The relationship between human erythrocyte glucose transporter (GLUT1) oligomeric structure and function was studied. GLUT1 was purified from human erythrocytes in the absence (GLUT1-DTT) or the presence (GLUT1+DTT) of dithiothreitol. Chemical cross-linking studies of lipid bilayer-resident purified GLUT1 and hydrodynamic studies of cholate-solubilized GLUT1 support the view that GLUT1-DTT is a homotetramer and GLUT1+DTT is a homodimer. Parallel studies on human erythrocyte, and studies employing conformation-specific antibodies (anti-GLUT1-DTT antibodies, ∂-IgGs), indicate that erythrocyte-resident GLUT1 resembles GLUT1-DTT (a homotetramer). While the D-glucose binding capacities of GLUT1-DTT and GLUT1+DTT are indistinguishable, GLUT1-DTT presents at least two population of binding sites to D-glucose whereas GLUT1+DTT presents only one population of sugar binding sites. The cytochalasin B (CCB) binding capacity of GLUT1-DTT (0.4 sites/monomer) is one half of that of GLUT1+DTT. GLUT1-DTT and GLUT1+DTT contain 2 and 6 free sulfhydryls per monomer respectively. The subunits (monomers) of tetrameric and dimeric GLUT1 are not linked by disulfide bridges. Erythrocyte resident GLUT1 presents at least two binding sites to D-glucose and binds CCB with a molar stoichiometry of 0.55 sites per GLUT1 monomer. Following treatment with high pH plus dithiothreitol, the sugar binding capacity of erythrocyte membrane resident transporter is unaltered but the transporter now presents only one population of binding sites to D-glucose, binds CCB with molar stoichiometry of 1.3 sites per GLUT1 monomer and displays significantly reduced affinity for ∂-IgGs. These findings demonstrate that erythrocyte resident glucose transporter is GLUT1-DTT (a GLUT1 tetramer) and that GLUT1 oligomeric structure determines GLUT1 functional properties. A model which rationalizes these findings is proposed.

The cytoplasmic surface of Sec61p is the binding site for the ribosome and has been proposed to interact with the signal recognition particle receptor during targeting of the ribosome nascent chain complex to the translocation channel. Point mutations in cytoplasmic loops six (L6) and eight (L8) of yeast Sec61p cause reductions in growth rates and defects in translocation of nascent polypeptides that utilize the cotranslational translocation pathway. Sec61 heterotrimers isolated from the L8 sec61 mutants have a greatly reduced affinity for 80S ribosomes. Cytoplasmic accumulation of protein precursors demonstrates that the initial contact between the large ribosomal subunit and the Sec61 complex is important for efficient insertion of a nascent polypeptide into the translocation pore. In contrast, point mutations in L6 of Sec61p inhibit cotranslational translocation without significantly reducing the ribosome binding activity, indicating that the L6 and L8 sec61 mutants impact different steps in the cotranslational translocation pathway. Integral membrane proteins are cotranslationally inserted into the endoplasmic reticulum via the protein translocation channel, which mediates the translocation of lumenal domains, retention of cytosolic domains and integration of transmembrane spans into the phospholipid bilayer. We analyzed the in vivo kinetics of integration of model membrane proteins in Saccharomyces cerevisiae using ubiquitin translocation assay reporters. A signal anchor sequence from a type II membrane protein gates the translocon pore less rapidly than a cleavable signal sequence from a secretory protein. Transmembrane spans and lumenal domains are exposed to the cytosol during integration of a poly topic membrane protein. The conformational changes in the translocon that permit opening of the lumenal and lateral channel gates occur less rapidly than elongation of the nascent polypeptide. Cytosolic exposure of transmembrane spans and lumenal domains poses a challenge to the fidelity of membrane protein integration.

TAX1BP1 is a pleiotropic multi-domain protein involved in many important biological processes such as signal transduction, cell growth and apoptosis, transcriptional coactivation, membrane trafficking, neurotransmission and autophagy. The N-terminus of TAX1BP1 contains a SKICH domain implicated in autophagy. SKICH domains are also present in four other proteins including NDP52, CALCOCO1, SKIP and PIPP. The SKICH domains of SKIP and PIPP mediate plasma membrane localization. The functions of the SKICH domains of NDP52 and CALCOCO1 are not known. We solved the crystal structure of the TAX1BP1 SKICH domain, which has an Ig-like fold similar to the NDP52 SKICH domain. Extensive pairwise and clustered aromatic π-stacking interactions are present in the TAX1BP1 SKICH domain. The aromatic residues mediating these interactions can be classified into four groups with varying degrees of conservation among different protein families. The interactions mediated by highly conserved residues are found in the interior and one outward face of the Ig-like β-barrel, representing common structural features of the SKICH domains. Three TAX1BP1-specific pairwise interactions locate in the loop regions, each augmented by a proline-aromatic interaction. The three proline-aromatic clusters are linked together by more generic hydrophobic interactions, forming a unique hydrophobic surface at one end of the TAX1BP1 SKICH domain. The structures and homologous models of SKICH domains from different proteins reveal substantial differences in electrostatic surface properties of the domains. Together with existing biochemical data, results from the structural study suggest that an intact SKICH domain is required for the autophagy function of TAX1BP1.

The Hedgehog signalling pathway is an essential developmental pathway present in all bilaterians that is involved in embryogenesis, body patterning and stem cell homeostasis. Dysregulation of the Hh pathway leads to various kinds of cancer, such as basal cell carcinoma and medulloblastoma. Smoothened (SMO), a Frizzled-type G-protein coupled receptor (GPCR), is the essential transmembrane signal transducer within the Hh pathway, conveying the signal from the upstream transmembrane protein, Patched1 (Ptc1), to the downstream intracellular proteins. The mechanisms by which SMO transmits the Hh signal from the extracellular environment, through the plasma membrane and to the intracellular proteins are not known. In this thesis, I present my work into the structural and functional characterisation of the extracellular and transmembrane domains (TMD) of human SMO in order to better understand the molecular mechanisms of its signal transduction. The extracellular region of SMO contains a highly conserved cysteine-rich domain (CRD) and a linker domain (LD). I present the first crystal structure of the CRD, LD and TMD of SMO, which is also the first crystal structure of a GPCR with a large functional extracellular domain. This structure revealed a domain architecture for SMO that enables regulation of its transmembrane domain by its extracellular domains. It also revealed a cholesterol molecule bound to the CRD, which we subsequently determined to be a new endogenous small-molecule agonist for SMO. I present five further structures of SMO bound to different small molecule agonists and antagonists. Together, these structures demonstrate that the position of the CRD relative to the TMD reflects the activation state of SMO. We also generated nanobodies against the extracellular region of SMO in order to stabilise its conformation. These studies not only improve our understanding of the workings of a key transmembrane protein within a fundamental signalling pathway but will also aid efforts to develop better therapeutics for an important cancer target.

Ubiquitin phosphorylation by PINK1 (PTEN-induced Putative Kinase 1) is crucial for mitochondrial quality control and loss or mutation of PINK1 can lead to autosomal recessive juvenile parkinsonism (AR-JP). PINK1 is an unusual kinase, as it is characterised by three unique insertions in its kinase N lobe and a C-terminal region after the kinase domain. Despite great effort, a structure of PINK1 could not be determined and the molecular mechanism of ubiquitin phosphorylation and the effect of the PINK1 AR-JP patient mutations remained elusive. The versatile modifier ubiquitin (Ub) is also an unusual kinase substrate, as its phosphorylation site (Ser65) is not exposed, but protected by the Ub fold. Hence, it was not clear how a kinase would be able to target Ser65 of Ub. This work shows that Ub needs to adopt a previously described conformation in order to be efficiently phosphorylated by PINK1. NMR experiments revealed that in a small population of Ub the last β-strand is retracted, resulting in a more accessible Ser65 loop. It could be shown that PINK1 binds the Ser65 loop in this C-terminally retracted conformation (Ub-CR), but not in the ‘common’ conformation. In addition, it could be shown that Ub trapped in the Ub-CR conformation by point mutations (Ub TVLN) is phosphorylated significantly faster than Ub wt, which only adopts the Ub-CR conformation at very low frequency. To further elucidate how PINK1 binds and phosphorylates Ub, the kinase domain of Pediculus humanus corporis (Ph)PINK1 was crystallised in complex with Ub TVLN stabilised by a nanobody. The structure revealed many peculiarities of PINK1, such as the architecture of the unique insertions and the C-terminal region. Together with NMR and mass spectrometry studies, the structure explains how PINK1 interacts with ubiquitin via insertion-3 and its activation segment, and how PINK1 utilises the Ub- CR conformation for efficient Ser65 phosphorylation. In addition, the structure shows that two autophosphorylation sites in the N lobe regulate PINK1, by stabilising the functionally important insertions. The structure helped our understanding of the molecular basis of over 40 AR-JP patient mutations and may guide the design of ARJP therapeutics in the future.

Toluene / o-xylene monooxyenase (ToMO) from Pseudomonas sp. OX1 is a multimeric metalloenzyme enzyme that efficiently catalyzes the hydroxylation of aromatic hydrocarbons with high specificity. Though included in a larger group of conserved bacterial multicomponent monooxygenases (BMMs) studied as potential biocatalysts for industrial hydrocarbon chemistry, the substrate specificity and oxygenated intermediates of ToMO differ greatly from its well-characterized, alkane-hydroxylating analog sMMO. Despite a shared global topology and near identical active sites, sMMO can cleave inert C-H bonds in alkanes while ToMO cannot - two seemingly similar structures give rise to vastly different chemistries. This work seeks to determine a structural basis for this difference by mutational analysis of residues thought to conformationally constrain the active site in ToMO, with the goal of replicating the terminal alkane hydroxylating activity of sMMO. To this end, a library of potential alkane-hydroxylating mutants was generated and kinetically characterized, revealing a range of novel behaviors including significant reaction rate enhancements. In combination with low-level computational modeling to quantify the bulk and local rigidity of both sMMOH and ToMOH, we propose a broader strategy for BMM scaffolds to achieve a variety of specific and efficient hydrocarbon chemistries.

A família das septinas caracteriza-se pela capacidade de ligar nucleotídeos de guanina e de se associarem formando filamentos. Diversas funções biológicas têm sido reportadas para esses filamentos e sua dissociação pode estar relacionada a patologias. A septina 12 humana expressa especificamente em testículos, foi identificada em filamentos que compõem o annulus do espermatozoide, cuja integridade está relacionada com a morfologia deste. Embora muitos estudos tenham sido reportados, vários aspectos das bases moleculares e fisiológicas de sua função e automontagem permanecem desconhecidos. Neste trabalho, procurou-se obter informações estruturais para o domínio de ligação ao nucleotídeo da SEPT12 (SEPT12G), do mutante SEPT12GT89M e do heterodímero SEPT7-SEPT12. A expressão destas proteínas foi realizada em células de E. coli da linhagem Rosetta(DE3) pelos vetores de expressão pET28a(+) e pETDuet-1. As etapas de purificação foram cromatografia de afinidade e exclusão molecular. A proteína SEPT12G foi submetida à avaliação do estado oligomérico, fluorescência intrínseca, ensaios de conteúdo de nucleotídeo, atividade GTPásica e transição térmica. O heterodímero SEPT7-SEPT12 foi submetido à avaliação do estado oligomérico e conteúdo de nucleotídeo. Ensaios de cristalização foram realizados para todas as proteínas. A coleta de dados realizada na linha I24 do Diamond Light Source (Didcot, Inglaterra) resultou em conjuntos de dados de alta resolução para a SET12G, SEPT12GT89M e baixa resolução para a SEPT7NGc. Os estudos biofísicos mostraram que a SEPT12G foi obtida em sua forma nativa ou, seja, capaz de ligar e hidrolisar o nucleotídeo GTP e que o heterodímero obtido apresentou ambas as proteínas. As estruturas cristalográficas foram resolvidas e permitiram realizar observações importantes para o grupo I das septinas humanas (SEPT3, SEPT9 e SEPT12). Para a SEPT12 pôde-se observar como a mudança que ocorre no motivo G4 pode alterar a estabilidade da interface G. No contexto do grupo I esta estrutura permitiu concluir que todas as proteínas deste subgrupo podem formar duas interfaces NC, dos tipos aberta e fechada. Além disso, reforçou a observação da orientação diferencial da hélice α5\', cuja função ainda não está esclarecida, mas sem dúvidas é um diferencial que caracteriza este grupo, possivelmente relacionado com a ancoragem da região polibásica na conformação aberta. A estrutura cristalográfica do mutante SEPT12T89M permitiu observar que a mutação levou a uma alteração na primeira esfera de coordenação do íon Mg2+, mudança que interrompe o mecanismo do switch universal e deixa a proteína catalíticamente inativa. Por fim, o estudo cristalográfica do complexo entre a SEPT12 e SEPT7 não foi possível, uma vez que todas as tentativas resultaram em cristais contendo apenas a SEPT7, o que pode ser consequência da precipitação da SEPT12 ou da condição de cristalização utilizada, que desestabiliza o heterodímero. / The septin family of proteins is characterized by their ability to bind guanine nucleotides and associate into filaments. Several biological functions have been reported for these filaments and their dissociation may be related to pathologies. Human septin is 12 specifically expressed in testes and has been identified in filaments that form the sperm annulus, whose integrity is related to its morphology. Although many studies have been reported, the molecular and physiological bases of septin filament function and self-assembly have yet to be completely elucidated. This study aims to obtain structural information for the nucleotide binding domain of SEPT12 (SEPT12G), the SEPT12GT89M mutant and the SEPT7-SEPT12 heterodimer. Expression of these proteins was performed in E. coli Rosetta(DE3) strain using the pET28a (+) and pETDuet-1 expression vectors. Purification was performed by affinity and size exclusion chromatography. The SEPT12G protein was submitted to an evaluation of its oligomeric state, intrinsic fluorescence, nucleotide content, GTPase activity and thermal transition. The oligomeric state and nucleotide content of SEPT7-SEPT12 was also evaluated. Crystallization assays were performed for all proteins. Data collection on line I24 of the Diamond Light Source (Didcot, England) resulted in high-resolution data sets for SET12G and SEPT12GT89M but only low resolution data for the SEPT7NGc. Biophysical studies showed that SEPT12G was obtained in its native form or, in other words, capable of binding and hydrolyzing GTP and that the purified heterodimer presented both proteins. The crystallographic structures were solved by molecular replacement allowing the identification of features characteristics of the group I septins (SEPT3, SEPT9 and SEPT12). The structure also confirmed that all the proteins of this group are able to form two different NC interfaces: open and closed. In addition, it reinforced the observation that the α5\' helix assumes a different orientation, whose function has not yet been clarified, but without doubt is a characteristic of this group which may be related to anchoring the polybasic regions whilst in the open conformation. The SEPT12T89M mutant crystal structure shows that the first shell coordination of the Mg2+ ion is altered, leading to an interruption of the universal switch mechanism and a consequent lack of catalytic activity. Finally, structural studies of the interaction between SEPT12 and SEPT7 were not possible, since all attempts resulted in crystals containing only SEPT7. This may be a consequence of SEPT12 precipitation or the crystallization condition used, destabilizing the heterodimeric interface.

Secondary multidrug transporters use the energy stored in transmembrane ion gradients to bind and extrude a variety of weakly related chemical structures. These polyspecific antiporters challenge the notions of high-affinity conformation and strict ion-substrate coupling, inherent to the alternating-access model of transport. In order to investigate the mechanism of secondary multidrug transport at a molecular level, we study LmrP, a Major Facilitator Superfamily (MFS) multidrug transporter from Lactococcus lactis, which relies on the proton-motive force to achieve the transport of its diverse substrates. We carried out Double Electron Electron (DEER) distance measurements to elucidate the conformational dynamics underlying the transport cycle. We monitored the conformational response of a library of labeled double cysteine mutants to the presence of ligand(s) and proton(s). We investigated the role of the lipid environment by performing the measurements on mutants reconstituted in nanoscale soluble lipid bilayers (nanodiscs). During this work, we have demonstrated that the transporter oscillates between two main conformations, the outward-open and the inward-open. We have shown that the protonation of conserved acidic residues is the driving force of the conformational transition. The lipid bilayer modulates the equilibrium and allows the transition to occur at higher and more physiological pH values. By using specific lipid compositions, we observe that the lipid headgroup is crucial in the regulation of the conformational equilibrium. Based on our data, we propose a model of secondary multidrug transport wherein substrate binding initiates the transport cycle by catalysing proton entrance from the extracellular side. Subsequent protonation of membrane-embedded acidic residues triggers a cascade of conformational changes that results in substrate extrusion to the extracellular side and proton release in the cytosol. We suggest the opening and closing of the extracellular site is tightly regulated while the cytoplasmic side is more flexible. To our knowledge, this work provides the first direct structural evidence of the role of the lipids in the regulation of the conformational dynamics of a membrane transporter. / La surexpression de transporteurs capables d’expulser des molécules cytotoxiques est un mécanisme connu de résistance aux antibiotiques de la cellule bactérienne. Certains transporteurs ont développé la capacité de reconnaitre et d’expulser des substrats de structures diverses, donnant lieu à une résistance multidrogue de la part de leur hôte. Ces transporteurs multidrogues sont présents dans une variété de classes de protéines, distribués dans tous les règnes du vivant. Parmi celles - ci, la famille MFS (Major Facilitator Superfamily) comprend la majorité des transporteurs multidrogues activé par une source d’énergie secondaire, et jouent un rôle crucial dans la propagation de maladies nosocomiales d’origine bactérienne. Une meilleure compréhension des mécanismes fondamentaux du transport multidrogue secondaire est le prérequis indispensable à l’élaboration de thérapies adaptées. En particulier, une description détaillée des changements conformationnels impliqués dans le transport, et une identification des mécanismes moléculaires qui permettent de lier la source d’énergie au transport fait actuellement défaut. Afin de pallier ce manque, ce travail vise à étudier LmrP (Lactococcus lactis multidrug resistance Protein) un transporteur MFS qui confère à son hôte Lactococcus lactis la résistance à divers antibiotiques et agents cytotoxiques de structure et de charge variable. Cette extrusion active est alimentée par un cotransport énergétiquement favorable de protons. Nous avons étudié le mécanisme de transport de LmrP à l’échelle moléculaire en utilisant la technique spectroscopique Double Electron Electron Resonance (DEER), qui permet de mesurer des variations de distances à l’échelle nanométrique, idéale pour observer les mouvements intramoléculaires d’un transporteur MFS. Différents aspects moléculaires susceptibles de réguler le cycle de transport sont étudiés de façon indépendante et couplée :le rôle des protons, des différents substrats, et de l’environnement lipidique. Sur base de cette cartographie conformationnelle, un mécanisme de transport couplant tous les acteurs moléculaires est proposé :la liaison du proton à un motif d’acides aminés conservé constitue la base de la transition conformationnelle, les divers substrats ayant pour rôle de permettre aux protons d’accéder à ce motif. La compétition substrat-proton est la base du transport couplé. Notre travail a mis en évidence le rôle fondamental de l’environnement lipidique, qui module l’équilibre conformationnel du transporteur en interagissant avec un ou plusieurs motif(s) conservé(s). Par ailleurs, notre étude questionne le paradigme actuel de transport au sein de la famille MFS car elle démontre que les changements conformationnels globaux passent par des réarrangements locaux et coordonnés. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

PepT1 and PepT2 are integral membrane proteins which couple the uptake of di- and tri-peptides to the proton electro-chemical gradient. PepT1 is predominantly expressed in the small intestine and is the main route through which dietary protein is absorbed. PepT2 shares 46% sequence identity with PepT1 and is expressed in the kidneys, lung and central nervous system. Many commonly prescribed drugs, such as penicillin are peptide mimetics, and PepT1 and PepT2 play a direct role in their transport and pharmacokinetic properties. Recent X-ray crystal structures and functional studies of the bacterial peptide transporters have provided significant insight into the likely mechanism by which such drugs are recognised by PepT1 and PepT2. The bacterial peptide transporters share approximately 30% sequence identity within their trans-membrane domains to the mammalian PepT1 and PepT2 transporters. However, a key structural difference exists; an additional 20 kDa extra-cellular loop is inserted between trans-membrane helices 9 and 10 in the animal peptide transporters, and this loop is absent in the bacterial homologues. It was not known, prior to this thesis, if this extra-cellular loop was structured and/or integral to the transport cycle, or whether it served an additional function to assist or regulate peptide transport. To investigate the role of this domain, the crystal structures of the Mus musculus PepT1 and Rattus norvegicus PepT2 'loops' were determined to 2.10 and 2.06 Å resolution respectively. The structures indicated that the loop region in both PepT1 and PepT2 forms a bi-lobal, all β-sheet, self-contained extra-cellular domain (ECD). Despite low sequence similarity, the ECDs from PepT1 and PepT2 share a common architecture; two transthyretin-like folds connected by a flexible linker. Sequence and structural analyses have indicated that the lobe interface of MmPepT^ECD is maintained by two highly conserved salt bridges, whereas in RnPepT2^ECD only one salt bridge is observed. Small-angle X-ray diffraction experiments indicated that the extra-cellular domains form a compact structural arrangement, although the lobe conformation of PepT2^ECD was more dynamic than PepT1. Using the X-ray crystal structures of the M. musculus and R. norvegicus ECDs, and the trans-membrane domain of PepT_so from Shewanella oneidensis, the first structure-based homology models of H. sapiens PepT1 and PepT2 were constructed. The hybrid models indicated that the ECD sits on top of the transporters. Two-electrode voltage clamp studies then revealed that the ECDs do not play a part in the transport mechanism of the transporter, although PepT1^ECD may play a role in transporter stability. Surface plasmon resonance binding assays were performed between the ECDs and the intestinal proteases trypsin and α-chymotrypsin. An interaction between both ECDs and α-chymotrypsin was observed, although this interaction could not be saturated using this assay. Trypsin binding however, could be saturated for both MmPepT1^ECD and RnPepT2^ECD giving K_ds of 90 ± 20 and 170 ± 30 μM. Physiologically the interaction would give trypsin a predisposition for the peptide transporter ECD; locating the protease in the vicinity of the transporter and aiding the presentation of substrate. The interaction between trypsin and PepT1^ECD was explored further with a mutational analysis of potential binding residues. The results could not locate the binding site definitively, however, the work did highlight the probable binding face which is perhaps conserved between PepT1 and PepT2 ECD.

Doctor of Philosophy / Biochemistry and Molecular Biophysics Interdepartmental Program / Brian V. Geisbrecht / The pathogenic bacterium Staphylococcus aureus actively evades many aspects of human innate immunity by expressing a series of secreted inhibitory proteins. A number of these proteins have been shown to specifically bind to and inhibit components of the complement system. Since complement is known to play a significant role in the pathophysiology of human inflammatory diseases, our long-term goal is to understand the structure, function, and mechanism of Staphylococcal immune evasion proteins to develop complement-targeted therapeutics. Since its discovery, the extracellular adherence protein (Eap) has been shown to be a crucial component in the pathogenesis and survival of S. aureus through its ability to interact and inhibit multiple aspects of the innate immune system. We have shown that Eap inhibits the classical and lectin pathways of complement by a previously undescribed mechanism. Specifically, Eap binds with nanomolar affinity to complement protein C4b, and thereby blocks binding of the classical and lectin pathway pro-protease C2 to C4b. This effectively eliminates formation of the CP/LP C3 proconvertase, which is required for amplification of downstream complement activity and subsequent inflammatory events. The full-length, mature Eap protein from S. aureus strain Mu50 consists of four ~97 residue domains, each of which adopt a similar beta-grasp fold, and are connected to one another through short linker regions that give rise to an elongated, but structured protein. Through multiple structural and functional assays, we have identified the 3rd and 4th domains of Eap as being critical for interacting with C4b and subsequent inhibition of the complement cascade. Alternative approaches to a standard co-crystal structure of Eap34 bound to C4b provided evidence that Eap domains 3 and 4 both contain a low affinity, but saturable binding site for C4b; we were able to map these sites to the α-chain and γ-chain, specifically the metal-ion-dependent adhesion site of the C345c domain, of C4b, both of which have been previously shown to be required for pro-protease binding. To provide higher resolution information, we took advantage of the abundance of surface exposed lysines in Eap34, and employed a lysine-acetylation foot printing mass spectrometry technique. This identified seven lysines in Eap34 that undergo changes in solvent exposure upon C4b binding and confirmation of these residues was done through site-directed mutagenesis, followed by direct binding and functional assays. Together, these results provide structural and functional insight into one of the many ways that Staphylococcus aureus can evade the killing powers of the innate immune system. Future plans are directed at conducting site-specific screens to identify small molecule/peptide compounds that target the Eap34 binding site on C4b. Such molecules would constitute attractive lead compounds in the search for specific inhibitors of the classical and lectin complement pathways.