Tesis sobre el tema "Receptor-ligand complexes"

Members of the Hedgehog (HH) family of morphogenic signalling molecules are key mediators of many fundamental processes in embryonic development. A relatively small change in HH concentration results in the specification of distinct cell types. Such fine-tuning necessitates a range of regulatory cell-surface proteins to control the concentration of HH to which responding cells are exposed. This thesis focuses on the structural and functional characterisation of three human extracellular modulators of the HH pathway, namely the hedgehog-interacting protein HHIP, the glypican GPC3 and the Growth Arrest Specific 1 (GAS1). Cell culture robot protocols were developed to allow large-scale expression of these targets in mammalian cells (Chapter 3). In Chapter 4, the structure of the HH antagonist HHIP alone and in complex with HH ligands is described. These studies combined with functional experiments reveal a binding mode distinct from previously defined ligand interaction sites, with the HH metal-binding sites playing key roles. The structural and functional analysis of GPC3, another negative HH regulator, is described in Chapter 5. Binding studies suggest that the GPC3 core domain does not bind directly to SHH and that the GPC3-attched heparan sulphate chains play an important role in HH regulation. Chapter 6 reveals crystal structures of the GAS 1 ectodomain, a HH agonist, allowing comparison to glial cell line-derived neurotrophic factor receptors, the identification of an unexpected ligand and mapping of the HH binding site. In summary, this work provides insights into the extracellular modulation of HH signalling and extends our current knowledge of this fundamental signalling pathway. It also offers a model to explain how both agonists and antagonists can adopt similar mechanisms of HH binding.

Thesis (Ph. D.)--University of Missouri-Columbia, 2007.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on February 26, 2008) Vita. Includes bibliographical references.

"Research conducted at the Department of Haematology, Hanson Centre for Cancer Research, Institute of Medical and Veterinary Science."--T.p. Includes bibliographical references (leaves 170-214). Elevated levels of receptor tyrosine kinases have been implicated in carcinogenesis. It is possible that high expression of c-Kit by the leukaemic cell provides them with a growth advantage over their normal counterparts in the bone marrow microenvironment. Thus, a means of inhibiting the interaction of c-Kit on these cells with ligand Steel Factor may remove proliferation and survival signals. Main aim of the study was to produce a biological inhibitor of this interaction and evaluate its ability to prevent ligand Steel Factor from binding to c-Kit on live cells.

Thesis (Ph.D.)--University of Adelaide, Dept. of Chemistry, 2002.
"September 2002" Includes as appendix: a list of publications by the author arising from this work; and, copies of some published journal articles. Includes bibliographical references.

Throughout the central nervous system (CNS), the Cys-loop superfamily of ligand-gated ion channels {LGICs), including nicotinic acetylcholine, serotonin type-3A, strychnine-sensitive glycine and y-aminobutyric acid A/C receptors, play important roles in synaptic transmission by converting chemical signals into electric signals. Designing potent and subtype-selective ligands with therapeutic value requires knowledge about how ligands interact with their binding sites. y-Aminobutyric acid (GABA) is the predominant inhibitory neurotransmitter in the mammalian CNS and its binding modes at GABA receptors have not been fully elucidated. GABAc receptors consist of p subunits (p1-p3) and they are known to form homomeric receptors. The five subunits are arranged around a central chloride selective ion channel pore. Each subunit contains a large extracellular N-terminal domain, four transmembrane domains {Ml-M4) of which the second (M2) lines the channel pore and a large M3-M4 intracellular loop. The orthosteric binding site is located at the interface between two subunits in the N-terminal domain and the key residues for ligand binding are found at the five discontinuous loops (A-E). This thesis describes how ligand binding and receptor gating are closely related and explores the effect of receptor conformational changes upon ligand binding. A series of point mutations in the N-terminal domain of the GABAc p1 receptor were created and expressed in Xenopus oocytes. The mutant receptors were then examined using a range of pharmacological tools to probe function which was measured using the two-electrode voltage clamp method. The GABA binding mode was explored at GABA receptors using the enantiomers of 3-fluoro-y-aminobutyric acid (3F-GABA) and stereoisomers of 2,3-difluoro-4-aminobutyric acids as conformational probes. Both enantiomers of 3F­GABA were full agonists, with the R-3F-GABA being approximately 3-fold more potent than 5-3F-GABA at GABAc receptors. In contrast, both enantiomers were partial agonists with similar efficacy and potency at GABAA receptors. These results suggest a different GABA binding mode at GABAc receptors to that found in the related but pharmacologically distinct GABAA receptors. The effect of the different stereoisomers of 2,3-difluoro-4-aminobutyric acids were also examined at GABAA, GABA8 and GABAc receptors. In the study, two enantiomeric GABAc receptor ligands were identified, one of which is an agonist (25,35-2,3-difluoro-4-aminobutyric acid) while the other is an antagonist (2R,3R-2,3-difluoro-4-aminobutyric acid). 4-Amino-3-hydroxybutanoic acid (GABOB) is an endogenous ligand found in the CNS in mammals and a metabolite of GABA. Homology modeling of the GABAc Pi receptor revealed a potential hydrogen (H-bond) interaction between the hydroxyl group of GABOB and threonine 244 (T244) located on loop C of the ligand binding site. Using site-directed mutagenesis, the effect of mutating T244 on the efficacy and pharmacology of GABOB and various ligands were examined. It was found that mutating T244 to amino acids that lacked a hydroxyl group in the side chain produced GABA insensitive receptors. Only by mutating PiT244 to serine (PiT2445) produced a GABA responsive receptor, albeit 39-fold less sensitive to GABA than Pi wild-type. It was also found that this mutation also changed the activity of GABAc receptor partial agonists, muscimol and imidazole-4-acetic acid (I4AA). At the concentrations tested, both muscimol and I4AA antagonized the currents produced by GABA at PiT2445 mutant receptors (Muscimol: PiWild-type, EC50 = 1.4 µM; PiT2445, IC50 = 32.8 µM. I4AA: Pi wild-type, EC50 = 8.6 µM; PiT2445, IC50 = 21.4 µM). This indicates that T244 is predominantly involved in channel gating. R-(-)-GABOB and 5-(+)-GABOB are full agonists at Pi wild-type receptors. In contrast, R-(-)-GABOB was a weak partial agonist at PiT2445 (lmM activates 26 % of the current produced by GABA ECso versus Pi wild-type, EC50 = 19 µM; lmax 100%), and 5-(+)-GABOB was a competitive antagonist at PiT2445 receptors (Pi wild-type, EC50 = 45 µM versus PiT2445, IC50 = 417.4 µM, Ks = 204 µM). This highlights that the interaction of GABOB with T244 is enantioselective. In contrast, the potencies of a range of antagonists tested, 3-aminopropyl(methyl)phosphinic acid (3-APMPA), 3-aminopropylphosphonic acid (3-APA), 5- and R-(3-amino-2-hydroxypropyl)methylphosphinic acid (5-(-)-CGP44532 and R-(+)-CGP44533), were not altered. This suggests that T244 is not critical for antagonist binding. Receptor gating is dynamic and this study highlights the role of loop C in agonist-evoked receptor activation, coupling agonist binding to channel gating. Ligands acting on receptors are considered to induce a conformational change within the ligand-binding site by interacting with specific amino acids. In this study, tyrosine 102 (Y102) located in the GABA binding site of the Pi subunit of the GABAc receptor was mutated to alanine (piY102A), serine (piY102S) and cysteine (piY102C) to assess the role of this amino acid plays on the action of 12 known and 2 novel antagonists. Of the mutated receptors, piY102S was constitutively active providing an opportunity to assess the activity of the antagonists on Pi receptors with a proportion of receptors existing in the open conformational state compared to those existing predominantly in the closed conformational state (pi wild-type, PiY102C and PiY102A). It was found that the majority of antagonists studied were able to inhibit the constitutive activity displayed by PiY1025, thus displaying inverse agonist activity. The exception was (±)-4-aminocyclopent-1-enecarboxamide ((±)-4-ACPAM) not exhibiting any inverse agonist activity, but acting explicitly on the closed conformational state of Pi receptors. It was also found that GABA antagonists were more potent at the closed compared to the open conformational states of Pi receptors suggesting that they may act by stabilizing the closed conformational state and thus reducing activation by agonists. Furthermore, of the antagonists tested, Y102 was found to have the greatest influence on the antagonist activity of gabazine (SR-95531) and its analogue (SR-95813). Our GABAc Pi receptor homology model identified a novel cavity, which extended beyond the GABA binding site. The model predicted phenylalanine 124(F124), one of the residues lining the cavity, was pointing towards the orthosteric binding site. In this study, F124 was mutated to various amino acids and only a modest effect on receptor pharmacology was observed. However, the mutations had a significant effect on the channel deactivation rate ('toeactivation)- This finding suggests that F124 may play a role in channel gating or stabilizing the open conformation of the receptor. Designing potent selective agents are the key for the further understanding of the physiological roles of GABAc receptors. Gabazine (SR-95531) is a potent GABAA receptor competitive antagonist. In this study, a series of novel gabazine analogues were tested at GABAA and GABAc receptors. Of the compounds studied, (p)-methoxy analogue without the butyric acid side-chain was 20-fold more potent at GABAc over GABAA receptors. As there was no butyric acid side chain, it is suggested that the carboxylic acid is not important for gabazine activity at this receptor. Establishing the structure-activity relationship based on this analogue will facilitate the development of selective GABAc receptor antagonists with possible physiological effects including memory-enhancement. Overall, our studies describe agonist and GABAc receptor antagonist induced conformational changes within the ligand binding site. Our findings also highlight the dynamic nature of receptor gating, initiated by ligand binding at a site physically distinct from the ion channel.

Low affinity Fcg receptor III (FcgRIII, CD16) triggers a variety of cellular events upon binding to the Fc portion of IgG. A real-time flow cytometry method was developed to measure the affinity and kinetics of such low affinity receptor/ligand interactions, which was shown as an easily operated yet powerful tool. Results revealed an unusual temperature dependence of reverse rate of CD16aTM dissociating from IgG. Except for a few studies using mammalian cell CD16s, most kinetics analyses use purified aglycosylated extracellular portion of the molecules, making it impossible to assess the importance of the receptor anchor and glycosylation on ligand binding. We used a micropipette adhesion frequency assay to demonstrate that the anchor length affects the forward rate and affinity of CD16s for IgG in a species specific manner, most likely through conformational changes. Receptor glycosylation dramatically reduced ligand binding by 100 folds. T cell receptor (TCR) is arguably the most important receptor in the adaptive human immune system. Together with coreceptor CD4 or CD8, TCR can discriminate different antigen peptides complexed with major histocompatibility complex (MHC) molecule (pMHC), which differ by as few as only one amino acid, and trigger different T cell responses. When T cell signaling was suppressed, TCR had similar affinity and kinetics for agonist and antagonist pMHC whose binding to CD8 was undetectable. TCR on activated T cell had a higher affinity for pMHCs, suggesting that TCRs organize themselves differently on activated T cells than on naïve T cells. In the absence of inhibitors for signaling, TCR binds agonist pMHC with several orders of magnitude higher affinity than antagonist pMHC. In addition, engagement of TCR by pMHC signals an upregulation of CD8 binding to pMHC, which is much stronger than the TCR-pMHC binding. The transition from weak TCR binding to the strong CD8 binding takes place around 0.75 second after TCR in contact with pMHC and can be reduced by several inhibitors of tyrosine and lipid phosphorylation, membrane rafts, and actin cytoskeleton. These results provide new insights to understanding T cell discrimination.

The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.

For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.

A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.

A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.

The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

Thesis (Ph. D.)--University of Oregon, 2001.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 163-175). Also available for download via the World Wide Web; free to University of Oregon users.

Membrane rafts are highly dynamic heterogeneous sterol- and sphingolipid-rich micro-domains on cell surfaces. They are generally believed to provide residency for cell surface molecules (e.g., adhesion and signaling molecules) and scaffolding to facilitate the functions of these molecules such as membrane trafficking, receptor transport, cell signaling, and endocytosis. Using laser scanning confocal microscopy and reflection interference microscopy (RIM), we studied the spatial and temporal distributions of membrane rafts and surface receptors, signaling molecules, and cell organelles during the formation of phagocytic contact areas. K562 cells, which naturally express CD32A, a cell surface receptor for the Fc portion of Immuno-globulin g (IgG), was chosen as a model for neutrophils. An opsonized target was modeled using a glass supported lipid bilayer reconstituted with IgG. CD32A was found to cluster and co-localize with membrane rafts. Placing the K562 cells on the lipid bilayer triggered a process of contact area formation that includes binding between receptors and ligands, their recruitment to the contact area, a concurrent membrane raft movement to and concentration in the contact area, and transport of CD32A, IgG, and membrane rafts to the Golgi complex. Characterization of these processes was performed using agents known to disrupt detergent resistant membranes (DRMs), dissolve actin microfilaments, and inhibit myosin motor activity, which abolished the CD32A clusters and prevented the contact area formation. The relevance to phagocytosis of contact area formation between K562 cells and lipid bilayers was demonstrated using micro-beads coated with a lipid bilayer reconstituted with IgG as the opsonized target instead of the glass supported planar lipid bilayer. Disruption of membrane rafts, salvation of the actin cytoskeleton, and inhibition of myosin II activity were found to inhibit phagocytosis. Here we have provided evidence that membrane rafts serve as platforms that are used to pre-cluster CD32A and transport CD32A along the actin cytoskeleton to the site of phagocytic synapse formation, followed by internalization to the Golgi complex.

Basic helix-loop-helix (bHLH) proteins are involved in the regulation of a multitude of developmental processes including cellular differentiation, cellular proliferation and xenobiotic metabolism. Among the members of the bHLH protein family are the products of the Pan gene Pan-1, Pan-2 and ITF -1. Pan proteins have been demonstrated to be required for proper B cell development, suggesting a unique role for Pan proteins during B cell formation. In our study we tested the function of ARNT (Ah receptor nuclear translocator) at the IgH (immunoglobulin heavy chain) enhancer. We were able to determine that ARNT appears to partially down-regulate activation at the IgH enhancer by Pan-1 in transient transfection assays by cotransfection of the multimerized murine form of the IgH enhancer elements 1-1E2, !-LE3 , and 1-1ES upstream of a luciferase reporter gene, a rodent Pan-1 (human homolog E47) expression vector, and an ARNT expression vector. Furthermore, during our investigation we discovered a putative ARNT -binding ligand that increases DNA-binding activity of the ARNT homodimer. This ligand was partially characterized by UV crosslinking studies and a variety of biochemical studies using electrophoretic mobility-shift assays. Preliminary data suggests that it is hydrophilic, heat-stable, small, and non-protein.

The main aim of work presented here is to design, develop and characterize a colorimetric model membrane (liposome) systems, which can bind with proteins, enzymes, bacteria, virus and other biomolecules. PDA molecules are utilized as a scaffold for the bilayer membrane, and a colorimetric assay is carried out. The holy grail of present work contributes towards the better understanding of protein interactions with the cell bilayer surface. Chapter 1 introduces a brief history on the advent of bilayer systems for cellular research exploration. We presented a literature survey about how liposome systems are used as a complementary technique to understand the fundamental principles of cellular membrane functions. Furthermore, we describe about membrane protein functions and recent findings on how proteins interact with the cell membrane. Finally, we explain conjugated systems and their exploration in bilayer membrane as a colorimetric scaffold. We also touch bases with major fluorescence techniques used in our experiments. Chapter 2 provides details on the preparation protocols of liposome and liposome-protein complexes. We confirmed protein-bilayer interactions by monitoring FRET between PDA and rhodamine molecules. Furthermore, we performed streptavidin-biotin binding studies on the PDA bilayer. Protein binding changed the spectral overlap (J) between PDA and rhodamine, which ultimately increased the fluorescence emission of rhodamine. The goal of performing these studies was to present a complete protocol for the preparation of liposome and protein-liposome complex. In chapter 3, we investigate how proteins bind on the cell membrane. Additionally, we propose a model of protein-bilayer complex. We reported that, by harnessing cell bilayer with specific bio-molecules, we monitored protein--bilayer, protein--protein and enzyme--substrate signal transduction. We have developed a colorimetric system for monitoring vital stimulations occur on the liposomal membrane surface. Bilayer was modified to covalently bind the amino group of lysine residues present on protein molecules. These bio-molecular interactions on bilayer surface provide differential stimulus, which turned out to be the major cause of differential spectroscopic signals depending upon size and shape of the protein bounded to the bilayer. Polydiacetylene (PDA) liposomes are the core of our color based system. These liposomes are used to monitor subtle interactions on the bilayer surface. We have also developed a semi-quantitative method based on the colorimetric response of PDA liposomes; we were able to detect protein molecules at sub-nanomolar concentrations in the solution. It's capability of distinguishing protein molecules based on their chemical and physical interactions to bilayer contributes towards the identity of our system. Interestingly, our mass spectroscopic data suggested non-specific enzymatic cleavage of membrane-bound proteins. These fragments were not present in bulk protein cleavage. We also proposed a model that depicts the covalent binding of protein at the bilayer of liposomes. These studies are intended to investigate protein-bilayer and enzyme-protein interaction occurring on the cell surface. In chapter 4, we focus on the kinetics of protein interaction on bilayer surface and we also attempt to visualize these interactions by exploring fluorescence microscopy. A self-assembled cell membrane is consisted of various lipids, which cluster themselves in their preferred phase separated regions. Lipid clusters are very important for lipid specific protein interactions. We investigated protein binding on such phase separated regions under a fluorescence microscope. Furthermore, we enzymatically catalyzed proteins, which were covalently bonded on the bilayer surface. This catalytic reaction was monitored both spectroscopically and under a fluorescence microscope. These studies were performed to help us in the better understanding of biological interactions at cell surface. Chapter 5, describes the encapsulation and controlled delivery of antimicrobial compounds from liposomes. Use of antimicrobial coatings on food packaging is one of the important technologies of active packaging for improving food safety. There is growing demand for natural antimicrobials because of fear of adverse health effects of synthetic preservatives. The main objective of this study is to compare antimicrobial activity of free versus encapsulated curcumin. Glass surfaces coated with nano-encapsulated curcumin may be used as an active packaging material in preserving liquid foods; however, further study is required to improve antimicrobial activities of polylactic acid PLA surfaces. In chapter 6, we investigate interactions between receptors and ligands at bilayer surface of polydiacetylene (PDA) liposomal nanoparticles using changes in electronic absorption spectroscopy and fluorescence resonance energy transfer (FRET). We study the effect of mode of linkage (covalent versus noncovalent) between the receptor and liposome bilayer. We also examine the effect of size-dependent interactions between liposome and analyte through electronic absorption and FRET responses. Glucose (receptor) molecules were either covalently or noncovalently attached at the bilayer of nanoparticles, and they provided selectivity for molecular interactions between glucose and glycoprotein ligands of E. coli. These interactions induced stress on conjugated PDA chain which resulted in changes (blue to red) in the absorption spectrum of PDA. The changes in electronic absorbance also led to changes in FRET efficiency between conjugated PDA chains (acceptor) and fluorophores (Sulphorhodamine-101) (donor) attached to the bilayer surface. Interestingly, we did not find significant differences in UV−Vis and FRET responses for covalently and noncovalently bound glucose to liposomes following their interactions with E. coli. We attributed these results to close proximity of glucose receptor molecules to the liposome bilayer surface such that induced stress were similar in both the cases. We also found that PDA emission from direct excitation mechanism was ∼2−10 times larger than that of the FRET-based response. These differences in emission signals were attributed to three major reasons: nonspecific interactions between E. coli and liposomes, size differences between analyte and liposomes, and a much higher PDA concentration with respect to sulforhodamine (SR-101). We have proposed a model to explain our experimental observations. Our fundamental studies reported here will help in enhancing our knowledge regarding interactions involved between soft particles at molecular levels. In chapter 7, we conclude the summary of all work carried out in previous chapters.

The human vitamin D receptor (hVDR) is a member of the nuclear receptor superfamily, involved in calcium and phosphate homeostasis; hence implicated in a number of diseases, such as Rickets and Osteoporosis. This receptor binds 1α,25-dihydroxyvitamin D3 (also referred to as 1,25(OH)2D3) and other known ligands, such as lithocholic acid. Specific interactions between the receptor and ligand are crucial for the function and activation of this receptor, as implied by the single point mutation, H305Q, causing symptoms of Type II Rickets. In this work, further understanding of the significant and essential interactions between the ligand and the receptor were deciphered, through a combination of rational and random mutagenesis. A hVDR mutant, H305F, was engineered with increased sensitivity towards lithocholic acid, with an EC50 value of 10 µM and 40 + 14 fold activation in mammalian cell assays, while maintaining wild-type activity with 1,25(OH)2D3. Furthermore, via random mutagenesis, a hVDR mutant, H305F/H397Y, was discovered to bind a novel small molecule, cholecalciferol, a precursor in the 1α,25-dihydroxyvitamin D3 biosynthetic pathway, which does not activate wild-type hVDR. This variant, H305F/H397Y, binds and activates in response to cholecalciferol concentrations as low as 100 nM, with an EC50 value of 300 nM and 70 + 11 fold activation in mammalian cell assays.

Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains xvii, 271 p.; also includes graphics. Includes bibliographical references (p. 245-269). Available online via OhioLINK's ETD Center

The relaxin-like peptide family consists of relaxin-1, 2 and 3, and the insulin-like peptides (INSL)-3, 4, 5 and 6. The evolution of this family has been controversial; points of contention include the existence of an invertebrate relaxin and the absence of a ruminant relaxin. Using the known members of the relaxin peptide family, all available vertebrate and invertebrate genomes were searched for relaxin peptide sequences. Contrary to previous reports an invertebrate relaxin was not found; sequence similarity searches indicate the family emerged during early vertebrate evolution. Phylogenetic analyses revealed the presence of potential relaxin-3, relaxin and INSL5 homologs in fish; dating their emergence far earlier than previously believed. Furthermore, estimates of mutation rates suggested that the expansion of the family (i.e. the emergence of INSL6, INSL4 and relaxin-1) during mammalia was driven by positive Darwinian selection. In contrast, relaxin-3 is constrained by strong purifying selection, implying a highly conserved function. (For complete abstract open document)

Synthèse de dérivés de métaux carbonyles d'hormones stéroïdes (progestatifs et glucocorticoïdes). Etude de l'affinité de ces produits pour les 2 récepteurs étudiés, avec sélection de 2 marqueurs potentiels. Spectrométrie IR.

Les récepteurs couplés aux protéines G (RCPG) sont impliqués dans la majeure partie des communications intercellulaires. Un grand nombre de RCPG ont été découverts en comparant la séquence des récepteurs connus avec les données fournies par le séquençage du génome humain. Pour plus d'une centaine de ces récepteurs, le ligand activateur ou agoniste est inconnu. Ces récepteurs sont dès lors qualifiés d'orphelins.

Les LGR forment une sous-famille de RCPG structurellement proches de la rhodopsine qui comprend les récepteurs aux hormones glycoprotéiques (TSH, LH, hCG, FSH) et à la relaxine. LGR4 est un membre de cette famille dont ni la fonction précise, ni l'agoniste ne sont connus.

Dans un premier temps, une cartographie détaillée de l'expression de Lgr4 chez la souris a été obtenue. Nous avons tiré parti de l'existence d'une lignée de souris transgéniques dont le gène Lgr4 a été interrompu par l'introduction d'une cassette comportant deux marqueurs histologiques. L'activité beta-galactosidase d'un de ces marqueurs a été analysée chez les souris hétérozygotes. Ces dernières ne présentent pas de phénotype particulier, ce qui permet d'estimer que l'expression des marqueurs rend effectivement compte de l'expression normale du gène Lgr4. Lgr4 est exprimé dans un grand nombre de structures, notamment dans le cartilage, le rein, les appareils reproducteurs mâle et femelle et certaines cellules du système nerveux.

Ensuite, le phénotype des souris homozygotes pour l'inactivation de Lgr4 (LGR4KO) a été exploré. Ces souris présentent à la naissance un poids inférieur à leurs congénères des autres phénotypes. Les mâles sont stériles à cause d'une malformation des tubules efférents et de l'épididyme. Un blocage au niveau des tubules efférents reliant le testicule à l'épididyme contraint les spermatozoïdes à s'accumuler à la sortie du testicule, dans la région du rete testis. De plus, les tubes de l'épididyme, pourtant normaux à la naissance, ne s'allongent pas pour former la structure convolutée habituelle. L'épithélium de ces tubes est aplati et est entouré d'une quantité anormalement élevée de mésenchyme.

Dans un troisième temps, des outils nécessaires aux futures tentatives d'identification de l'agoniste naturel de LGR4 ont été réalisés. Il s'agit :(1) d'anticorps monoclonaux dirigés contre la partie extracellulaire du récepteur humain. (2) d'un appât moléculaire pour la ‘pêche au ligand’. Cet appât est constitué du domaine extracellulaire du récepteur humain couplé à un marqueur histologique. (3) d'une construction peptidique constituée du domaine extracellulaire du récepteur humain couplé à une queue poly-histidine. Cette construction est destinée à servir de greffon lors de chromatographies d'affinités devant permettre de purifier le ligand. (4) de lignées cellulaires exprimant le récepteur LGR4 humain ainsi que le système æquorine devant permettre de détecter l'activation de ce récepteur.

Les données apportées par ce travail montrent un rôle important du récepteur LGR4 au cours du développement et permettent de circonscrire le champ des recherches futures. Ceci, ainsi que les outils moléculaires développés, constitue une base pour l'identification future de l'agoniste et la détermination précise de la fonction de LGR4.
Doctorat en Sciences biomédicales et pharmaceutiques
info:eu-repo/semantics/nonPublished

La signalisation des brassinostéroïdes (BR) est importante pour presque tous les aspects du développement des plantes, comme en témoigne le phénotype extrêmement nain et stérile des mutants défectueux du récepteur des brassinostéroïdes BRASINOSTEROID INSENSITIVE 1 (BRI1). De plus, il est un régulateur clé de la réponse des plantes à l'augmentation de la température ambiante (thermomorphogenèse) dans les parties aériennes de la plante, associé à la signalisation auxine et au facteur de transcription PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Cependant, les rôles des mécanismes moléculaires de la thermomorphogenèse des racines restent insaisissables. Dans cette thèse, je décris en détail les mécanismes moléculaires conduisant à la thermomorphogenèse des racines des plantes exposées à une température ambiante élevée à la suite de la germination. Pour que les plantes allongent leur racine primaire à 26 ° C, par rapport à 21 ° C, elles régulent sélectivement la signalisation BR via la dégradation de BRI1 en fonction de la température. De manière surprenante, dans nos propres conditions, la signalisation auxine n’est pas nécessaire pour la thermomorphogenèse radiculaire, ce qui suggère une différence entre les réponses de thermomorphogenèse aérienne et racinaire. En utilisant une approche de mutagenèse dirigée, nous avons pu déterminer que la dégradation est déclenchée par une modification post-traductionnelle ciblant les lysines, probablement l’ubiquitination K63. Pour découvrir l’ubiquitine ligase E3 impliquée dans la dégradation de BRI1 induite par la température, nous avons effectué un criblage double hybride en levure en utilisant le domaine cytoplasmique de BRI1. Nous avons obtenu trois protéines candidates nommées DENSE AND ERECT PANICLE (DEP), qui se localisent de manière surprenante dans des microtubules corticaux (MTc) et sont apparues en même temps que la signalisation par le BR, suggérant un lien fonctionnel. L'interaction entre DEP1 et BRI1 a été confirmée par trois techniques différentes et, par conséquent, les mutants simples dep sont défectueux dans la perception de BR. D'un côté, ils sont hyposensibles à la réduction de la longueur de l'hypocotyle induite par le BR, mais de l'autre, ils sont hypersensibles au gravitropisme induit par le BR. Ces données suggèrent une interaction entre la signalisation par BR, la dynamique sous-cellulaire de BRI1 et les microtubules corticaux. Des recherches futures permettront de mieux comprendre l'importance biologique de l'interaction BRI1-MTc en général et de l'interaction BRI1-DEP1 en particulier
Brassinosteroid (BR) signaling is important for nearly all aspects of plant development, as attested by the extremely dwarf and sterile phenotype of mutants defective in the brassinosteroid receptor BRASINOSTEROID INSENSITIVE 1 (BRI1). In addition, it is a key regulator of plant responses to increase in ambient temperature (thermomorphogenesis) in the above-ground parts of the plant together with auxin signaling and the transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4). However, the roles molecular mechanisms of root thermomorphogenesis remain elusive. In this thesis, I describe in great detail the molecular mechanisms leading to root thermomorphogenesis of plants exposed to elevated ambient temperature from germination. In order for plants to elongate their primary root at 26°C, compared to 21°C, they selectively downregulate BR signaling via the temperature-specific degradation of BRI1. Surprisingly, under our own conditions, auxin signaling is not required for root thermomorphogenesis, suggesting a difference between aerial and root thermomorphogenesis responses. Using a site-directed mutagenesis approach, we are able to pinpoint that the degradation is triggered by a post-translational modification targeting lysines, probably K63 ubiquitination. To find out the E3 ubiquitin ligase involved in the BRI1 temperature-induced degradation we carried out a yeast two hybrid screen using BRI1’s cytoplasmic domain. We obtained three candidate proteins named DENSE AND ERECT PANICLE (DEP) that surprisingly localize to cortical microtubules (cMTs) and arose at the same time as BR signaling, suggesting a functional link. The interaction between DEP1 and BRI1 was confirmed by three different techniques and, consequently dep single mutants are defective in BR percepton. On one hand, they are hyposensitive to the BR-induced reduction in hypocotyl length but on the other hand they are hypersensitive regarding BR-induced agravitropism. This data suggest an interplay between BR signaling, BRI1 subcellular dynamics and cortical microtubules. Future research will shed light on the biological significance of the BRI1-cMTs interaction in general and the BRI1-DEP1 interaction in particular

La maladie d’Alzheimer (MA) est une maladie neurodégénérative complexe caractérisée par une perte progressive de la mémoire et de la cognition. C’est la première cause de démence chez le sujet âgé et affecte environs 4.6 millions de personnes par an, selon un rapport de l’association « Alzheimer’s disease International », le nombre de patients pourrait s’élever à 135.5 millions en 2050. Du fait de sa complexité, la MA reste incurable et seuls 4 médicaments aux vertus palliatives dont 3 visant à inhiber l’acétylcholinestérase (AChE) ont reçu une autorisation de mise sur le marché à ce jour. L’approche multi-cible parait particulièrement adaptée du fait du grand nombre de cibles potentielles de la pathologie, et du caractère multifactoriel de la maladie. Cette approche consiste à associer sur une seule molécule, plusieurs pharmacophores afin qu’ils puissent agir simultanément sur différentes cibles impliquées dans le processus neurodégénératif. Dans ce contexte, en parallèle de la resynthèse d’un ligand multi-cible conjugué alliant un inhibiteur d’AChE (IAChE) et un antioxydant, deux nouvelles familles de ligands multi-cibles conjuguées, combinant un IAChE et un agoniste des récepteurs nicotiniques α7 (α7 nAChR) ont été conçues et leur synthèse abordée. Dans le cas de la première famille, le fragment ivastigmine a été choisi pour sa capacité à inhiber de manière pseudo-irréversible l’AChE et a été conjugué à un motif quinuclidine, un puissant agoniste des α7 nAChRs impliqués dans la MA. En combinant ces deux fragments, il a été observé que les propriétés biologiques in vitro de chaque pharmacophore étaient améliorées. La structure de la seconde famille est basée sur le Donepezil, un IAChE réversible de plus forte affinité, combiné au même motif quinuclidine que dans la série précédente. Si des intermédiaires avancés ont été obtenus, un ou deux étapes restent à finaliser pour finaliser la synthèse de cette troisième famille de MTDL
Alzheimer’s disease (AD) is a complex neurodegenerative disease characterised by a progressive loss of memory and cognition. Nowadays, 4.6 million new patients are identified every year and according to the “Alzheimer’s diseases International” association, the number of patients could reach 135.5 million in 2050. Due to its complexity, AD remains uncurable and only 4 palliative drugs, of which 3 are acetylcholinesterase (AChE) inhibitors (AChEI), have been approved by FDA to date. AD being a multifactorial illness, with many potential targets involved in the pathology, the MTDL approach seems promising. This strategy associates in one single molecule, different pharmacophores (at least) acting on different targets involved in this CNS-related disorder. In this context, in parallel with the upscaled synthesis of a conjugated MTDL combining an AChEI inhibitor and an antioxidant, two new families of conjugated MTDLs associating an AChEI and a α7 nicotinic receptor (α7 nAChR) agonist have been investigated. The structure of the first family was based on a Rivastigmine scaffold, known to be a pseudo-irreversible AChE inhibitor, and a quinuclidine fragment, a potent α7 nAChR agonist. By combining these two fragments, it was brought to light that the in vitro biological properties were improved on both targets. The second family was based on a donepezil fragment, a more potent AChEI, and the same quinuclidine fragment than in the first family. Advanced intermediates have been obtained, and two last steps remain to be achieved for the completion of this third MTDL series

Humans have two plasminogen activators (PAs), tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA), which generate plasmin to breakdown fibrin and other barriers to cell migration. Both PAs are used as pharmaceuticals but their efficacies are limited by their rapid clearance from the circulation, predominantly by parenchymal cells of the liver. At the commencement of the work presented here, the hepatic receptors responsible for mediating the catabolism of the PAs were little understood. tPA degradation by hepatic cell lines was known to depend on the formation of binary complexes with the major PA inhibitor, plasminogen activator inhibitor type-1 (PAI-1). Initial studies presented here established that uPA was catabolised in a fashion similar to tPA by the hepatoma cell line, HepG2. Other laboratories around this time found that the major receptor mediating the binding and endocytosis of the PAs is Low Density Lipoprotein Receptor-related Protein (LRP1). LRP1 is a giant 600 kDa protein that binds a range of structurally and functionally diverse ligands including, activated α2 macroglobulin, apolipoproteins, β amyloid precursor protein, and a number of serpin-enzymes complexes, including PA??PAI-1 complexes. Further studies for the work presented here centred on this receptor. By using radiolabelled binding assays, ligand blots, and Western blots on cultured cells, the major findings are that: (1) basal LRP1 expression on HepG2 is low compared to a clone termed, HepG2a16, but appears to increase in long term culture; (2) a soluble form of LRP1, which retains ligand-binding capacity, is present in human circulation; (3) soluble LRP1 is also present in cerebral spinal fluid where its role in neurological disorders such as Alzheimer??s disease is a developing area of interest; and (4) the release of LRP1 is a mechanism conserved in evolution, possibly as distantly as molluscs. The discovery, identification, and characterisation of soluble LRP1 introduces this protein in the human circulation, and presents a possible further level of regulation for its associated receptor system.

De nombreuses études révèlent que le domaine de liaison au ligand de RXRα est très dynamique, même en présence d'un ligand agoniste. Nous avons utilisé les données expérimentales (HDX, RMN et X-ray) disponibles sur ce domaine pour mettre en place un protocole, basé sur la dynamique moléculaire accélérée, permettant d'explorer efficacement la dynamique conformationnelle du domaine de liaison au ligand de RXRα et de valider les ensembles conformationnels obtenus. Ce protocole a été appliqué pour analyser l'influence de la phosphorylation pSer260, située à proximité de la surface d'interaction avec les protéines coactivatrice et impliquée dans le développement de carcinomes hépatocellulaires, sur la structure de ce domaine et sa dynamique. Parallèlement, une méthode de réduction de la dimensionnalité a été développé afin d'analyser de longues trajectoires de dynamique moléculaire. Ainsi grâce à cette méthode, nous avons pu identifier plusieurs nouvelles conformations alternative stables du domaine de liaison au ligand de RXRα
Many studies reveal that the ligand binding domain of RXRα is very dynamic, still even in a presence of an agonist ligand. Therefore, the availability of experimental data (HDX, NMR and X-ray) on the domain was used as a leverage in order to set up a protocol, based on accelerated molecular dynamics, to explore its conformational dynamic and to validate it. This protocol was applied to understand the influence of the pSer260 phosphorylation, closed to the binding surface of coactivator proteins and implied in the hepatocellular carcinoma growth, on its structure and its dynamic. At the same time, a dimensional reduction method was developed to analyse long molecular dynamic trajectories. Thus, with this approach, we identified a couple of new alternative and stable conformations of the ligand binding domain of RXRα

Le récepteur de la vitamine D (VDR) est un facteur de transcription activé par la forme active de la vitamine D3. VDR est une cible thérapeutique potentielle pour de multiples pathologies telles que les maladies auto-immunes et neurodégénératives et certains cancers. VDR module l’expression de gènes par le recrutement sélectif de corégulateurs. Les données structurales disponibles à ce jour pour des complexes de récepteur nucléaire-corégulateurs sont très limitées. Cette étude se focalise sur l’architecture du complexe formé par VDR et un grand fragment du coactivateur MED1, une sous-unité du complexe Médiateur qui fait le lien entre les récepteurs nucléaires et la machinerie basale de transcription. Les résultats obtenus nous sont permis de caractériser l'interaction du récepteur avec le coactivateur et de révéler l'architecture globale du complexe. Ce travail fournit une base solide pour la détermination structurale d’autres complexes impliqués dans le contrôle de la transcription
The vitamin D nuclear receptor (VDR) is a transcription factor activated by the biologically active form of vitamin D3. VDR is a potential candidate to treat neurodegenerative and autoimmune disorders, and cancer. VDR modulates the expression of vitamin D3-regulated genes by selective recruitment of coregulators of transcription which are, in turn, attractive targets in epigenetic-oriented drug discovery. Available structural data for receptor-coregulator complexes are limited; investigation of such complexes is highly important. The present work focuses on the architecture of the complex between VDR and a large part of the coactivator MED1, a subunit of the Mediator complex linking nuclear receptors to the basal transcription machinery. Obtained results revealed important details of the interaction, as well as the overall organization of the complex. This work provides a solid background for the structural investigation of similar complexes involved in the transcriptional control

L'acide rétinoïque (AR) joue un rôle important dans plusieurs processus cellulaires à travers la régulation de la différentiation cellulaire, de la prolifération et de l'apoptose. Ces propriétés sont à la base de l'utilisation de l'AR dans le traitement de plusieurs cancers dont la leucémie aiguë promyélocytaire. Décrypter comment l'AR contrôle l'expression de gènes spécifiques est un défi permanent pour l'étude des cancers. Les effets de l'AR sont médiés in vivo principalement par les récepteurs à l'acide rétinoïque (RARs). Il a été récemment démontré que la phosphorylation des RARs par différentes kinases est une étape nécessaire dans la régulation de leurs fonctions. Dans ce contexte, ma thèse a porté sur l’étude des mécanismes moléculaires de la régulation par phosphorylation des RARs. Nous nous sommes intéressés en particulier à deux aspects : l’effet de la phosphorylation sur le domaine de liaison au ligand (LBD) et sur le domaine N-terminal (NTD). Dans le cas du LBD, la phosphorylation induit la fixation de la Cycline H qui est une sous-unité du facteur de transcription TFIIH, alors que la phosphorylation du NTD induit une diminution d’affinité de liaison à la Vinexine beta qui est un co-répresseur. Nous avons étudié les effets de la phosphorylation par des simulations de dynamique moléculaire. Cette technique permet de caractériser la dynamique structurale et de quantifier les interactions qui stabilisent les états phosphorylés et non phosphorylés. Ce projet a permis de définir les bases moléculaires de la communication entre le RA et les cascades de phosphorylation et d’obtenir des informations originales sur des mécanismes régulateurs d’une grande importance
Retinoic Acid (RA) plays a critical role in many cellular processus through regulatory effects on cellular differentiation, proliferation and apoptosis. This proprety is at the basis of RA therapy in the treatment of several diseases and cancers such as Acute Promyelocytic Leukemia. Deciphering how RA controls the expression of specific subsets of genes is therefore a permanent challenge in oncology. The effects of RA are mediated in vivo by the retinoic acid receptor (RAR), which consistsof three subtypes. A new concept has recently emerged according to which phosphorylation of RARs by different kinases is a necessary step in the regulation of their function. In this context, the specific aim of this thesis was the elucidation of the molecular mechanisms of the regulation of RAR mediated by phosphorylation. In particular, we focused on two aspects, the effects of phosphorylation of the ligand binding domain (LBD) and the effects on the N-terminal domain (NTD). In the case of the LBD, phosphorylation enhanced binding to cyclin H, a component of the TFIIH transcription factor, while phosphorylation of the NTD decreased binding to vinexinB, a corepressor protein. We used molecular dynamics simulations to characterize the structural dynamics of these proteins in both phosphorylated and unphosphorylated states and to quantify theirinteractions. From this project, we were able to define the molecular basis of the communication between RA-induced phosphorylation cascades and regulatory mechanisms of high importance

Cette thèse vise à réaliser une étude approfondie sur le développement de méthodologies pour l’analyse de systèmes complexes. Cela comprend l’étude des systèmes hors d’équilibre, des systèmes d’auto-assemblage, et les systèmes biologiques désordonnés. Les méthodes développées recouvrent principalement la RMN, tel que la mesure de diffusion (DOSY) mais également d’autres techniques telles que la spectrométrie de masse, le dichroïsme circulaire (CD), la microscopie électronique (EM) et diffusion des rayons X aux petits angles (SAXS). La partie N-terminale du récepteur des androgènes (AR) est utilisée comme un système complexe. D’après la littérature, il est connu que cette région joue un rôle important pour l’activité du récepteur, et elle est également décrite comme étant intrinsèquement désordonnée. Les résultats que j’ai acquis durant la thèse m’ont permis d’identifier une courte région de ce domaine, impliquée dans la formation réversible de fibres amyloïdes, par modulation des conditions d’oxydo-réduction du milieu. Les résultats révèlent un aspect inconnu du mécanisme de AR
My PhD project was focused on the development of methods for the analysis of complex systems and their biophysical characterization. This includes the study of large chemical libraries, self assembly systems, protein-ligand interaction studies and disordered biological systems. A wide range of biophysical methods were used for this purpose. Specially, Nuclear Magnetic Resonance(NMR) but also other techniques such as mass spectrometry, circular dichroism (CD), electron microscopy (EM) and small angle X-ray scattering (SAXS). The N-terminal Domain of the Androgen Receptor is studied as an example of a complex system. This region plays an important role in receptor activity, and is also described as being intrinsically disordered. The results obtained during my thesis shown a short conserved region involved in the amyloid fibers formation under oxidative conditions. These results open new possibilities to understand the mechanism of the AR activity

Les récepteurs couplés aux protéines G (GPCRs en anglais) représentent la famille de récepteurs intégrales de membrane plus vaste dans la majorité des cellules eucaryotes. Ils jouent un rôle clé dans la transduction de signal, ainsi que la compréhension de leur mécanisme de signalisation représente une des questions principales dans la biologie d'aujourd'hui. Dans la caractérisation du paysage énergétique de ces récepteurs à l'échelle atomique, les structures cristallographiques publiées pendant la décennie dernière par cristallographie aux rayons X représentent la percée scientifique majeure et donnent une contribution fondamentale dans la biologie structurelle de GPCRS. Ces structures représentent un point de départ précieux dans la compréhension du mécanisme de transduction de signal, en plaçant des structures dans l'ensemble conformationnel de ces récepteurs le long du processus d'activation. Pour compléter ce cadre de structures statiques qui correspondent aux états à basse l'énergie et fortement peuplés, une caractérisation de l'ensemble conformationnel et des barrières cinétiques qui sont associées est un point nécessaire et fondamentale. À ce but nous proposons une approche innovant avec la finalité d'observer le paysage conformationnel dynamique des GPCR et étudier la modulation de ces récepteurs par des ligands et des lipides, qui sont connus pour jouer un rôle clé dans la structure et les fonctions des protéines de membrane (e.g.). Un des outilles le plus approprié pour explorer les barrières cinétiques de GPCR c'est la résonance magnétique nucléaire (RMN) en solution. Pour tirer profit au mieux de cette technique, nous avons utilisé des sondes marqués 13CH3 immergées dans un environnement perdeuteré, qui constitue le marquage isotopique le plus approprié en RMN pour examiner les paysages conformationnels des protéines de grosses dimensionnes ou des complexes de protéines. Nous avons choisi Escherichia coli comme système d'expression pour sa capacité de pousser dans des conditions très hostiles comme des solutions 100%-D2O. Pour surmonter les difficultés habituellement rencontrées lors de l'expression des GPCRs, nous avons appliqué un protocole innovant qui cible l'expression de GPCRs directement aux corps d'inclusion. Ceci permet la production des bonnes quantités de protéines (jusqu’à 6 mg/litres de culture de pur 13CH3-u-2H-GPCRs). Une fois purifié, le récepteur est foldé en amphipols et transféré ensuite à une double couche lipidique appelée nanometric lipid bilayer ou nanodisc (NLB). De façon très important, les mesures pharmacologiques quantitatives indiquent que les récepteurs incorporés dans des NLBs après ce protocole sont stables et entièrement actifs dans les conditions des expériences de NMR.Les investigations par RMN conduites sur le GPCR en NLB ont donné lieu à une résolution jamais obtenue dans le domaine, grâce à la biochimie finement accordée et à la perdeuteration du récepteur. Selon les données obtenues, notre récepteur modèle, le récepteur 2 pour le leukotriene B4 (BLT2), est capable d'explorer plusieurs conformations différentes, même dans l'état pas lié aux ligands, y compris l'état actif. Ce paysage conformationnel est également modulé par des ligands et des lipides. Dans le cas spécifiques, nous avons observé que un incrément dans le contenu de stérol dans la membrane modifie la distribution des différents états conformationnels du récepteur, en favorisant l'état actif, qui indique une régulation allosteric positif du stérol sur l'activation de ce récepteur, comme confirmé aussi par les mesures de liaison du GTP à la protéine G. Cette propriété du stérol est probablement importante pour le contrôle de mécanisme de signalisation de GPCRs
G protein-coupled receptors (GPCRs) are the largest family of integral membrane protein receptors present in most eukaryotic cells. They play a key role in signal transduction and understanding their signalling mechanism represents one of the main issues in biology today. In the characterization of the energy landscape of these receptors, at the atomic scale, X-ray crystal atomic structures published during the last decade represent the major breakthrough and contribution in the structural biology of GPCRs. They represent a precious starting point in the understanding of the mechanism of signal transduction by placing structures in the conformational ensemble of these receptors along the activation pathway. To complete these static snapshots that correspond to low energy and highly populated states, a characterization of the whole conformational ensemble and associated kinetic barriers is fundamental to complete the picture. To this aim we proposed an innovative approach to observe GPCRs dynamic conformational landscape and how it is modulated by ligands and lipids, that are known to play a key role in membrane protein structures and functions (e.g.). One of the most appropriate tool to explore GPCR kinetic barriers is solution state NMR. To do so, we used 13CH3 probes immersed in a perdeuterated environment, the most appropriate isotope-labelling scheme to investigate conformational landscapes of large proteins or protein complexes with this spectroscopy. We chose Escherichia coli as expression system for its ability to grow in very hostile conditions like 100%-D2O solutions. In order to overcome the usual expression issues concerning GPCRs, we applied an innovative protocol which targets the expression directly to inclusion bodies. This allows the production of high amounts of proteins (up to 6 mg/litre of culture of pure 13CH3-u-2H-GPCRs). Once purified, receptors are folded in amphipols and then transferred to nanometric lipid bilayers or nanodiscs. Importantly quantitative pharmacological measurements indicate that receptors embedded in NLBs following this protocol are stable and fully active in the conditions of the NMR experiments. NMR investigation of a GPCR in a NLB gave rise to a resolution never achieved in the field thanks to a fine tuned biochemistry and a perdeuteration of the receptor. According to our data, the prototypical receptor, the leukotriene B4 receptor (BLT2), is able to explore multiple different conformations, even in the unliganded state, including the active state. This conformational landscape is further modulated by ligands and lipids. In particular, we observed that an increment in the sterol content of the membrane modifies the distribution of the different conformational states of the receptor in favour of the active one, indicating a positive allosteric regulation of the sterol on the activation of this receptor, as confirmed by GTP-to-G protein binding measurements. This property of the sterol is likely important for the control of the signalling properties of GPCRs

"September 2002" Includes as appendix: a list of publications by the author arising from this work; and, copies of some published journal articles Includes bibliographical references. Describes the synthesis, properties and reactions of transition metal complexes containing poly-ynyl ligands

"September 2002"
Includes as appendix: a list of publications by the author arising from this work; and, copies of some published journal articles
Includes bibliographical references.
[12], 209 leaves, [35] pages : ill. ; 30 cm.
Describes the synthesis, properties and reactions of transition metal complexes containing poly-ynyl ligands
Thesis (Ph.D.)--University of Adelaide, Dept. of Chemistry, 2002

Thesis (M. Sc.)--York University, 2001. Graduate Programme in Biology.
Typescript. Includes bibliographical references (leaves 106-118). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pMQ66399.

How does a bacteria integrate a variety of signals received at its surface and respond with flagella rotation either in CCW or in CW? Several experimental approaches have been used to identify possible mechanism of transmembrane signaling. The different studies suggest different mechanisms of transmembrane signaling (Milburn et al., 1991; Lynch and Koshland, 1992; Chervitz and Falke, 1996; Maddock and Shapiro, 1993; Long and Weis, 1992; Liu et al., 1997; Li et al., 1997). However, most of the evidence including the one from this study either directly or indirectly points out that a receptor cluster probably serves as a working unit for signal integration and processing upon ligand binding. In this study we have observed that the level of covalent modification on the serine receptor strongly influences serine binding affinity while the receptor is in a complex. The ligand concentration dependence is construed as a change in the ligand binding affinity. Certainly, we consider that these binding affinity changes are the result of receptor covalent modification.

The glycoprotein hormones, Luteinizing Hormone (LH), human Chorionic Gonadotropin (hCG), Follicle Stimulating Hormone (FSH) and Thyroid Stimulating Hormone (TSH) are heterodimeric proteins with an identical α-subunit associated non-covalently with the hormone specific β-subunit and play important roles in reproduction and overall physiology of the organism [1]. The receptors of these hormones belong to the family of G-protein coupled receptors (GPCR) and have a large extracellular domain (ECD) comprising of 9-10 leucine rich repeats (LRR) followed by a flexible hinge region, a seven helical transmembrane domain (TMD) and a C terminal cytoplasmic tail [2]. Despite significant sequence and structural homologies observed between the ECDs of the receptors and the specific β-subunits of the hormones, the hormone-receptor pairs exhibit exquisite specificity with very low cross-reactivity with other members of the family. The TSH receptor (TSHR) is an especially interesting member of this family as it not only recognizes is cognate ligand, i.e. TSH, but also binds to the non-cognate ligands such as autoantibodies. TSHR autoantibodies come in different flavors; inhibitory antibodies that compete with the hormone for receptor binding and block its action, stimulatory antibodies that activate the receptor in a hormone independent manner and neutral antibodies that bind to the receptor but do not directly influence its functions. The inhibitory autoantibodies cause hypothyroidism and are responsible for Hashimoto’s Thyroiditis, whereas the stimulatory autoantibodies cause Graves’ thyrotoxicosis characterized by hyperthyroid condition [3]. The exact epitopes of these autoantibodies are not well delineated although it has been hypothesized that the blocking type- and the stimulatory type- autoantibodies have predominant epitopes in the TSHR ECD that overlap with hormone binding regions [4]. Insights into the mode of hormone or autoantibody binding to the receptor was primarily derived from the crystal structure of FSHR leucine rich repeat domain (LRRD) bound to single chain analog of FSH, and the crystal structures of TSHR LRRD bound to the stimulatory type human monoclonal antibody M22 [5] and the inhibitory type- monoclonal antibody K1-70 [6]. Both these crystal structures propose LRRDs as the primary ligand binding site which interacts with the hormone through its determinant loop in a hand-clasp fashion [7] while the autoantibodies mimics the hormone binding to a large extent [8] . These structures, while providing detailed understanding of the molecular interactions of the LRRs with the hormone, shed little light on the mechanism by which the signal generated at the LRRD are transduced to the downstream effector regions at the distally situated TMD. Hence, while one understands the ligand binding to a large extent, the activation process is not well understood, one of the central objective of the present study. Ligand-receptor interactions are typically studied by perturbing ligand/receptor structure by mutagenesis or by mapping conformational changes by biophysical or computational approaches. In addition to the above-mentioned approaches, the present work also uses highly specific antibodies against different domains of the receptor as molecular probes due to the ability of antibodies to distinguish between conformations likely to arise during the activation process. Use of antibodies to understand the receptor activation process is especially apt for TSHR due to the presence of physiologically relevant TSHR autoantibodies and their ability to influence hormone binding and receptor activation [9, 10]. Chapter 2 attempts to provide a comparison between the interactions of the hormone and the autoantibodies with TSHR. For this purpose, two assays were developed for identification of TSHR autoantibodies in the sera of patients suffering from autoimmune thyroid diseases (AITD), the first assay is based on the ability of TSHR autoantibodies to compete for radiolabeled hormone (The TSH binding inhibition (TBI), assay) and the second based on the capability of stimulatory antibody to produce cAMP in cells expressing TSHR (TSHR stimulatory immunoglobin (TSI) assay). A stable cell line expressing TSHR capable of recognizing both TSH and TSHR autoantibodies was thus created and used for prospective and retrospective analysis of AITD patients. Based on the TBI and TSI profiles of IgGs, purified from AITD patient's sera, it was recognized that TSHR stimulatory and TSH binding inhibitory effects of these antibodies correlated well, indicating overlap between hormone binding and IgG binding epitopes. It was also recognized that stimulatory IgGs are not affected by negative regulatory mechanism that governs TSH secretion substantiating the persistence of these antibodies in circulation. Kinetics of cAMP production by Graves’ stimulatory IgG was found to be fundamentally distinct, where the autoantibodies displayed pronounce hysteresis during the onset of the activation process when compared to the hormone. This could possibly be explained by the oligoclonality of the autoantibody population, a different mechanism of receptor activation or dissimilarity in autoantibody and hormone epitopes. To gain additional insights into the epitopes of TSHR autoantibodies and the regions that might be critical in the activation process, different overlapping fragments encompassing the entire TSH receptor ECD were cloned, expressed in E.coli as GST fusion proteins and purified: 1] the first three LRRs (TLRR 1-3, amino acid (aa) 21-127), 2] the first six LRRs (TLRR 1-6, aa 21-200), 3] the putative major hormone binding domain (TLRR 4-6, aa 128-200), and 4] the hinge region of TSH receptor along with LRR 7 to 9, (TLRR 7-HinR, aa 201-413). The receptor fragment TLRR 7-HinR was further subdivided into LRR 7-9 (TLRR 7-9, aa 201-161) and the hinge region (TSHR HinR, aa 261-413), expressed as N-terminal His-Tagged protein and purified using IMAC chromatography. Simultaneously, the full-length TSHR ECD was cloned, expressed and purified using the Pichia pastoris expression system. ELISA or immunoblot analysis of autoantibodies with the TSHR exodomain fragments suggested that Graves’ stimulatory antibody epitopes were distributed throughout the ECD with LRR 4-9 being the predominant site of binding. Interestingly, experiments involving neutralization of Graves’ IgG stimulated cAMP response by different receptor fragment indicated that fragments corresponding to the TSHR hinge region were better inhibitors of autoantibody stimulated receptor response than corresponding LRR fragments, suggesting that the hinge region might be an important component of the receptor activation process. This was in contrast to prevalent beliefs that considered the hinge region to be an inert linker connecting the LRRs to the TMD, a structural entity without any known functional significance. Mutagenesis in TSHR hinge region and agonistic antibodies against FSHR and LHR hinge regions, reported by the laboratory, recognized the importance of the hinge regions as critical for receptor activation and may not simply be a scaffold [11-13]. Unfortunately, the mechanism by which the hinge region regulates binding or response or both have not been well understood partially due to unavailability of structural information about this region. In addition poor sequence similarity within the GpHR family and within proteins of known structure, make this region difficult to model structurally. In chapter 3, effort is made to model the hinge regions of the three GpHR based on the knowledge driven and Ab initio protocols. An assembled structure comprising of the LRR domain (derived from the known structures of FSHR and TSHR LRR domains) and the modeled hinge region and transmembrane domain presents interesting differences between the three receptors, especially in the manner the hormone bound LRRD is oriented towards the TMD. These models also suggested that the α-subunit interactions in these three receptors are fundamentally different and this was verified by investigating the effects of two α-subunit specific MAbs C10/2A6 on hCG-LHR and hTSH-TSHR interactions. These two α-subunit MAbs had inverse effects on binding of hormone to the receptor. MAb C10 inhibited TSH binding to TSHR but not that of hCG, whereas MAb 2A6 inhibited binding of hCG to LHR but not of hTSH. Investigation into the accessibility of their epitopes in a preformed hormone receptor complex indicated that the α-subunit may become buried or undergo conformational change during the activation process and interaction may be different for LHR and TSHR. Fundamental differences in TSHR and LHR were further investigated in the next chapter (Chapter 4), especially with regards to the ligand independent receptor activation. Polyclonal antibodies were developed against LRR 1-6, TLRR 7-HinR and the TSHR HinR receptor fragments. The LRR 1-6 antibodies were potent inhibitor of receptor binding as well as response, similar to that observed with antibodies against the corresponding regions of LHR. Interestingly, the antibodies against the hinge region of TSHR were unable to inhibit hTSH binding, but were effective inhibitors of cAMP production suggesting that this region may be involved in a later stage of a multi-step activation process. This was also verified by studying the mechanism of inhibition of receptor response and their effect on ligand-receptor association and dissociation kinetics. Hinge region-specific antibodies immunopurified from TLRR 7-HinR antibodies behaved akin to those of the pure hinge region antibodies providing independent validation of the above results. This result was, however, in contrast to those observed with a similar antibody against LHR hinge region. As compared to the TSHR antibody, the LHR antibody inhibited both hormone binding and response. In addition, this antibody could dissociate a preformed hormone-receptor complex which was not observed for TSHR hinge region antibodies. Although unable to dissociate preformed hormone-receptor complex by itself, the TSHR HinR antibodies augmented hormone induced dissociation of the hormone-receptor complex suggesting that this region may be involved in modulation of negative cooperativity associated with TSHR. Molecular dissection of the role of hinge region of TSHR was further carried out by using monoclonal antibodies against LRR 1-3 (MAb 413.1.F7), LRR 7-9 (MAb 311.87), TSHR hinge region (MAb 311.62 and MAb PD1.37). MAb 311.62 which identifies the LRR/Cb-2 junction (aa 265-275), increased the affinity of TSHR for the hormone while concomitantly decreasing its efficacy, whereas MAb 311.87 recognizing LRR 7-9 (aa 201-259) acted as a non-competitive inhibitor of TSH binding. MAb 413.1.F7 did not affect hormone binding or response and was used as the control antibody for different experiments. Binding of MAbs was sensitive to the conformational changes caused by the activating and inactivating mutations and exhibited differential effects on hormone binding and response of these mutants. By studying the effects of these MAbs on truncation and chimeric mutants of thyroid stimulating hormone receptor (TSHR), this study confirms the tethered inverse agonistic role played by the hinge region and maps the interactions between TSHR hinge region [14] and exoloops responsible for maintenance of the receptor in its basal state. Mechanistic studies on the antibody-receptor interactions suggest that MAb 311.87 is an allosteric insurmountable antagonist and inhibits initiation of the hormone induced conformational changes in the hinge region, whereas MAb 311.62 acts as a partial agonist that recognizes a conformational epitope critical for coupling of hormone binding to receptor activation. Estimation of apparent affinities of the antibody to the receptor and the cooperativity factor suggests that epitope of MAb 311.87 (LRR 7-9) may act as a pivot involved in the initial events immediate to hormone binding at the LRRs. The anatgonsitic effect of MAB 311.62 on binding and response also suggested that binding of hormone is conformationally selective rather than an induced event. The hinge region, probably in close proximity with the α-subunit in the hormone-receptor complex, acts as a tunable switch between hormone binding and receptor activation. In contrast to the stimulatory nature of Cb-2 antibody such as MAb 311.62, MAb PD1.37, which identified residues aa 366–384 near Cb-3, was found to be inverse agonistic. Unlike other known inverse agonistic MAbs such as CS-17 [15] and 5C9 [16], MAb PD1.37 did not compete for TSH binding to TSHR, although it could inhibit hormone stimulated response. Moreover, unlike CS-17, MAb PD1.37 was able to decrease elevated basal cAMP of hinge region constitutively activated mutations only but not those in the extracellular loops. This is particularly important as interaction of hinge region residues with those of ECLs had been thought to be critical in maintenance of the basal level of receptor activation and are responsible for attenuating the constitutive basal activity of the mutant and wild-type receptors in the absence of the hormone. This was demonstrated by a marked increase in the basal constitutive activity of the receptor upon the complete removal of its extracellular domain, which returned to the wild-type levels upon reintroduction of the hinge region. However, careful comparison of the activities of the mutants (receptors harboring deletions and gain-of-function mutations) with maximally stimulated wild-type TSHR indicated that these mutations of the receptor resulted primarily in partial activation of the serpentine domain suggesting that only the ECD in complex with the hormone is the full agonist of the receptor. Confirmation of the above proposition has been difficult to verify primarily due to a highly transient conformational change in the tripartite interaction of the hinge region/hormone and the ECLs. The current approaches of using antibodies to probe the ECLs are difficult due to the conformational nature of the antigen as well as difficulty in obtaining a soluble protein. In chapter 5, the ligand induced conformational alterations in the hinge regions and inter-helical loops of LHR/FSHR/TSHR were mapped using the exoloop specific antibodies generated against a mini-Transmembrane domain (mini-TMD) protein. This mini-TMD protein, designed to mimic the native exoloop conformations, was created by joining the TSHR exoloops, constrained through the helical tethers and library derived linkers. The antibody against mini-TMD specifically recognized all three GpHRs and inhibited the basal and hormone stimulated cAMP production without affecting hormone binding. Interestingly, binding of the antibody to all three receptors was abolished by prior incubation of the receptors with the respective hormones suggesting that the exoloops are buried in the hormone-receptor complexes. The antibody also suppressed the high basal activities of gain-of-function mutations in the hinge regions, exoloops and TMDs such as those involved precocious puberty and thyroid toxic adenomas. Using the antibody and point/deletion/chimeric receptor mutants, dynamic changes in hinge region-exoloop interactions were mapped. The computational analysis suggests that mini-TMD antibodies act by conformationally locking the transmembrane helices by restraining the exoloops and juxta-membrane regions. This computational approach of generating synthetic TMDs bears promise in development of interesting antibodies with therapeutic potential, as well as, explains the role of exoloops during receptor activation. In conclusion (Chapter 6), the study provides a comprehensive outlook on the highly dynamic interaction of ligand and different subdomains of the TSHR (and to a certain extent of LHR and FSHR) and proposes a model of receptor activation where the receptor is in a dynamic equilibrium between the low affinities constrained state and the high affinity unconstrained state and bind to the hormone through the LRR 4-6. Upon binding the βL2 loop of the hormone contact LRR 8-10 that triggers a conformational change in the hinge region driving the α-subunit to contact the ECLs. Upon contact, the ECLs cooperatively causes helix movement in the TMH and ultimately in ICLs causing the inbuilt GTP-exchange function of a GPCR.

Resveratrol is a polyphenolic phytoestrogen that has been shown to exhibit potent anti-oxidant, anti-inflammatory, and anti-catabolic properties. Increased osteoclastic and decreased osteoblastic activities result in bone resorption and loss of bone mass. These changes have been implicated in pathological processes in rheumatoid arthritis and osteoporosis. Receptor activator of NF-kappaB ligand (RANKL), a member of the TNF superfamily, is a major mediator of bone loss. In this study, we investigated the effects of resveratrol on RANKL during bone morphogenesis in high density bone cultures in vitro. Untreated bone-derived cell cultures produced well organized bone-like structures with a bone-specific matrix. Treatment with RANKL induced formation of tartrate-resistant acid phosphatase-positive multinucleated cells that exhibited morphological features of osteoclasts. RANKL induced NF-kappaB activation, whereas pretreatment with resveratrol completely inhibited this activation and suppressed the activation of IkappaBalpha kinase and IkappaBalpha phosphorylation and degradation. RANKL up-regulated p300 (a histone acetyltransferase) expression, which, in turn, promoted acetylation of NF-kappaB. Resveratrol inhibited RANKL-induced acetylation and nuclear translocation of NF-kappaB in a time- and concentration-dependent manner. In addition, activation of Sirt-1 (a histone deacetylase) by resveratrol induced Sirt-1-p300 association in bone-derived and preosteoblastic cells, leading to deacetylation of RANKL-induced NF-kappaB, inhibition of NF-kappaB transcriptional activation, and osteoclastogenesis. Co-treatment with resveratrol activated the bone transcription factors Cbfa-1 and Sirt-1 and induced the formation of Sirt-1-Cbfa-1 complexes. Overall, these results demonstrate that resveratrol-activated Sirt-1 plays pivotal roles in regulating the balance between the osteoclastic versus osteoblastic activity result in bone formation in vitro thereby highlighting its therapeutic potential for treating osteoporosis and rheumatoid arthritis-related bone loss.