Protein-protein interactions are of vital importance to the cell as they mediate the assembly of protein complexes that carry out diverse biological functions. Many proteins involved in cellular signaling are built by the combinatorial use of peptide recognition modules (PRMs), which are small protein domains that bind to their cognate ligands by recognizing short linear peptide motifs. Thousands of PRMs are found in nature, requiring improved methods to better elucidate their molecular determinants of binding and to allow accurate mapping of their interaction networks. In this thesis, I describe the development and application of phage-displayed peptide libraries to map the binding specificities of two common PRMs. First, I generated specificity profiles for 82 C. elegans and human PDZ domains that could be organized into a specificity map. The map revealed that PDZ domains have far greater substrate sequence specificity than previously believed, providing significant insights into the relationships between PDZ structure and specificity, and allowing specificity prediction for uncharacterized domains. My results were used to predict both endogenous and pathogenic PDZ interactions. This analysis revealed that viruses have evolved ligands that specifically mimic PDZ domains to subvert host cell immunity. Second, I analyzed the binding specificity for the SH3 domain family in S. cerevisae. I found that, like PDZ domains, SH3 domains have binding specificities that are more detailed than the conventional classification system. The phage-derived specificity profiles were combined with data from oriented peptide and yeast two-hybrid screening to generate a highly accurate SH3 domain interaction network. Given the prominent role of SH3 domains in endocytosis, the SH3 domain interaction data was used to predict the dynamic localization of several uncharacterized endocytosis proteins, which was subsequently confirmed by cell-based assays. The application of the techniques described here to other PRM families will significantly improve protein interaction maps for signaling pathways, which will illuminate our understanding of the cell circuitry, allow the use of PRMs as general affinity reagent and detection tools, and guide the development of small molecule inhibitors that mimic their peptide ligands for therapeutic intervention.

Protein-protein interactions are of vital importance to the cell as they mediate the assembly of protein complexes that carry out diverse biological functions. Many proteins involved in cellular signaling are built by the combinatorial use of peptide recognition modules (PRMs), which are small protein domains that bind to their cognate ligands by recognizing short linear peptide motifs. Thousands of PRMs are found in nature, requiring improved methods to better elucidate their molecular determinants of binding and to allow accurate mapping of their interaction networks. In this thesis, I describe the development and application of phage-displayed peptide libraries to map the binding specificities of two common PRMs. First, I generated specificity profiles for 82 C. elegans and human PDZ domains that could be organized into a specificity map. The map revealed that PDZ domains have far greater substrate sequence specificity than previously believed, providing significant insights into the relationships between PDZ structure and specificity, and allowing specificity prediction for uncharacterized domains. My results were used to predict both endogenous and pathogenic PDZ interactions. This analysis revealed that viruses have evolved ligands that specifically mimic PDZ domains to subvert host cell immunity. Second, I analyzed the binding specificity for the SH3 domain family in S. cerevisae. I found that, like PDZ domains, SH3 domains have binding specificities that are more detailed than the conventional classification system. The phage-derived specificity profiles were combined with data from oriented peptide and yeast two-hybrid screening to generate a highly accurate SH3 domain interaction network. Given the prominent role of SH3 domains in endocytosis, the SH3 domain interaction data was used to predict the dynamic localization of several uncharacterized endocytosis proteins, which was subsequently confirmed by cell-based assays. The application of the techniques described here to other PRM families will significantly improve protein interaction maps for signaling pathways, which will illuminate our understanding of the cell circuitry, allow the use of PRMs as general affinity reagent and detection tools, and guide the development of small molecule inhibitors that mimic their peptide ligands for therapeutic intervention.

LNX1 belongs to a family of multi-PDZ domain containing RING-type E3 ligases. Several interactions have been mapped to its PDZ domains, but the role of each domain in LNX function has not yet been determined. To study individual PDZ domain function in the context of full length protein I generated point mutations in peptide binding sites of each of PDZ domain, and in a putative phosphoinositide binding site of LNX1 PDZ4. Peptide binding was successfully disrupted by an arginine or lysine to alanine mutation in the peptide binding cleft. A LNX1 PDZ4 mutant with lysine residues in a putative phosphoinositide binding site mutated to glutamate displayed decreased membrane localization. The impact of each PDZ mutation on cell morphology and substrate ubiquitination was also investigated. I identified a potential role for PDZ binding in auto-inhibition of RING function. Additionally, novel interactions between LNX1 and Frizzled family members were identified and characterized.

LNX1 belongs to a family of multi-PDZ domain containing RING-type E3 ligases. Several interactions have been mapped to its PDZ domains, but the role of each domain in LNX function has not yet been determined. To study individual PDZ domain function in the context of full length protein I generated point mutations in peptide binding sites of each of PDZ domain, and in a putative phosphoinositide binding site of LNX1 PDZ4. Peptide binding was successfully disrupted by an arginine or lysine to alanine mutation in the peptide binding cleft. A LNX1 PDZ4 mutant with lysine residues in a putative phosphoinositide binding site mutated to glutamate displayed decreased membrane localization. The impact of each PDZ mutation on cell morphology and substrate ubiquitination was also investigated. I identified a potential role for PDZ binding in auto-inhibition of RING function. Additionally, novel interactions between LNX1 and Frizzled family members were identified and characterized.

Le détournement de la machinerie cellulaire par un pathogène est souvent essentiel à sa propagation dans l'organisme de l'hôte. Les voies de signalisation qui contrôlent l'homéostasie cellulaire constituent une cible stratégique de nombreux virus lors d'une infection. Le virus de la rage possède la particularité d'induire la survie des neurones qu'il infecte. Le site de fixation à des domaines PDZ (PDZ-BS) de la glycoprotéine du virus de la rage a été identifié comme étant un élément clef dans le contrôle des voies de survie et d'apoptose. Ce PDZ-BS reconnaît uniquement deux isoformes de la famille des " Microtubule Associated Serine/Threonine kinase " (MAST1 et MAST2). La kinase MAST2 possède une fonction inhibitrice de survie en contrôlant l'élongation des neurites et interagit, par ailleurs, avec le PDZ-BS de la phosphatase PTEN, autre inhibiteur essentiel de la survie neuronale. Nous avons montré in vitro que les domaines C-terminaux de PTEN (PTEN13-Cter) et de la glycoprotéine (Cyto13-vir) entrent en compétition pour la fixation domaine PDZ de MAST2. La résolution de la structure du domaine PDZ de MAST2 et PTEN13-Cter, son ligand endogène, révèle un mode d'interaction original avec une large surface d'interaction. Ce réseau d'interaction est conservé dans la structure du domaine PDZ de MAST2 complexé au ligand viral Cyto13-vir. En parallèle, nous avons démontré que le PDZ-BS de la glycoprotéine est nécessaire pour induire la survie des cellules infectées et qu'il module la distribution spatiale de PTEN in cellulo. Cette localisation est dépendante de la phosphorylation de PTEN-Cter.

PSD95 is the canonical member of the Membrane Associated Guanylate Kinase class of scaffold proteins. PSD95 is a five-domain major scaffolding protein abundant in the postsynaptic density (PSD) of the neuronal excitatory synapse. Within PSD95 three PDZ domains modulate protein-protein interactions by selectively binding to short peptide motifs of target proteins. Under the direction of the multivalent PDZ domain interactions, the interacting proteins tend to cluster at the PSD, a phenomenon that is critical for synaptic signalling regulation. Earlier studies have shown that the N-terminal PDZ domains of PSD95 are obligatory for the clustering to occur. This thesis focuses on the strong inwardly rectifying potassium channel, Kir2.1 as the PSD95 binding partner. Kir2.1 is known to maintain membrane resting potential and control cell excitability. Previous studies have reported that Kir2.1 clustered into ordered tetrad complexes upon association with PSD95.This study investigates the detailed clustering mechanisms of Kir2.1 by PDZ domains. To achieve this, components that are involved in the formation of a complex namely PSD95 sub-domains comprising single PDZ and the tandem N terminal PDZ double domain (PDZ1-2), and Kir2.1 cytoplasmic domains(Kir2.1NC) are studied in detail via different structural and biophysical approaches; 1) PDZ1-2 is examined in apo- and bound ligand form with a Kir2.1 Cterminal peptide in crystal and solution via X-ray crystallography and small angle X-ray scattering; 2) the tandem and the single PDZ domain interaction with ligand are measured thermodynamically via isothermal calorimetry (ITC); 3) the complex of full length PSD95 with Kir2.1NC is analyzed with electron microscopy (EM). The protein components are produced in high quality by protein expression and multiple-step protein purification techniques. PDZ1-2 crystallographic structures were solved at 2.02A and 2.19A in theapo- and the liganded forms respectively. The solution state analysis showed domain separation and structural extension of the tandem domain when incorporated with the ligand. The ITC experiment revealed PDZ1-2 to have greater affinity towards the peptide ligand relative to the single PDZ domains. These combinatorial outcomes lead to the conclusion that PSD95 clusters Kir2.1 by adopting an enhanced binding interaction which is associated with increased PDZ1-2 inter-domain separation. The preliminary analysis of PSD95-Kir2.1NC complex with cryo-EM showed the establishment of a tetrad and led to a reconstruction at 40A resolution. The work in obtaining a higher resolution complex structure is promising with further data collection required to allow the employment of more sophisticated model reconstruction processes.

An understanding of the underlying mechanisms by which proteins engage and communicate within the complex cellular environment is critical to the elucidation of the molecular basis of disease states and the development of safer, more efficacious drug therapies. Diverse cellular functions, including replication, transcription, cell growth and intracellular signal transduction, are governed by extensive networks of protein-protein interactions (PPIs). Disruption of the finely-tuned cellular networks due to the formation of aberrant or unregulated PPIs is implicated in the development and progression of cancer. As a result, over the last decade, PPI modulation has developed as an attractive molecular target for novel cancer therapies and as a powerful research tool in chemical biology to provide insight into the cellular transformations involved in carcinogenesis. Chapter 1 provides a review of the physiological importance of PPIs and the role they play in the development and progression of cancer. A summary of the challenges associated with targeting PPIs is given, highlighting the changing perception regarding the drugabbility of PPIs and the technological and conceptual advances driving this transformation. A brief overview of the approaches used to identify PPI modulators links the reader to the appropriate chapter for further discussion and utilisation of a selection of these methods. Chapter 2 describes the application of a virtual screening approach to discover PPI modulators. In particular, the development of an in silico – in vitro screening method to identify modulators of the protein interactome of the AAA+ protein reptin. The synthesis and optimisation of two hit compounds is outlined, with a discussion of their predicted binding modes, mode of action, potential as chemical tools and lead molecules for an anti-cancer drug discovery programme. Chapter 3 highlights the potential to discover PPI modulators from Nature's rich source of structurally complex, bioactive molecules. A synthetic approach to a sub-family of tetramic acid natural products is outlined, involving the development of a short, asymmetric synthesis of unnatural 4,4-disubstituted glutamic acid derivatives. The first total syntheses of the potent siderophore harzianic acid and the PAC3 PPI inhibitor JBIR-22 are reported. In addition, the potential role of a Diels-Alderase enzyme in the biosynthesis of JBIR-22 and the development of a chiral catalysed intramolecular Diels-Alder of an advanced JBIR-22 intermediate is investigated. Chapter 4 discusses the use of structure based design techniques in the development of PPI modulators. The process involved in the design of two series of inhibitors of PICK PDZ domain mediated interactions is outlined. This leads to the development and optimisation of synthetic routes to both series of inhibitors, including the utilisation of a strategic sp3-sp2 cross coupling reaction. Finally, preliminary biological assessment of the inhibitors is reported. Chapter 5 gives a brief overview of high-throughput screening (HTS) methods used to identify PPI modulators. The utilisation of a forward chemical genetics screen to identify the p53 activator MJ05 is described. A racemic and asymmetric route to MJ05 is developed and biochemical analysis of the two enantiomers of MJ05 is reported including the investigation of MJ05 as an adjuvant therapy for the treatment of cancer. Chapter 6 provides a general overview of the outcome of the different approaches used in this research to discover PPI modulators. Particular emphasis is placed on the development of chemical tools for the elucidation and dissection of the physiological role of protein-protein interactions and the identification of novel drug targets, in addition to the identification of lead molecules for PPI drug development programmes.

La fonction des protéines de signalisation est déterminée par la nature des domaines qui les composent. Une meilleure compréhension des voies de signalisation passe par l'étude de ces domaines et de leur régulation. PTPN4 est une tyrosine phosphatase qui joue un rôle anti-apoptotique. Lors de l'infection par une souche atténuée du virus de la rage, sa fonction est perturbée, conduisant à la mort des cellules. Cette perturbation est due à l'interaction du motif de reconnaissance au domaine PDZ (PBM) de la glycoprotéine virale avec le domaine PDZ de PTPN4. Nous avons montré que ce domaine PDZ a un rôle d'inhibiteur allostérique de l'activité catalytique de la phosphatase de PTPN4. Ceci représente la première description de la régulation d'une phosphatase par un domaine PDZ. Cette inhibition est levée lors de la fixation d'un ligand au domaine PDZ, tel que le PBM de la glycoprotéine virale. Notre étude structurale révèle que la fixation d'un PBM perturbe les interactions transitoires entre les deux domaines et rétablit ainsi les propriétés catalytiques de la phosphatase. Nous avons par ailleurs identifié un ligand endogène de PTPN4, la MAP Kinase p38 qui, à travers son interaction avec PTPN4, participerait à la régulation de l'homéostasie cellulaire. La formation du complexe implique le recrutement du PBM de p38 par le domaine PDZ de PTPN4. Ainsi, en plus d'avoir une fonction de régulation du domaine phosphatase, le domaine PDZ permet également le recrutement de partenaires et la présentation de substrats au site actif de la phosphatase de PTPN4. Cette étude contribue ainsi à améliorer notre connaissance du rôle des domaines PDZ dans les voies de signalisation cellulaires. / The function of signaling proteins is determined by the nature of the domains from which they are made up. A better understanding of cell signaling pathways will result from the study of these domains and their regulation. PTPN4 is a non-receptor tyrosine phosphatase with an anti-apoptotic function. Upon infection with an attenuated rabies virus, its function is hijacked, which subsequently leads to cell death. This phenotype is arises from the interaction of the PDZ binding motif (PBM) of the viral glycoprotein with the PDZ domain of PTPN4. In this study, we show that this PDZ domain is an allosteric inhibitor of the catalytic activity of the PTPN4 phosphatase domain. This is the first description of the regulation of a phosphatase by a PDZ domain. This inhibition is released by the interaction of a ligand to the PDZ domain, such as the viral glycoprotein PBM. Our structural study revealed that the PBM recognition disrupts the transient inter-domain interactions and restores the complete phosphatase catalytic properties. As well, we identified a PTPN4 endogenous ligand, the MAP Kinase p38, which may participate in the regulation of the cellular homeostatic through its interaction with PTPN4. Thus, in addition to its phosphatase regulatory role, the PDZ domain also allows the recruitment of partners and the introduction of substrates to the PTPN4 phosphatase active site. This study contributes to our understanding of the role played by PDZ domains in cell signaling pathways.

ABCB4/MDR3 est le transporteur canaliculaire de la phosphatidylcholine. Il est exprimé à la membrane canaliculaire des hépatocytes et est essentiel à la sécrétion biliaire. Un défaut d’ABCB4 entraîne des pathologies hépatobiliaires, dont la PFIC3 (cholestase intrahépatique familiale progressive de type 3), caractérisée par une cholestase précoce qui progresse vers la cirrhose et l’insuffisance hépatique avant l’âge adulte. Dans la majorité des cas, la seule thérapie efficace est la transplantation hépatique. Cette thèse s’intéresse aux rôles de l’extrémité C-terminale dans la régulation de la stabilité et l’expression de ce transporteur au canalicule biliaire. Nous avons délété le motif Q-N-L de cette extrémité et montré que cette délétion affecte la stabilité d’ABCB4/MDR3 en augmentant son endocytose. Son interaction avec des protéines à domaines PDZ est alors étudiée. Nous avons montré une interaction par le motif Q-N-L avec la protéine à domaines PDZ, EBP50. Cette interaction est nécessaire pour l’expression canaliculaire et la stabilité du transporteur. / ABCB4 is a phosphatidylcholine translocator specifically expressed at the bile canalicular membrane of hepatocytes. Mutations of the ABCB4 gene cause progressive familial intrahepatic cholestasis type 3 (PFIC3), a rare genetic disease characterized by early onset of cholestasis and evolution to cirrhosis and liver failure before adulthood. Little is known regarding the molecular mechanisms which control the canalicular expression and membrane stabilization of ABCB4 in hepatocytes. The aim of this work was to study the role of the C-terminal domain of ABCB4 for its expression and stability. potential interaction with EBP50, a PDZ protein highly expressed in hepatocytes. The experimental approach consisted in the deletion of the QNL motif at the C-terminus of ABCB4. The truncation of the QNL motif leds to a reduction of ABCB4 stability by increasing its endocytosis. ABCB4 co-precipitated with EBP50, an interaction that required the QNL motif. This interaction plays a critical role in the canalicular expression and stabilization of ABCB4.

Voltage-gated Ca2+ (Cav) channels are activated upon depolarization. They specifically allow Ca2+ ions to come into the cell. These Ca2+ ions are bi-functional because they not only control cell excitability but also couple electrical activity to complex downstream signaling events, such as excitation-contraction coupling in muscles and neurotransmitter release in neurons. In the brain, Cav channels are expressed in the pre- or post-synaptic membrane of most excitable cells, neurons. In the past few years, their expression and function have also been characterized in many nonexcitable cells such as astrocytes. This dissertation focuses on the regulation of one subtype of postsynaptic Cav channels, Cav1.2, in neurons. In the first part of chapter I, I provide a literature overview of Cav channels in terms of their subtypes, localizations, physiological functions, and biophysical properties. For years, Cav channels were studied as single entities. But now, based on multiple proteomic studies, we know that these channels actually do not live alone. They interact with numerous proteins depending on the physiological conditions. Such interactions can anchor the channels to optimal sites of action, and tether Cav channels to their modulatory molecules. Therefore, it is crucial to understand how Cav channels are regulated by their macromolecular assembly. Among these protein partners, our lab studied the regulation of Cav channels by a subset of PDZ-domain containing proteins. Because these proteins play an important role in scaffolding and they colocalize with both pre- and post-synaptic Cav channels. Indeed, previous studies from our lab and other groups have revealed that PDZ proteins participate in a multitude of Cav regulation. The second part of chapter I introduces the diverse modulation of neuronal Cav channels by numerous PDZ proteins. In neurons, Cav1.2 channels regulate neuronal excitability and synaptic plasticity. Their functions have been implicated in learning, memory, and mood regulation. A study published in the journal Lancet showed that the gene encoding Cav1.2 is a common risk factor for five major psychiatric disorders. A PDZ protein, densin-180 (densin) is an excitatory synapse protein that promotes Ca2+-dependent facilitation of voltage-gated Cav1.3 Ca2+ channels in transfected cells. Mice lacking densin exhibit similar behavioral phenotypes that closely match those in mice lacking Cav1.2. In chapter II and III, we investigated the functional impact of densin on Cav1.2 channels and their auxiliary subunit β2a. Besides the regulation of Cav channels by their interactome, we have also known for a long time that Ca2+ currents undergo a negative feedback regulation. This regulation is called Ca2+-dependent inactivation (CDI) and it is mediated by Ca2+ that directly traverses the pore. CDI has been described for Cav channels in multiple cell types. In the heart, CDI prevents excessively long cardiac action potentials, which in turn can prevent activity-dependent arrhythmia. In neurons, CDI may be neuroprotective by preventing excitotoxic Ca2+ overloads. In the last 18 years, two essential components have been revealed in the mechanism of CDI. One is the protein calmodulin (CaM). CaM interacts directly with sites on the C-terminus of Cav channels. It binds to the incoming Ca2+ ions and produces a mysterious conformational change that determines the conductance of the channel. The other molecular player is Cavβ protein family. Cavβ comprises four subfamilies β1 through β4, which generally enhance the channel inactivation, except β2a. In chapter IV, Xiaohan Wang from Roger Colbran’s lab in Vanderbilt University, and I identified a new molecular determinant for Cav1.2 CDI. The α2δ subunit is an extracellular component of the Cav channel complex. Similar to Cavβ subunits, α2δ subunits are essential for the biophysical properties, surface level, and trafficking of Cavα1 subunits. There are four isoforms of α2δ subunits (α2δ1 to α2δ4). They display distinct tissue distributions. Although the roles of α2δ subunits in Cav channel regulation were studied extensively, studies have proposed that the function of α2δ subunits may be in part or entirely independent of Cav channel complex, such as synaptogenesis. Considering the important role of α2δ in physiology and pathology, it is imperative to identify the factors that regulate the properties of α2δ. In chapter V, I explored the trafficking dynamics of α2δ1 and revealed a potential regulator of α2δ1 for its protein stability and localization. One beauty of doing research is that it always motivates us to think and ask more questions on our journey of demystifying nature. While looking at the evidence that I find, I realize how much more we could do in the future. In chapter VI, I conclude the findings of each chapter and share my perspectives on the future direction for these research projects.