Complex I (NADH:ubiquinone oxidoreductase), located in the mitochondrial inner membrane, is a major electron entry point to the respiratory chain. It couples the energy released from electron transfer (from NADH to ubiquinone) to the concomitant pumping of protons across the membrane, to generate an electrochemical proton motive force. Mammalian complex I is composed of 45 subunits, 14 of which comprise its simpler bacterial homologues. It is encoded by both the mitochondrial and nuclear genomes, and pathological mutations in both sets of subunits result in severe neuromuscular disorders such as Leigh syndrome. Several structures of mammalian complex I from various organisms have been determined, but the limited resolutions of the structures, which typically refer to poorly characterised enzyme states, has hampered detailed analyses of mechanistic features. The first part of this thesis describes development of a method for purifying complex I from the genetically amenable and medically relevant model organism Mus musculus (mouse), in a pure, stable and active state. The enzyme from mouse heart mitochondria was then comprehensively characterised, to ensure the presence of all the expected subunits and co-factors, and to define its kinetic properties. The second part of this thesis describes structural studies by single particle electron cryomicroscopy (cryo-EM) on the purified mouse enzyme in two distinct states, the 'active' and 'de-active' states. The active state was determined to 3.3 Å resolution, the highest resolution structure of a eukaryotic complex I so far. Subsequently, comparison of the two mouse structures, together with previously determined mammalian and bacterial structures, revealed variations in key structural elements in the membrane domain, which may be crucial for the catalytic mechanism. Moreover, in the high-resolution active mouse complex I structure a nucleotide co-factor was observed bound to the nucleoside kinase subunit NDUFA10. Finally, complex I from the Ndufs4 knockout mouse model, which recapitulates the effects of a human mutation that causes Leigh syndrome, was purified and subjected to kinetic and proteomic analyses. Following cross-linking and preliminary structural studies, it was concluded that the detrimental effects of deleting NDUFS4 are due to lack of stability of the mature complex.

Ubiquitination is a post-translational modification tht mediates sorting of integral membrane proteins to lysosomes for their degradation. ESCRTs (Endosomal Sorting Complex Required For Transport) bind and sequester ubiquitinated membrane proteins and direct them into multivesicular bodies (MVBs). ESCRTs themselves become covalently ubiquitinated, simply by virtue of non-covalently binding Ub. However, it is unclear whether this regulates a critical aspect of ESCRT function. In yeast, many MVB cargo proteins are ubiquitinated by the HECT-type Ub-ligase Rsp5, sometimes via the action of Rsp5 adaptor proteins. While many Rsp5 targets are modified by polyubiquitination, it remains unclear whether polyubiquitination is a necessary signal for their incorporation into MVBs. Despite years of research, these and related questions have been difficult to resolve because it is technically quite challenging to control the level of a given protein's ubiquitination. The aim of this research was to develop a novel technique, which can render proteins resistant to ubiquitination. The technique involved the fusion of the Ub-peptidase to a protein of interest via a flexible linker, essentially creating a "DUb module". The intent of this module would be to cleave any Ub form the target protein, essentially immunizing it from the effects of ubiquitination. This novel method was used in combination with several conventional methods to examine the role of ubiquitination within the endocytic pathway and in particular focus on the questions of what type of ubiquitin signal was sufficient for sorting into MVB vesicles and whether ubiquitination of ESCRTs was required for their sorting activity. We found that a single Ub was sufficient for membrane protein entry into MVBs in the absence of ESCRT ubiquitination.

Photoreceptors are highly compartmentalized neurons in the retina, and they function by detecting light and initiating signaling through the visual network. The photoreceptor contains several compartments including the outer segment (OS) which is a sensory cilium for detecting photons and the inner segment (IS) that carries out important modulatory functions via its resident channels and transporters. Those proteins are membrane proteins that function together to shape electrical properties of the cell membrane during both rest and active states. Therefore it is essential to maintain proper function of the membrane proteins in the IS. One important way to regulate the function of a membrane protein is via controlling its trafficking to ensure a proper amount of the protein in the proper cellular compartment. To date, little is known about how IS membrane protein trafficking is controlled in photoreceptors. In this study, our goal is to understand those mechanisms using cell biology and biochemistry approaches. To achieve the goal, we investigated trafficking of two unrelated IS resident proteins: the hyperpolarization-activated cyclic nucleotide-gated channel 1 (HCN1) that mediates a feedback current in photoreceptors, and the sodium potassium ATPase (NKA) which maintains the basic electrochemical property of the cell. In order to study trafficking of HCN1, we first investigated the dependence of HCN1 trafficking in photoreceptors on TRIP8b, an accessory subunit that influences trafficking of HCN1 in hippocampal neurons. By studying TRIP8b knockout mice we found that TRIP8b is dispensable for HCN1 trafficking in photoreceptors but required for maintaining the maximal expression level of HCN1. Since we revealed that HCN1 trafficking can be regulated in a cell-type specific manner, we subsequently focused on the amino acid sequence of HCN1 to identify novel trafficking signals that function in photoreceptors. By examining localization of a series of HCN1 mutants in transgenic Xenopus photoreceptors, we discovered a di-arginine ER retention motif and a leucine-based ER export motif. These two sequence motifs must function together to maintain equilibrium of HCN1 level between the endomembrane system and the cell surface. The study of HCN1 uncovered a mechanism for the photoreceptor to control membrane protein trafficking via the early secretory pathways. To reveal additional trafficking machineries in photoreceptors, we investigated trafficking of NKA. We first tested for an interaction with ankyrin, an adaptor protein that regulates NKA trafficking in epithelial cells, and found these proteins do not co-localize in photoreceptors. We then aimed to identify novel trafficking signals by studying the trafficking behavior of two NKA isozymes: NKA-α 3 and NKA-α 4. When expressed in transgenic Xenopus photoreceptors, these two proteins localize to the IS and the OS respectively. By studying localization of multiple chimeras and truncation mutants, we found that the distinct localization pattern is due to a VxP OS/ciliary targeting motif present in NKA-α 4. Since NKA-α 4 is naturally expressed in the ciliary compartment of the sperm, our finding in the photoreceptor suggests a mechanism for NKA-alpha 4 trafficking in its native environment. Overall, our studies of HCN1 and NKA together provide new insights into controlling membrane protein trafficking in photoreceptors and help establish the basics for future therapeutic intervention targeting trafficking pathways that are linked to about one third of proteins reported in retinal diseases.

This thesis reports the characterisation of a novel outer membrane protein (OMP) from M. catarrhalis, designated M35, with a molecular mass of 36.1 kDa. This protein is structurally homologous to classic Gram-negative porins, such as OMP C from E. coli and OMP K36 from K. pneumoniae, with a predicted structure of 8 surface loops connecting 16 antiparallel -sheets. Comparison of the DNA sequences of the M35 genes from 18 diverse clinical isolates showed that the gene was highly conserved (99.6-100 % of nucleotides) with only one isolate (ID78LN266) having base variations that resulted in amino acid substitutions. A single amino acid mutation in the 3rd external loop of M35 in isolate ID78LN266 significantly affected antibody recognition, indicating that loop 3 contains an immunodominant B-cell epitope. The reduction in antibody-binding to M35 from ID78LN266 was similar to that caused by complete removal of loop 3. Since loop 3 folds into the porin channel in the classic structure, the antibody specificity to loop 3 was hypothesised to be a potential mechanism for evasion of host immune responses targeted to M35, potentially explaining the high degree of conservation across isolates. A series of recombinant proteins were constructed to analyse the binding to M35 of antibodies specificity for loop 3 or the remainder of the protein. It was found that loop 3- specific antibodies were not able to bind to M35 on the surface of M. catarrhalis and that this corresponds both with a lack of ability to enhance opsonophagocytosis in vitro and bacterial clearance in vivo. Additionally, antibodies raised against a version of M35 lacking loop 3 and M35 from the variant isolate ID78LN266 were both no less effective than the full consensus M35 by both these measures. It therefore appears that while the majority of antibodies raised against M35 are specific for loop 3 these antibodies do not mediate anti-M. catarrhalis actions. Two deletion mutant strains of M. catarrhalis that do not contain the outer membrane protein M35 were created by insertional inactivation of the M35 gene. Growth comparisons between these mutant strains and their wildtype parent strains initially led to the hypothesis that M35 is necessary for efficient glutamic acid uptake by M. catarrhalis, however this hypothesis was later shown to be incorrect. Efficient uptake of glutamic acid seemed to be mediated by a novel 40 kDa protein that was up-regulated in the deletion mutant strains, presumably to compensate for the lack of M35. M35 was also found to be essential for in vivo survival of M. catarrhalis in the nasal cavities of mice, indicating that it is an essential functional protein for colonisation of the mucosal surface.

<p>Membrane proteins are of broad interest since they constitute a large fraction of the proteome in all organisms, up to 20-30%. They play a crucial role in many cellular processes mediating information flow and molecular transport across otherwise nearly impermeable membranes. Traditional three-dimensional structural analyses of membrane proteins are difficult to perform, which makes studies of other structural aspects important. The topology of an α-helical membrane protein is a two-dimensional description of how the protein is embedded in the membrane and gives valuable information on both structure and function.</p><p>This thesis is focused on predicting the topology of α-helical membrane proteins and on assessing and improving the prediction accuracy. Reliability scores have been derived for a number of prediction methods, and have been integrated into the widely used TMHMM predictor. The reliability score makes it possible to estimate the trustworthiness of a prediction.</p><p>Mapping the full topology of a membrane protein experimentally is time-consuming and cannot be done on a genome-wide scale. However, determination of the location of one part of a membrane protein relative to the membrane is feasible. We have analyzed the impact of incorporating such experimental information <i>a priori </i>into TMHMM predictions and show that the accuracy increases significantly. We further show that the C-terminal location of a membrane protein (inside or outside) is the optimal information to use as a constraint in the predictions.</p><p>By combining experimental techniques for determining the C-terminal location of membrane proteins with topology predictions, we have produced reliable topology models for the majority of all membrane proteins in the model organisms <i>E. coli </i>and <i>S. cerevisiae</i>. The results were further expanded to ~15,000 homologous proteins in 38 fully sequenced eukaryotic genomes. This large set of reliable topology models should be useful, in particular as the structural data for eukaryotic membrane proteins is very limited.</p>

The multidrug and toxic compounds extrusion (MATE) family includes hundreds of functionally uncharacterised proteins from bacteria and all eukaryotic kingdoms except the animal kingdom, that function as drug/toxin::Na⁺ or H⁺ antiporters. In <i>Arabidopsis thaliana</i> the MATE family comprises 56 members, one of which is NIC2 (Novel Ion Carrier 2). Using heterologous expression systems including <i>Escherichia coli</i> and <i>Saccharomyces cerevisiae</i>, and the homologous expression system of <i>Arabidopsis thaliana</i>, the functional characterisation of NIC2 was performed. It has been demonstrated that NIC2 confers resistance of <i>E. coli</i> towards the chemically diverse compounds such as tetraethylammonium chloride (TEACl), tetramethylammonium chloride (TMACl) and a toxic analogue of indole-3-acetic acid, 5-fluoro-indole-acetic acid (F-IAA). Therefore, NIC2 may be able to transport a broad range of drug and toxic compounds. In wild-type yeast the expression of NIC2 increased the tolerance towards lithium and sodium, but not towards potassium and calcium. In <i>A. thaliana</i>, the overexpression of NIC2 led to strong phenotypic changes. Under normal growth condtions overexpression caused an extremely bushy phenotype with no apical dominance but an enhanced number of lateral flowering shoots. The amount of rossette leaves and flowers with accompanying siliques were also much higher than in wild-type plants and the senescence occurred earlier in the transgenic plants. In contrast, RNA interference (RNAi) used to silence NIC2 expression, induced early flower stalk development and flowering compared with wild-type plants. In additon, the main flower stalks were not able to grow vertically, but instead had a strong tendency to bend towards the ground. While NIC2 RNAi seedlings produced many lateral roots outgrowing from the primary root and the root-shoot junction, NIC2 overexpression seedlings displayed longer primary roots that were characterised by a 2 to 4 h delay in the gravitropic response. In addition, these lines exhibited an enhanced resistance to exogenously applied auxins, i.e. indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) when compared with the wild-type roots. Based on these results, it is suggested that the NIC2 overexpression and NIC2 RNAi phenotypes were due to decreased or increased levels of auxin, respectively. The Pro_NIC2:GUS fusion gene revealed that NIC2 is expressed in the stele of the elongation zone, in the lateral root cap, in new lateral root primordia, and in pericycle cells of the root system. In the vascular tissue of rosette leaves and inflorescence stems, the expression was observed in the xylem parenchyma cells, while in siliques it was also in vascular tissue, but as well in the dehiscence and abscission zones. The organ- and tissue-specific expression sites of NIC2 correlate with the sites of auxin action in mature Arabidopsis plants. Further experiments using Pro_NIC2:GUS indicated that NIC2 is an auxin-inducible gene. Additionally, during the gravitropic response when an endogenous auxin gradient across the root tip forms, the GUS activity pattern of the Pro_NIC2:GUS fusion gene markedly changed at the upper side of the root tip, while at the lower side stayed unchanged. Finally, at the subcellular level NIC2-GFP fusion protein localised in the peroxisomes of <i>Nicotana tabacum</i> BY2 protoplasts. Considering the experimental results, it is proposed that the hypothetical function of NIC2 is the efflux transport which takes part in the auxin homeostasis in plant tissues probably by removing auxin conjugates from the cytoplasm into peroxisomes. / &quot;Multidrug and Toxic Compounds Extrusion&quot; (MATE) &ndash; Proteine sind Membranproteine, die eine Vielzahl komplexer und giftiger Substanzen transportieren können. Sie sind weit verbreitet und kommen in Bakterien und Höheren Organismen mit Ausnahme des Tierreichs vor. Insgesamt gibt es hunderte von bisher kaum untersuchten Genen dieser Familie, die eine hohe Sequenzhomologie aufweisen. In der Pflanze Arabidopsis thaliana wurden 56 Gene der MATE - Familie zugeordnet. Eines von ihnen, der &quot;Novel Ion Carrier 2&quot; (NIC2) wurde näher charakterisiert. Dafür wurden heterologe Expressionssysteme wie Bakterien (Escherichia coli) und Hefe (Saccharomyces cerevisiae) genutzt und transgene Pflanzen (Arabidopsis thaliana) hergestellt. Es wurde gezeigt, dass NIC2 Bakterien eine Resistenz gegenüber mehreren giftigen Stoffen verlieh. In Hefe erhöhte NIC2 die Salztoleranz gegenüber Lithium und Natrium, aber nicht gegenüber Kalium und Kalzium. Das deutet darauf hin, dass NIC2 diese Stoffe transportieren kann und so zur Entgiftung beziehungsweise erhöhter Stresstoleranz beiträgt. In Pflanzen führte die Überexpression von NIC2 zu dramatischen Änderungen im Wachstum. Die Pflanzen waren buschig ohne zentralen Blütenstand, hatten jedoch eine höhere Anzahl von Blättern und Blüten und längere Wurzeln mit einer im Vergleich zu den Wildtyppflanzen verzögerten gravitropen Antwort. In Gegensatz dazu entwickelten Pflanzen, in denen die Expression von NIC2 gehemmt wurde, früh einen zentralen Blütenstand, der allerdings nicht gerade wuchs, sondern die Tendenz hatte, sich zum Boden zu biegen. Das Wurzelsystem bestand aus einer Hauptwurzel und vielen sekundären Wurzeln und war im Vergleich zu den Wildtyppflanzen besser entwickelt. Vermutlich kann die Wuchsform auf einen veränderten Gehalt des Pflanzenhormons Auxin zurückgeführt werden. Die Expression von NIC2 wird durch Auxin induziert. Experimente, in denen die Aktivität eines Gens mit Hilfe eines Reportergens nachgewiesen wird, zeigten, dass NIC2 in Wurzeln, Blättern, Blütenstielen, Blüten und Schoten aktiv ist. Innerhalb der Zelle ist NIC2 in Peroxisomen lokalisiert. Peroxisomen sind kleine Organellen, die eine Rolle im Hormonstoffwechsel spielen können, wie z.B. im Fall von Auxinen. Die Daten sprechen dafür, dass NIC2 eine Funktion beim Auxintransport und somit bei der Auxin-Homöostase hat.

Membrane proteins are essential for life, and roughly one-quarter of all open reading frames in sequenced genomes code for membrane proteins. Unfortunately, our understanding of membrane proteins lags behind that of soluble proteins, and is best reflected by the fact that only 0.5% of the structures deposited in the protein data-bank (PDB) are of membrane proteins. This discrepancy has arisen because their hydrophobicity - which enables them to exist in a lipid environment - has made them resistant to most traditional approaches used for procuring knowledge from their soluble counter-parts. As such, novel methods are required to facilitate our knowledge acquisition of membrane proteins. In this thesis a generic approach for rapidly obtaining information on membrane proteins from the classic bacterial encyclopedia Escherichia coli is described. We have developed a Green Fluorescent Protein C-terminal tagging approach, with which we can acquire information as to the topology and ‘expressibility’ of membrane proteins in a high-throughput manner. This technology has been applied to the whole E. coli inner membrane proteome, and stands as an important advance for further membrane protein research.

Membrane proteins are of broad interest since they constitute a large fraction of the proteome in all organisms, up to 20-30%. They play a crucial role in many cellular processes mediating information flow and molecular transport across otherwise nearly impermeable membranes. Traditional three-dimensional structural analyses of membrane proteins are difficult to perform, which makes studies of other structural aspects important. The topology of an α-helical membrane protein is a two-dimensional description of how the protein is embedded in the membrane and gives valuable information on both structure and function. This thesis is focused on predicting the topology of α-helical membrane proteins and on assessing and improving the prediction accuracy. Reliability scores have been derived for a number of prediction methods, and have been integrated into the widely used TMHMM predictor. The reliability score makes it possible to estimate the trustworthiness of a prediction. Mapping the full topology of a membrane protein experimentally is time-consuming and cannot be done on a genome-wide scale. However, determination of the location of one part of a membrane protein relative to the membrane is feasible. We have analyzed the impact of incorporating such experimental information a priori into TMHMM predictions and show that the accuracy increases significantly. We further show that the C-terminal location of a membrane protein (inside or outside) is the optimal information to use as a constraint in the predictions. By combining experimental techniques for determining the C-terminal location of membrane proteins with topology predictions, we have produced reliable topology models for the majority of all membrane proteins in the model organisms E. coli and S. cerevisiae. The results were further expanded to ~15,000 homologous proteins in 38 fully sequenced eukaryotic genomes. This large set of reliable topology models should be useful, in particular as the structural data for eukaryotic membrane proteins is very limited.

Inorganic cations play decisive roles in many cellular and physiological processes and are essential components of plant nutrition. Therefore, the uptake of cations and their redistribution must be precisely controlled. Vacuolar antiporters are important elements in mediating the intracellular sequestration of these cations. CAXs (for CAtion eXchanger) are members of a multigene family and appear to predominately reside on vacuoles. Defining CAX regulation and substrate specificity have been aided by utilizing yeast as an experimental tool. Studies in plants suggest CAXs regulate apoplastic Ca2+ levels in order to optimize cell wall expansion, photosynthesis, transpiration and plant productivity. CAX studies provide the basis for making designer transporters that have been used to develop nutrient enhanced crops and plants for remediating toxic soils. In my second study, I have characterized and defined autoinhibitory domain of Arabidopsis CAX3. Several CAX transporters, including CAX1, appear to contain an approximately 40 amino acid N-terminal regulatory regions (NRR) that modulates transport through N-terminal autoinhibition. Deletion of the NRR from several CAXs (sCAX) enhances function in plant and yeast expression assays; however, to date, there are no functional assays for CAX3. In this report, we create a series of truncations in the CAX3 NRR and demonstrate activation of CAX3 in both yeast and plants by truncating a large portion of the NRR. Experiments on endomembrane-enriched vesicles isolated from yeast expressing activated CAX3 demonstrate that the gene encodes Ca2+/H+ exchange with properties distinct from CAX1. These studies demonstrate shared and unique aspects of CAX1 and CAX3 transport and regulation. My third study is to express and purify CAX proteins for X-ray crystallographic analysis. In this study, I initiated crystallization of vacuolar membrane localized CAX protein from eukaryotes. Membrane proteins continue to be challenging targets for structural biology because of their hydrophobic nature. We have demonstrated here that eukaryotic Ca2+/H+ exchanger can be successfully expressed in E. coli based expression system. Collectively, our findings suggest that CAX protein can be successfully expressed, detergent solublized and purified from E. coli with a yield sufficient for functional and structural studies.

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.