Misfolding of membrane proteins as a result of mutations that disrupt their functions in substrate transport across the membrane or signal transduction is the cause of many significant human diseases. Yet, we still have a limited understanding of the direct consequences of these mutations on folding and function - a necessary step toward the rational design of corrective therapeutics. This thesis addresses the gap in understanding the residue-specific implications for folding through a series of experiments that utilize the cystic fibrosis transmembrane conductance regulator (CFTR) as a model in various contexts. We first examined the thermodynamic implications of mutations in the soluble nucleotide binding domain 1 (NBD1) of CFTR. We found that mutations can have a significant effect on thermodynamic stability that is masked in non-physiological conditions. Our studies were then focussed on a membrane-embedded hairpin CFTR fragment comprised of transmembrane segments 3 (TM3) and 4 (TM4) to evaluate the direct effects of mutations on folding in a systematic manner. It was found that the translocon-mediated membrane insertion of helices closely parallels a basic hydrophobic-aqueous partitioning event. This study was then extended to determine residue-specific effects on helix-helix association. We found that this process is not solely dependent on hydropathy, but there is a context dependence of these results with regard to residue position within the helix. Overall, these findings constitute a key step in relating mutation-derived effects on membrane protein folding to the underlying basis of human disease such as cystic fibrosis.

The DrrAB proteins of Streptomyces peucetius belong to the ABC family of ubiquitous membrane transporters. The DrrA and DrrB proteins together form a drug efflux pump that carries out the transport of the anticancer drug doxorubicin by carrying out ATP hydrolysis. The present study is the first where the intrinsic factors involved in the assembly of the DrrAB functional complex have been elucidated. The drrA and drrB genes in the wild type operon have overlapping stop and start codons (ATGA) which indicates translational coupling between the two genes. On insertion of a fortuitous stop codon in DrrA it was shown that the expression of DrrB is coupled to that of the upstream gene drrA. Furthermore, it was observed that a functional complex could be achieved only when the genes were maintained in cis in a translationally coupled manner. Translational regulation in DrrA was found to be involved in the control of optimal levels of DrrB. Inhibitory interactions within drrA sequence were speculated to cause translational arrest at the C terminus of DrrA. A novel assembly domain that forms the interface between DrrA containing the Nucleotide Binding Domain (NBD) and DrrB comprising the TransMembrane Domain (TMD) was found. Based on the data presented in this study a model is proposed for the biogenesis of the DrrAB drug pump. The model suggests that translational coupling between DrrA and DrrB is crucial for functional complex formation. Further, there is evidence of regulation of translation by attenuation in the intergenic region of drrA and drrB. The regulation seems to involve the last 30 nucleotides of the mRNA of drrA and some upstream sequences within drrA that cause translational arrest within the C terminus of DrrA. Since DrrB is translationally coupled to drrA, this translational arrest in conjunction with coupling causes lowering in the levels of DrrB. Finally, since the DrrA-DrrB interaction domain lies in the C terminus of DrrA, only the fully translated DrrA product will be competent to form a complex with DrrB. This interaction between the C terminus of DrrA and the N terminus of DrrB may be crucial for initial targeting of the complex to the membrane. The model is expected to serve as primer and open up an interesting yet insufficiently understood subject of membrane protein biogenesis.

Adenosine triphosphate (ATP) is the molecular currency of intracellular energy transfer in living organisms. The enzyme ATP synthase is primarily responsible for ATP production in eukaryotes. In archaea and some bacteria, ATP is synthesized by V-ATPase that is related to ATP synthase both in structure and function. Both of these enzymes are reversible rotary motors capable of catalyzing ATP synthesis or hydrolysis. The rotation of the central rotor, which is powered by the flow of proton (or sometimes sodium ion) down the electrochemical gradient through the membrane-bound Fo/Vo region, leads to the chemical synthesis of ATP in F1/V1 region. The F1/V1 region, on the other hand, can catalyze ATP hydrolysis, which in turn leads to proton (or sodium) pumping across the membrane through rotation of the central rotor in the opposite direction. This thesis describes structure determination of both the intact F-type and V-type enzymes using single particle electron cryomicroscopy (cryo-EM), with the aim of better understanding their overall architecture, subunit organization and the mechanism of proton translocation. Our cryo-EM structural analysis on the F-type ATP synthase from Saccharomyces cerevisiae uncovered the arrangement of subunits a, b, c, and the two dimer-specific subunits e and g within the membrane-bound region of Fo. A model of oligomerization of the ATP synthase involving two distinct dimerization interfaces was proposed.The rotor-stator interaction within the membrane-bound region of both enzymes is responsible for proton translocation. Our cryo-EM structures of the V-ATPase from Thermus thermophilus reveal that the interaction between the rotary ring (rotor) and the I-subunit (stator) is surprisingly small, with only two subunits from the ring making contact with the I-subunit near the middle of the membrane. Furthermore, the spatial arrangement of transmembrane helices resolved in subunit I can form two passageways that could provide proton access through the membrane-bound region and is consistent with a two-channel model of proton translocation.

Cellular life, as we know it, is absolutely dependent on biological membranes; remarkable superstructures made of lipids and proteins. For example, all living cells are surrounded by at least one membrane that protects the cell and holds it together. The proteins that are embedded in the membranes carry out a wide variety of key functions, from nutrient uptake and waste disposal to cellular respiration and communication. In order to function accurately, any integral membrane protein needs to be inserted into the cellular membrane where it belongs, and in that particular membrane it has to attain its proper structure and find partners that might be required for proper function. All membrane proteins have evolved to be inserted in a specific overall orientation, so that e.g. substrate-binding parts are exhibited on the ‘right side’ of the membrane. So, what determines in which way a membrane protein is inserted? Are all membrane proteins inserted just so? The focus of this thesis is on these fundamental questions: how, and when, is the overall orientation of a membrane protein established? A closer look at the inner membrane proteome of the familiar gram-negative bacterium Escherichia coli revealed a small group of proteins that, oddly enough, seemed to be able to insert into the membrane in two opposite orientations. We could show that these dual-topology membrane proteins are delicately balanced, and that even the slightest manipulations make them adopt a fixed orientation in the membrane. Further, we show that these proteins are topologically malleable until the very last residue has been synthesized, implying interesting questions about the topogenesis of membrane proteins in general. In addition, by looking at the distribution of homologous proteins in other organisms, we got some ideas about how membrane proteins might evolve in size and complexity. Structural data has revealed that many membrane bound transporters have internal, inverted symmetries, and we propose that perhaps some of these proteins derive from dual-topology ancestors. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

In cellular respiration, electron transfer from the breakdown of foodstuff is coupled to the formation of an electrochemical proton gradient. This is accomplished through proton translocation by respiratory complexes, and the proton gradient is subsequently used e.g. to drive ATP production. Consequently, proton- and electron-transfer reactions through the hydrophobic interior of membrane proteins are central to cellular respiration. In this thesis, proton- and electron transfer through an aa3-type terminal oxidase, cytochrome c oxidase (CytcO) from Rhodobacter sphaeroides, have been studied with the aim of understanding the molecular proton-transfer machinery of this proton pump. In the catalytic site of CytcO the electrons combine with protons and the terminal electron acceptor O2 to form water in an exergonic reaction that drives proton pumping. Therefore, CytcO must transfer both protons that are pumped and protons for the oxygen chemistry through its interior. This is done through its two proton-transfer pathways, termed the D pathway and the K pathway. Our studies have shown that the protons pumped during oxidation of CytcO are taken through the D pathway, and that this process does not require a functional K pathway. Furthermore, our data suggests that the K pathway is used for charge compensation of electron transfer to the catalytic site, but only in the A2 → P3 state transition. Our data also show that the water molecules identified in the crystal structures of CytcO play an important role in proton transfer through the D pathway. Finally, the effects of liposome reconstitution of CytcO on D-pathway proton transfer were investigated. The results suggest that the membrane modulates the rates of proton transfer through the D pathway, and also influences the extent of electron transfer between redox-active sites CuA and heme a.

Misfolding of membrane proteins as a result of mutations that disrupt their functions in substrate transport across the membrane or signal transduction is the cause of many significant human diseases. Yet, we still have a limited understanding of the direct consequences of these mutations on folding and function - a necessary step toward the rational design of corrective therapeutics. This thesis addresses the gap in understanding the residue-specific implications for folding through a series of experiments that utilize the cystic fibrosis transmembrane conductance regulator (CFTR) as a model in various contexts. We first examined the thermodynamic implications of mutations in the soluble nucleotide binding domain 1 (NBD1) of CFTR. We found that mutations can have a significant effect on thermodynamic stability that is masked in non-physiological conditions. Our studies were then focussed on a membrane-embedded hairpin CFTR fragment comprised of transmembrane segments 3 (TM3) and 4 (TM4) to evaluate the direct effects of mutations on folding in a systematic manner. It was found that the translocon-mediated membrane insertion of helices closely parallels a basic hydrophobic-aqueous partitioning event. This study was then extended to determine residue-specific effects on helix-helix association. We found that this process is not solely dependent on hydropathy, but there is a context dependence of these results with regard to residue position within the helix. Overall, these findings constitute a key step in relating mutation-derived effects on membrane protein folding to the underlying basis of human disease such as cystic fibrosis.

Organic cation (OC) secretion across renal proximal tubules (RPTs) involves basolateral OCT2- mediated uptake from the blood, followed by apical MATE1/2-mediated efflux into the tubule filtrate. Whereas OCT2 supports electrogenic OC uniport, MATE is an OC/H exchanger. OCs make up ~40% of all prescribed drugs and renal secretion plays a major role in clearing them. This study looked at two aims with the intent of resolving two outstanding issues dealing with the mechanism of MATE-mediated OC transport. First: Understanding the nature of intracellular sequestration of OC in cells that express hMATE1 as an integral part of characterizing 'the potential difference of substrate selectivity between the intracellular and extracellular face of MATE1.' Second: Testing whether structurally distinct MATE substrates can display different quantitative profiles of inhibition when interacting with structurally distinct ligands to determine 'the potential influence of the substrate on the profile of ligand interaction with MATE1.' All uptake experiments were realized with CHO cells that stably expressed hMATE1, hMATE2K or hOCT2. By epifluorescence microscopy cultured CHO-hMATE1 cells accumulated the fluorescent OC, N,N,N-trimethyl-2-[methyl(7-nitrobenzo[c][l,2,5]oxadiazol-4- yl)amino]ethanaminium (NBD-MTMA) in the cytoplasm and in a smaller, punctate compartment; accumulation in hOCT2 expressing cells was restricted to the cytoplasm. A second intracellular compartment was also evident in the multicompartmental kinetics of efflux of the prototypic OC, 1-methyl-4-phenylpyridinium, [³H]MPP, from MATE1-expressing CHO cells. Punctate accumulation (20 min) of NBD-MTMA was markedly reduced by coexposure of MATE1-expressing cells with 5 μM bafilomycin (BAF), an inhibitor of the V-Type H-ATPase, and 20 min accumulations of [³H]MPP and [³H]NBD-MTMA were reduced by >30% by coexposure with 5 μM BAF. BAF had no effect on the initial rate of MATE1-mediated uptake of NBD-MTMA (10-300 sec) suggesting that the effect of BAF was a secondary effect involving inhibition of the V-type H-ATPase. The 15 min accumulation of [³H]MPP by isolated single non-perfused rabbit RPTs was also reduced >30% by coexposure to 5 μM BAF. Thus, the native expression in RPTs of MATE protein within endosomes can increase steady-state OC accumulation. However, the rate of [³H]MPP secretion by isolated single perfused rabbit RPTs was not affected by 5 μM BAF suggesting that vesicles loaded with OCs are not likely to recycle into the apical plasma membrane at sufficient rates to provide a parallel pathway for OC secretion. The uptake of three structurally distinct MATE substrates: MPP, triethylmethylammonium (TEMA) and NBD-MTMA into CHO-hMATE1 and CHO-hMATE2K cells was inhibited by three structurally similar cationic ionic liquids (ILs, salts in the liquid state: N-butylpyridinium, NBuPy; 1-methyl-3-butylimidazolium, Bmim; and N-butyl-N-methylpyrrolidinium, BmPy). The three ILs displayed a higher affinity for the pyridinium-based NBuPy (IC50 values, 2-4 μM) than for either the pyrrolidinium- (BmPy; 20-70 μM) or imidazolium-based ILs (Bmim; 15-60 μM). Inhibition of MPP, TEMA, and NBD-MTMA transport by NBuPy was competitive, with comparable Ki values against all substrates. Bmim also competitively blocked the three substrates but with Ki values that differed significantly (20 μM against MPP and 30 μM against NBD-MTMA versus 60 μM against TEMA). By trans-stimulation, all three ILs were transported by both MATE transporters. Together, these data indicate that renal secretion of ILs by the human kidney involves MATE transporters and suggest that the mechanism of transport inhibition is ligand-dependent, supporting the hypothesis that the binding of substrates to MATE transporters involves interaction with a binding surface with multiple binding sites. In order to further verify this hypothesis the uptake of four structurally distinct MATE substrates: MPP, NBD-MTMA, Cimetidine and Metformin into CHO-hMATE1 cells was characterized. Inhibition by ~400 drugs from the NIH clinical collection (NCC) was determined, and the rank order and level of inhibition seen were comparable against all substrates. IC₅₀ were measured for ~20 drugs selected from the NCC using principal component analysis (PCA); their IC₅₀ values were very similar against all four substrates, showing no systematic influence of substrate structure on inhibitory profile. The development and comparison of pharmacophores for each individual substrate revealed no substantial difference among them as proved by cluster analysis, leading to the conclusion that contrary to what was predicted based on the preliminary IL data, the substrates tested appear to have no influence on the inhibitory profile of ligands with hMATE1.

abstract: Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet would bring fully hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses ( 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. At the initial experiments at the AMO beamline using 6.9- &Aring; wavelength, Bragg peaks were recorded to 8.5- &Aring; resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage. Recently, femtosecond X-ray protein nanocrystallography experiments were done at the CXI beamline of the LCLS using 1.3- &Aring; wavelength, and Bragg reflections were recorded to 3- &Aring; resolution; the data are currently being processed. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins. / Dissertation/Thesis / Ph.D. Chemistry 2011

Le virus d’Epstein-Barr (EBV) est un herpèsvirus humain qui infecte plus de 90% de la population généralement de façon bénigne et asymptomatique. Cependant, de nombreuses données démontrent que ce virus peut également contribuer à certains processus de cancérisation. En effet, l’EBV est associé à de nombreuses pathologies malignes telles que le lymphome de Burkitt, le lymphome hodgkinien et le carcinome du nasopharynx. Dans la grande majorité de ces cancers associées à ce virus, l’EBV exprime un programme de latence de type II durant lequel la protéine LMP1 est exprimée. Elle est décrite comme l’oncogène majeur de l’EBV car son expression est nécessaire à la survie et à la prolifération des lignées transformées in vitro. Cette protéine membranaire est fonctionnellement apparentée aux membres de la famille des récepteurs du TNF. LMP1 est constitutivement active et son expression conduit à l’activation de voies de signalisation telles que les voies NF-&#954;B, PI3K et des MAPK. L’activation de ces voies de signalisation cellulaire confère à LMP1 des propriétés oncogéniques, cependant, des effets toxiques liés à son expression ont également été décrits. Effectivement, LMP1 est capable d’induire l’apoptose dans différents types cellulaires. Dans ce contexte, nous avons d’abord développé et caractérisé, des variants dérivés de LMP1 constitués de sa partie C-terminale signalisatrice, complète ou partielle, fusionnée à la protéine GFP. Nous montrons que ces variants sont capables de séquestrer les protéines adaptatrices se fixant à LMP1 ou au récepteur TNFR1, et d’inhiber le signal et les phénotypes induits par ces derniers. Ces protéines à effet dominant négatif peuvent ainsi contrecarrer les effets transformants de LMP1 dans des modèles de latence II et III. Ces dominants négatifs peuvent aussi inhiber l’activation du TNFR1 et les phénotypes qui en découlent. Puis, nous avons étudié les propriétés de LMP1 en dehors d’un contexte infectieux et son rôle dans la transformation épithéliale. Nous démontrons que LMP1 induit la mort des cellules épithéliales MDCK mais certaines cellules outrepassent ses effets cytotoxiques générant des lignées qui expriment stablement LMP1 et dans lesquelles cet oncogène viral favorise la survie et exacerbe les phénotypes induits par le facteur de croissance HGF. Le caractère ambivalent de LMP1 pourrait limiter le pouvoir oncogène de l’EBV mais en contrepartie favoriser l’émergence de cellules résistantes à l’apoptose et capables de répondre de façon accrue à des facteurs de croissance. Nos travaux ont permis de mieux comprendre la dualité fonctionnelle de LMP1, d’une part ses effets oncogènes favorisant la survie cellulaire et d’autre part ses propriétés pro-apoptotiques, induites directement ou révélées suite à son inhibition, limitant la tumorigenèse. La caractérisation des mécanismes moléculaires impliquant LMP1 pourrait ainsi participer à la définition de potentielles stratégies thérapeutiques pour le traitement de cancers associés à l’EBV et où LMP1 est exprimée. / Epstein-Barr virus (EBV) is a human herpesvirus that infects more than 90% of worldwide population, generally asymptomatically. However, numerous studies show that EBV promotes tumorigenesis. Indeed, EBV infection is associated with many human malignancies including Burkitt’s lymphoma, Hodgkin’s lymphoma and nasopharyngeal carcinoma. In most of these cancers associated with EBV, it expresses latency II program in which the latent membrane protein 1 (LMP1) is expressed. LMP1 is described as the major EBV oncogene because its expression is necessary in vitro for survival and proliferation of transformed cell lines. This membrane protein is functionally related to members of the TNF receptors superfamily. LMP1 is constitutively active and its expression leads to activation of NF-&#954;B, PI3K and MAPK signaling pathways. These activation confers oncogenic properties to LMP1, however, toxic effects associated with its expression are also described. Indeed, LMP1 can induce cell death in different cell types. In this context, we first developed and characterized LMP1 derivative variants consisting of its C-terminal signal, complete or partial, fused to GFP. We show that these variants are able to sequester adaptors binding to LMP1 and TNFR1, and inhibit signal and phenotypes induced by them. These proteins have dominant negative effect and may counteract LMP1 transformant properties in latency II cellular models. In addition, these dominant negatives impair TNFR1 signaling and associated phenotypes. Then, we studied LMP1 properties outside infectious context and its involvement in epithelial transformation. We show that LMP1 induces cell death in MDCK epithelial cells, but some go beyond its cytotoxic effects generating lines stably expressing LMP1 and in which this viral oncogene promotes survival and exacerbates HGF-induced phenotypes. Ambivalent character of LMP1 could limit the oncogenic potential of EBV but in return support the emergence of cells resistant to apoptosis and able to enhance growth factor responses. Our work allowed us to better understand the functional duality of LMP1 on the one hand its oncogenic effects favoring cell survival and other pro-apoptotic properties, induced directly or reveal by its inhibition, limiting tumorigenesis. Thus, characterization of molecular mechanisms involving LMP1 could participate in the definition of potential therapeutic strategies for treating cancers associated with EBV and where LMP1 is expressed.

abstract: Transient receptor potential vanilloid member 1 (TRPV1) is a membrane protein ion channel that functions as a heat and capsaicin receptor. In addition to activation by hot temperature and vanilloid compounds such as capsaicin, TRPV1 is modulated by various stimuli including acidic pH, endogenous lipids, diverse biological and synthetic chemical ligands, and modulatory proteins. Due to its sensitivity to noxious stimuli such as high temperature and pungent chemicals, there has been significant evidence that TRPV1 participates in a variety of human physiological and pathophysiological pathways, raising the potential of TRPV1 as an attractive therapeutic target. However, the polymodal nature of TRPV1 function has complicated clinical application because the TRPV1 activation mechanisms from different modes have generally been enigmatic. Consequently, tremendous efforts have put into dissecting the mechanisms of different activation modes, but numerous questions remain to be answered. The studies conducted in this dissertation probed the role of the S1-S4 membrane domain in temperature and ligand activation of human TRPV1. Temperature-dependent solution nuclear magnetic resonance (NMR) spectroscopy for thermodynamic and mechanistic studies of the S1-S4 domain. From these results, a potential temperature sensing mechanism of TRPV1, initiated from the S1-S4 domain, was proposed. Additionally, direct binding of various ligands to the S1-S4 domain were used to ascertain the interaction site and the affinities (Kd) of various ligands to this domain. These results are the first to study the isolated S1-S4 domain of human TRPV1 and many results indicate that the S1-S4 domain is crucial for both temperature-sensing and is the general receptor binding site central to chemical activation. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2019