use as a potential source of cells for tissue repair and regeneration of various organs and tissues. Little is known about the molecules secreted by MSCs into the extracellular matrix (ECM), present at cell-matrix interface and present on intracellular signal transduction. Thus, the aim of this study was to evaluate gene expression profile of ECM remodeling enzymes (matrix metalloproteinases MMPs: 15 members) and their inhibitors (tissue inhibitors of matrix metalloproteinases TIMPs: 4 members and RECK) and plasma membrane proteins (Caveolin-1) that participate in signaling pathways during osteogenic differentiation in vitro from human dental pulp stem cells (DPSCs). Normal human impacted third molars were collected from adults (18-32 years-old n=3) and DPSCs isolated were immunophenotyping by flow cytometry, evaluated the proliferation ratio, induced to osteogenic (1, 7, 14, 21 and 28-days) and adipogenic differentiation (28-days) and the transcript levels evaluated by Real Time PCR. These cells are positive for CD29, CD105, STRO -1, CD44, and CD90 markers and negative for CD31, CD45, CD34, and CD14 markers and are capable of differentiating into osteoblasts and adipocytes. We found that MMP- 2, MMP -3, MMP -13, MMP -14, MMP -25, TIMP-3, TIMP-4 and Caveolin-1 were differentially expressed during osteogenic differentiation, being upregulated only at 28 days post-induction and TIMP-1 upregulated from the first day of induction. MMP-11 and MMP-16 were not detected in DPSCs neither during differentiation. Thus, we conclude that MMPs, Caveolin-1 found as well as TIMP-3 and TIMP-4 may be participating in the event of bone differentiation in DPSCs, TIMP-1 may participate in biological events related to the properties of the undifferentiated state DPSCs and osteogenic differentiation, MMP-11 and MMP-16 are not also expressed by DPSCs and are not involved in osteogenic differentiation.

O trabalho aqui desenvolvido teve como objeto o estudo estrutural e funcional de várias proteínas do fitopatógeno Xanthomonas axonopodis pv citri (Xac), dentre as quais se destacam as proteínas hipotéticas conservadas YaeQ e SufE, as proteínas RpfC, RpfF e RpfG envolvidas em quorum sensing e proteínas PilZ, FimX e PilB envolvidas na biogênese do pilus tipo IV. Para o desenvolvimento deste trabalho foram utilizadas diferentes técnicas incluindo: clonagem, expressão, purificação, desnaturação térmica, cristalografia, difração de raios-X, RMN, ensaios de 2-híbrido, produção de nocautes, mutação sítio dirigida, Western- e Far- Western, entre outras. Dentre os resultados mais importantes obtidos temos a determinação estrutural das proteínas YaeQ e PilZ pela técnica MAD. Em ambos os casos, as estruturas representaram topologias inéditas. Com base nos dados estruturais, mostramos que YaeQ pertence à família PD-(D/E)XK presente em endonucleases dependentes de magnésio, e a partir de ensaios funcionais obtivemos evidências que sugerem que YaeQ está envolvida em alguma via de reparo de DNA em Xac. A estrutura tridimensional de PilZ revelou uma inesperada variedade estrutural dentro da família PilZ e mostrou de forma clara porque ortólogos não interagem com o segundo mensageiro bacteriano, c-diGMP. A cadeia principal de PilZ foi assinalada por RMN e a estrutura secundária de PilZ em solução é consistente com aquela determinada por cristalografia. Duas proteínas que interagem com PilZ foram identificadas: PilB e FimX. Como PilZ, ambos exercem papéis na biogênese do pilus tipo IV (T4P). Mostramos que PilZ interage especificamente com o domínio EAL de FimX e que resíduos conservados na região do C-terminal de PilZ estão envolvidos na interação com PilB, mas não com FimX. Ensaios de mutação sítio dirigida mostraram que a Y22 de PilZ pode estar envolvida na regulação da interação de PilZ com FimX e com PilB. Apesar de PilZ não interagir com c-diGMP seu parceiro, FimX, interage. PilZ consegue interagir com PilB ao mesmo tempo em que interage com FimX, formando um complexo ternário que é independente da interação de FimX com c-diGMP. Com base em todos estes resultados propusemos possíveis mecanismos de ação de PilZ e FimX no controle da biogênese do T4P. Além dos resultados acima descritos, determinamos a estrutura de SufE e mostramos que esta aumenta a atividade cisteína dessulfarase de seu parceiro, SufS, em torno de 10 vezes, como ocorre com SufE-SufS de E.coli. Clonamos, expressamos, purificamos e fizemos ensaios de cristalização de algumas proteínas envolvidas no controle de quorum sensing em Xac. Tivemos êxito na cristalização do domínio HPT (histidina fosfotransferase) da proteína chave deste sistema, RpfC / The aim of the project was to perform structural and functional studies of different Xanthomonas axonopodis pv citri (Xac) proteins including the hypothetical proteins YaeQ and SufE; RpfC, RpfF and RpfG involved in the quorum sensing and PilZ, FimX and PilB that play roles in type IV pilus (T4P) biogenesis. Several experimental techniques were employed including cloning, expression and purification of recombinant proteins, thermal denaturation, protein crystallography, X-ray diffraction, NMR, two-hybrid assays, Western- and Far-Western Blotting assays, site direct mutagenesis, and the production of Xac knockouts strains. The most important results include the determination of the three-dimensional crystal structures of PilZ and YaeQ using the MAD technique. In both cases, the structures reveled new protein topologies. The comparison of the YaeQ structure with others deposited in public databases revealed that YaeQ proteins represent a new variation within the PD-(D/E)XK magnesium dependent endonucleases superfamily. Functional assays suggest that YaeQ may be envolved in DNA repair in Xac. The PilZ three-dimensional structure revealed an unexpected structural variation within the PilZ domain superfamily and showed why PilZ orthologs are not able to bind the important bacterial second messenger, c-diGMP. We assigned the PilZ main chain by NMR and used this information to demonstrate that the PilZ secondary structure in solution is consistent with the PilZ crystal structure. We identified two proteins that interact with PilZ: PilB and FimX. As with PilZ, both PilB and FimX are involved in T4P biogenesis. PilZ binds specifically to the EAL domain of FimX and the conserved residues located in the PilZ unstructured C-terminal region contribute to binding with PilB but not with FimX. Site direct mutagenesis studies showed that PilZ residue Y22 is necessary for its capability to interact with both PilB and FimX. Although PilZ does not bind c-diGMP, her partner, FimX, does. We present evidence that PilZ can bind simultaneously to FimX and PilB, forming a ternary complex that is independent of c-diGMP. These results allow us to propose possible mechanisms by which PilZ and FimX control T4P biogenesis. Other results obtained during this period include the resolution of the crystal structure of the SufE protein from Xac using the molecular replacement technique. We show that SufE induces a 10-fold increase in the cysteine desulfurase activity of SufS, similar to that observed for the SufE-SufS complex from E. coli. Several proteins involved in quorum sensing and c-di-GMP signaling were cloned, expressed and submitted to crystallization trials. Crystals of the HPT (histidine phophotransferase) domain) of the RpfC sensor histidine kinase were obtained

Unnatural amino acids (uAA) expand the structural and functional possibilities of proteins. Numerous previous studies have demonstrated uAA as a powerful tool for protein engineering, but challenges also remain. Three notable such challenges include: (1) the fitness of uAA-incorporated proteins are difficult to predict and time-consuming to screen with conventional methods, (2) uAA incorporation in difficult-to-express proteins (e.g. membrane proteins such as G-protein coupled receptors) remain challenging, and (3) the incorporation of multiple types of uAA are still limited. In response, we pose cell-free protein synthesis (CFPS), a rapid and versatile in vitro expression system, as a platform to explore solutions to these challenges. The "cell-free" nature of CFPS enables it to accelerate protein expression and tolerate extensive modifications to its translational environment. In this work, these advantages were utilized to address the aforementioned challenges by: (1) rapidly expressing and screening uAA-containing proteins, (2) incorporating uAA in functional G-protein coupled receptor in the presence of membrane-mimicking lipid additives, and (3) engineer the translational environment extensively towards multiple uAA incorporation.

Ce travail de thèse repose sur le développement de méthodes en spectrométrie de masse native et mobilité ionique pour la caractérisation structurale de protéines d’intérêt thérapeutique et de complexes multiprotéiques. L’optimisation fine et conséquente de la préparation d’échantillon et des conditions analytiques ont permis la caractérisation de protéines membranaires solubilisées en milieu détergent, protéines hydrophobes habituellement réfractaires à l’analyse par MS. D’autre part, une nouvelle approche de mobilité ionique appelée Collision Induced Unfolding a été évaluée et mise en place au laboratoire. Elle a permis une caractérisation conformationnelle approfondie et originale de plusieurs formats d’anticorps monoclonaux thérapeutiques. Enfin, les techniques de MS native et de mobilité ionique ont été utilisées pour caractériser des complexes multiprotéiques d’hétérogénéité variable mettant ainsi en lumière leurs avantages et les progrès réalisés dans le domaine de la MS structurale. / This PhD work focuses on developments in native mass spectrometry and ion mobility methods for the structural characterization of therapeutic proteins and multiprotein complexes. First, careful optimizations of sample preparation and analytical conditions allowed the characterization of membrane proteins, which are hydrophobic proteins difficult to analyze by MS approaches in detergent environment. Then, a new ion mobility-based activation approach called Collision Induced Unfolding has been set up and evaluated. CIU allowed extensive and original conformational characterization of several therapeutic monoclonal antibody formats. Finally, native MS and ion mobility techniques were used for the characterization of heterogeneous multiprotein complexes depicting their benefit when combined to other biophysical techniques for the structural characterization of multiprotein complexes.

Transport across the membrane of a cell is of crucial importance for cellular functions. The solute carrier family,SLC38 is a family of membrane proteins that transports various substances through the membrane and thusperforms many physiologically important functions, for example, transport of glutamine from astrocyte toneurons in the central nervous system. In this paper, we demonstrate that one of the transporters in this familynamed SLC38A6 forms several protein complexes with a variety of proteins in the membrane and in synapticvesicles, suggesting that SLC38A6 is involved in the synaptic release of neurotransmitters in synapses. Weperformed sensitive protein interaction analysis between the protein of interest and a variety of proteinsexpressed at different sites in the neuronal cell. We showed that SLC38A6 interacts with proteins in the cellmembrane as well as in the membrane of synaptic vesicles. The current theory is that SLC38A6 interact withthese proteins when the synaptic vesicles are in close proximity with the cell membrane during the release of theneurotransmitters.

Single-molecule force spectroscopy (SMFS) with atomic force microscope (AFM) has advanced our knowledge of the mechanical aspects of biological processes, and helped us take big strides in the hitherto unexplored areas of protein (un)folding. One such virgin land is that of membrane proteins, where the advent of AFM has not only helped to visualize the difficult to crystallize membrane proteins at the single-molecule level, but also given a new perspective in the understanding of the interplay of molecular interactions involved in the construction of these molecules. My PhD work was tightly focused on exploiting this sensitive technique to decipher the intra- and intermolecular interactions in membrane proteins, using bacteriorhodopsin and bovine rhodopsin as model systems. Using single-molecule unfolding measurements on different bacteriorhodopsin oligomeric assemblies - trimeric, dimeric and monomeric - it was possible to elucidate the contribution of intra- and interhelical interactions in single bacteriorhodopsin molecules. Besides, intriguing insights were obtained into the organization of bacteriorhodopsin as trimers, as deduced from the unfolding pathways of the proteins from different assemblies. Though the unfolding pathways of bacteriorhodopsin from all the assemblies remained the same, the different occurrence probability of these pathways suggested a kinetic stabilization of bacteriorhodopsin from a trimer compared to that existing as a monomer. Unraveling the knot of a complex G-protein coupled receptor, rhodopsin, showed the existence of two structural states, a native, functional state, and a non-native, non-functional state, corresponding to the presence or absence of a highly conserved disulfide bridge, respectively. The molecular interactions in absence of the native disulfide bridge mapped onto the three-dimensional structure of native rhodopsin gave insights into the molecular origin of the neurodegenerative disease retinitis pigmentosa. This presents a novel technique to decipher molecular interactions of a different conformational state of the same molecule in the absence of a high-resolution X-ray crystal structure. Interestingly, the presence of ZnCl2 maintained the integrity of the disulfide bridge and the nature of unfolding intermediates. Moreover, the increased mechanical and thermodynamic stability of rhodopsin with bound zinc ions suggested a plausible role for the bivalent ion in rhodopsin dimerization and consequently signal transduction. Last but not the least, I decided to dig into the mysteries of the real mechanisms of mechanical unfolding with the help of well-chosen single point mutations in bacteriorhodopsin. The monumental work has helped me to solve some key questions regarding the nature of mechanical barriers that constitute the intermediates in the unfolding process. Of particular interest is the determination of altered occurrence probabilities of unfolding pathways in an energy landscape and their correlation to the intramolecular interactions with the help of bioinformatics tools. The kind of work presented here, in my opinion, will not only help us to understand the basic principles of membrane protein (un)folding, but also to manipulate and tune energy landscapes with the help of small molecules, proteins, or mutations, thus opening up new vistas in medicine and pharmacology. It is just a matter of a lot of hard work, some time, and a little bit of luck till we understand the key elements of membrane protein (un)folding and use it to our advantage.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2008. / Härtill 4 uppsatser. Includes bibliographical references.

Diss. (sammanfattning) Umeå : Umeå universitet, 2009. / Härtill 4 uppsatser. Även tryckt utgåva.