Morphine-6-glucuronide is a minor metabolite. representing 5% of an administered dose of morphine. The metabolite has analgesic activity exceeding that of morphine and may contribute to analgesia following morphine administration. The aims of the study were to attempt to identify the reasons behind the improved activity of morphine-6-glucuronide over the parent compound and to examine a series of 6-substituted compounds, based on 6-substituted benzoate esters, as potential mimics of morphine-6-glucuronide. Morphine-6-glucuronide was seen to have similar affinity to morphine at l1-opioid receptors as assessed by ligand-binding assays in mouse brain homogenates. However a three-fold improved affinity at S-opioid receptor binding sites was observed and a ten-fold reduction in affinity at K-opioid sites. Using in vitro bioassay systems the glucuronide showed a two-fold improved potency over morphine in both the guinea-pig ileum and the mouse vas deferens preparations. Following in vivo (s.c.) administration in the mouse the glucuronide was seen to be equipotent with morphine in the tail-flick test, but was of much longer duration, lasting up to 9 hours. Exvivo binding assays confirmed that morphine-like material was still present in the central nervous system six hours after administration of the glucuronide, but was not observed at a similar time after morphine administration. Activity was retained if the hydroxyl groups of the sugar moiety of the glucuronide were protected as esters. In contrast the more prevalent morphine metabolite morphine-3-glucuronide was inactive in all in vitro and in vivo tests used and did not antagonise morphine in vitro or in vivo. A group of 3-substituted derivatives containing saturated and unsaturated substituents did show affinity for opioid receptors but no agonist activity of the compounds could be demonstrated in vitro. A series of synthetic 6-substituted compounds showed a variety of affinities for, and agonist potencies at, opioid receptors, though low affinity at Kopioid receptors was a general finding. For example, morphine-6- nitrobenzoate was l1-opioid receptor preferring, while morphine-6- phthalate had improved O-opioid receptor affinity and acted via Il-opioid receptors in the mouse vas deferens and in vivo. However the compounds were weaker than morphine and the duration of action in vivo was shorter than morphine-6-glucuronide. The conclusions from these studies are that morphine-6-glucuronide and morphine have similar in vitro affinities at the l1-receptor, although morphine-6-glucuronide has somewhat improved binding affinity for Il receptor sites, it has less affinity for K receptor sites. Pharmacokinetic reasons are probably responsible for the improved activity and duration of action of morphine-6-glucuronide over morphine. None of the synthetic compounds examined are potentially useful as direct mimics of the glucuronide because morphine-6-glucuronide is more potent and has a longer duration of action than the synthetic derivatives, though alteration at the 6-position of the morphine nucleus can lead to dramatic changes in selectivity and potency of ligands for the differing opioid receptors.

Hyperpolarization-activated, cyclic-nucleotide gated ion channels (HCN channels) are activated by membrane hyperpolarization and modulated by cyclic nucleotides. HCN channels are important to maintain the resting membrane potential and input resistance in neurons and have important physiological functions in the brain and heart. Four mammalian HCN isoforms, HCN1-4, and the isoform cloned from sea urchin, spHCN, have been extensively studied. Among these, only spHCN channel shows a voltage dependent inactivation. Previous studies have shown that the ligand binding in mHCN2 channel is activity dependent: cAMP binding increases along with channel opening or channels in the open state have higher binding affinity for cAMP. But to date, information pertaining to the ligand binding to an inactivated ion channel or desensitized receptor is lacking. To address this gap, we used fluorescently labelled cAMP analogues in conjunction with patch clamp fluorometry (PCF) to study the ligand binding to the spHCN channel in various conformational states. We show that inactivated spHCN channel shows reduced binding affinity for cAMP, compared to that of the closed or open channel. Parallelly, we noticed significant changes to channel function when a combination of laser and photosensitizer was used to study ligand binding. A reactive oxygen species called singlet oxygen has been confirmed to be the major player in this process. Both photo-dynamically generated and chemically generated singlet oxygen modifies spHCN channel by removing the inactivation. The effect of singlet oxygen on channel can be abolished by the mutation of a key histidine (H462) residue in the ion conducting pore. Taken together, these two projects expanded our understanding about the physicochemical nature of fluorophores from two aspects: (i) the release of photon as a valuable tool to study the conformational dynamics in proteins; (ii) the generation of singlet oxygen as an effective modulator of protein function.

Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. The thermodynamic integration technique is used to calculate pKa values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pKa values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pKa shifts in wild-type and mutant epoxide hydrolase. The calculated pKa values support a model that can explain some of the pH dependent properties of this enzyme. Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase. Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.

In the past 30 years, the discovery of capabilities of nucleic acids far beyond their well-known information-bearing capacity has profoundly influenced our understanding of these polymers. The discovery by the Cech and Altman labs that nucleic acids could perform catalytic functions, coupled with the Gold and Szostak groups’ demonstration of the de novo evolution of nucleic acids that bind arbitrary ligands, has resulted in a proliferation of newfound roles for these molecules. Nucleic acids have found utility in both engineered systems, such as aptamer therapeutics, as well as in newly appreciated roles in extant organisms, such as riboswitches. As a result of these discoveries, many have pondered the potential importance of the dual (catalytic and informational) roles of nucleic acids in early evolution. A high-yielding synthetic route for the nonenzymatic polymerization of nucleic acids, based on the aqueous self-assembly of their components, would provide a powerful tool in nucleic acid chemistry, with potential utility in prebiotic and contemporary nucleic acid systems alike – however, such a route remains elusive. In this thesis, I describe several steps towards such a synthetic route. In these systems, a nucleic-acid binding ligand drives the assembly of short DNA and RNA duplexes, promoting the production of long nucleic acid polymers, while suppressing the production of short, cyclic species. Additionally, the use of a reversible covalent linkage allows for the production of long polymers, as well as the incorporation of previously cyclized products into these polymers. I also report several explorations of novel base pairings, nucleic acid-ligand interactions, and nucleic acid-ion interactions that have informed our studies of self-assembling nucleic acid systems.

Ligand-gated ion channels couple intra- and extracellular chemical signals to cellular excitability. In response to a specific ligand, these channels change their permeability to certain ions by opening or closing their ion conductive pathway, a controlling mechanism known as channel gating. Although recent studies with X-ray crystallography and site-directed mutagenesis have revealed several structures potentially important for channel gating, the gating mechanism is still elusive. Ligand-dependent channel gating involves a series of transient events and asymmetric movements of individual subunits. Understanding of these events appears to be a challenge to current approaches in gating studies by using the homomeric wild-type or mutant channels. I therefore took an alternative approach by constructing heteromeric channels. Subunit stoichiometric studies of the Kir1.1 channel showed that a minimum of one functional subunit was required for the pH-dependent gating of the channel. Four subunits in this channel were coordinated as dynamic functional dimers. In Kir6.2 channel, stoichiometry for proton-binding was almost identical to that for channel gating in the M2 helix, suggesting a one-to-one direct coupling of proton binding in C-terminus to channel gating in M2 helix. Positive cooperativity was suggested among subunits in both the proton binding and channel gating. Ligand binding can be differentiated from channel gating by studying the ATP-dependent gating of Kir6.2 channel. Disruptions in ATP binding were found to change both the potency and efficacy of the concentration-dependent curves, while the baseline activity instead of maximum inhibition was affected by disruptions of channel gating. Four subunits in the Kir6.2 channel undergo negative cooperativity in ATP binding and positive cooperativity in channel gating. The ligand binding was coupled to the gating mechanism in the same subunit and neighboring subunits, although the intrasubunit coupling was more effective. These results are well described with the operational model which we have applied to ion channel studies for the first time. By manipulating the relative distance and the interaction of two transmembrane helices, the inner helix bundle of crossing was found to not only serve as a gate but also determine the consequence of ligand binding.

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.

This thesis describes studies directed towards understanding structure-function relationships of triosephosphate isomerase (TIM), from a protozoan parasite Plasmodium falciparum and a thermophilic archaea Methanocaldococcus jannaschii. Triosephosphate isomerase, a ubiquitous glycolytic enzyme, has been the subject of biochemical, enzymatic and structural studies for the last five decades. Studies on TIM have been central to the development of mechanistic enzymology. The present study investigates the role of specific residues in the structure and function of Plasmodium falciparum triosephosphate isomerase (PfTIM). The structure and stability of a tetrameric triosephosphate isomerase from Methanocaldococcus jannaschii (MjTIM) is also presented. Chapter 1 provides a general introduction to the glycolytic enzyme triosephosphate isomerase, conservation of TIM sequences, its fold and three dimensional organization. The isomerisation reaction interconverting dihydroxyacetone phosphate and glyceraldehyde 3phosphate catalyzed by triosephosphate isomerase is an example of a highly stereospecific proton transfer process (Hall & Knowles, 1975; Rieder & Rose, 1959). This chapter briefly reviews mechanistic features and discusses the role of active site residues and the functional flexible loop 6. Triosephosphate isomerase adopts the widely occurring ( β/ α)8 barrel fold and mostly occurs as a dimer (Banner et al., 1975). Protein engineering studies, related to folding, stability and design of monomeric TIM are also addressed. A brief introduction to thermophilic TIMs and higher oligomeric TIMs is given. The role of this enzyme in disease states like hemolytic anemia and neuromuscular dysfunction is surveyed. The production of methylglyoxal, a toxic metabolite, as a byproduct of the TIM reaction is also considered. Many proteins utilize segmental motions to catalyze a specific reaction. The omega loop (loop 6) of triosephosphate isomerase is important for preventing the ene-diol intermediate from forming the cytotoxic byproduct, methylglyoxal. The active site loop-6 of triosephosphate isomerase moves about 7Ǻ on ligand binding. It exhibits a hinged lid motion alternating between two well defined, “open” and “closed”, conformations (Joseph et al., 1990). Though the movement of loop 6 is not ligand gated, in crystals the ligand bound forms invariably reveal a closed loop conformation. Plasmodium falciparum TIM is an exception which predominantly exhibits “open” loop conformations, even in the ligand bound state (Parthasarathy et al., 2002). Phe 96 is a key residue that is involved in contacts between the flexible loop-6 and the protein body in PfTIM. Notably, in all TIM sequences determined thus far, with the exception of plasmodial sequences, this residue is Ser 96. In Chapter 2 the mutants F96S, F96H and F96W are reported. The crystal structures of the mutant enzymes with or without bound ligand are described. In all the ligand free cases, loop-6 adopts an “open” conformation. Kinetic parameters for all the mutants establish that residue 96 does not play an essential role in modulating the loop conformation but may be important for ligand binding. Structural analysis of the mutants along with WT enzyme reveals the presence of a water network which can modulate ligand binding. Subunit interfaces of oligomeric proteins provide an opportunity to understand protein- protein interactions. Chapter 3 describes biochemical and biophysical studies on two separate dimer-interface destabilizing mutants C13E and W11F/W168F/Y74W of PfTIM. The intention was to generate a stable monomer by disrupting the interaction hubs. C13 is a part of a large hydrophobic patch (Maithal et al., 2002a) at the dimer interface. Introduction of a negative charge at position 13 destabilizes the interface and reduces activity. Y74 is a part of an aromatic cluster of the interface (Maithal et al., 2002b). The Y74W triple mutant was designed to disrupt the aromatic cluster by introducing additional atoms. Tryptophan is also a fluorophore, allowing studies of the dimer disruption by fluorescence, after mutating the two inherent tryptophan residues, W11 and W168 to phenylalanine. The mutants showed reduced activity and were more sensitive than the wild type enzyme to chemical denaturants as well as thermal denaturation. Evidenced for monomer formation is presented. These studies together with previous work reveal that the interface is important for both activity and stability. In order to develop a model for understanding the relationship between protein stabilization and oligomeric status, characterization of the TIM from Methanocaldococcus jannaschii (MjTIM) has been undertaken. Chapter 4 describes the purification and characterization of MjTIM. The MjTIM gene was cloned and expressed in pTrc99A and protein was isolated from AA200 E. coli cells. Hyperexpressed protein was purified to homogeneity and relevant kinetic parameters have been determined. The tetrameric nature of MjTIM is established by gel filtration studies. Circular dichroism (CD) studies establish the stability of the overall fold, even at temperatures as high as 95ºC. A surprising loss of enzyme activity upon prolonged incubation at high temperature was observed. ESI-MS studies establish that oxidation of thiol groups of the protein may be responsible for the thermal inactivation. Chapter 5 describes the molecular structure of MjTIM, determined in collaboration with Prof. MRN Murthy’s group at the Indian Institute of Science (Gayathri et al., 2007). The crystal structure of the recombinant triosephosphate isomerase (TIM) from the archaeabacteria Methanocaldococcus jannaschii has been determined at a resolution of 2.3 Å. MjTIM is tetrameric, as suggested by solution studies and from the crystal structure, as in the case of two other structurally characterised archaeal TIMs. The archaeabacterial TIMs are shorter compared to the dimeric TIMs, with the insertions in the dimeric TIMs occurring in the vicinity of the putative tetramer interface, resulting in a hindrance to tetramerization in the dimeric TIMs. The charge distribution on the surface of archaeal TIMs also facilitates tetramerization. Analysis of the barrel interactions in TIMs suggests that these interactions are unlikely to account for the thermal stability of archaeal TIMs. A feature of the unliganded structure of MjTIM is the complete absence of electron density for the loop 6 residues. The disorder of the loop may be ascribed to a missing salt bridge between residues at the N- and C- terminal ends of the loop in MjTIM. Chapter 6 is a follow up of an interesting observation made by Vogel and Chmielewski (1994), who noticed that subtilisin cleaved rabbit muscle triosephosphate isomerase religated spontaneously upon addition of organic solvents. Further extension of this nicking and religation process with PfTIM emphasizes the importance of tertiary interactions in contributing to the stability of the (β/α)8 barrel folds (Ray et al., 1999). This chapter establishes that subtilisin nicking and religation is also facile in thermophilic MjTIM. Fragments generated by subtilisin nicking were identified using MALDI mass spectrometry at early and late stages of the cleavage for both the dimeric PfTIM and tetrameric MjTIM. This chapter also describes the comparative thermal and denaturant stability of both the enzymes. The accessibility of the Cys residues of MjTIM has been probed by examining the rates of labeling of thiol groups by iodoacetamide. The differential labeling of Cys residues has been demonstrated by mass spectrometry. Chapter 7 summarizes the main results and conclusions of the studies described in this thesis.

El trabajo presentado en esta tesis cubre varios campos de investigación relacionados con el desarrollo de moléculas bioactivas. Se compone de cinco partes distintas que se resumen aquí. Predicción de la utilidad farmacológica de dianas terapéuticas. El desarrollo de fármacos está generalmente dirigido a inhibir la función de una proteína específica. Pero para validar esta proteína como diana terapéutica, al principio de un proyecto de descubrimiento de fármacos se tiene que saber si una molécula de tipo fármaco puede unirse con suficiente afinidad a la proteína como para alterar su función. Existen métodos que predicen si una potencial diana terapéutica es tratable o no por vía farmacológica, lo que se ha dado en llamar ‘druggability’. El problema es que estos métodos no están accesibles libremente y su validación es discutible. En la primera parte de la tesis se ha compilado un conjunto extensivo de datos de cavidades en proteínas cuyo novel de ‘druggability’ es conocido, haciéndolo accesible en una plataforma web pública (http://fpocket.sourceforge.net/dcd). Estos datos pueden ser modificados por cualquier persona que quiera contribuir al desarrollo de este conjunto de datos, aumentando su volumen o mejorando su calidad. En estudios previos, los sitios druggable se han asociado a cavidades profundas e hidrofóbicas, ignorando la importancia que tiene los grupos polares en el sitio de unión y su posible relación con la ‘druggability’. Utilizando el set de datos compilado previamente, hemos encontrado que aunque las cavidades ‘druggables’ son mas hidrofóbicas, también tienen grupos polares más expuestos pero con poca superficie de interacción. Esta observación es objeto de posteriores investigaciones en la segunda parte de la tesis. Finalmente, se ha utilizado un algoritmo de búsqueda de sitios de unión, fpocket, que empecé a desarrollar como proyecto de master. Este programa se ha utilizado para extraer todas las características de las cavidades ‘druggables’ y no ‘druggables’ y estos parámetros se han utilizado para entrenar un modelo logístico capaz de predecir si un sitio es druggable o no. Demostramos que el algoritmo y la función de puntuación desarrollado durante esta primera parte predice la ‘druggability’ de manera fiable. Los resultados son de igual calidad a los obtenidos con el único otro programa accesible con funcionalidad parecida (SiteFinder, de Schrödinger), pero nuestro programa tiene las siguientes importantes ventajas: 1) es libre; 2) es mucho más eficiente computacionalmente; y 3) trabaja sobre cavidades detectadas automáticamente por el programa, lo que permite aplicaciones a gran escala. En otras partes de la tesis se verá como su aplicación al conjunto del PDB permite novedosas aplicaciones en el área del diseño de fármacos. Análisis de movilidad de cavidades de las proteínas Existen una gran variedad de algoritmos que permiten identificar posibles sitios de unión en las estructuras tridimensionales de las proteínas. El trabajo presentado en la sección anterior de esta tesis permitía extender uno de estos algoritmos para caracterizar la ‘druggability’ de las cavidades. Un problema de gran calado en el estado actual de la técnica, tanto de detección de sitios de unión como en diseño de fármacos en general,4 es que las proteínas se tratan como un cuerpo rígido a pesar de que en realidad gozan de una gran movilidad estructural. El objetivo de esta sección era otorgar todavía otra funcionalidad a fpocket, el programa de predicción de sitios de unión, para permitir también la detección y el análisis de cavidades de proteínas en movimiento. Habitualmente, los movimientos de las proteína se pueden simular usando la dinámica molecular (MD). Una herramienta capaz de analizar conjuntos de estructuras derivados de MD u otras fuentes puede ser, por tanto, extremadamente útil para observar la aparición de cavidades transitorias y su plasticidad. Como resultado final de este trabajo, se presenta un nuevo programa informático, llamado MDpocket y que se enmarca dentro del paquete fpocket. Para cada conformación de la proteína, se ejecuta un ciclo de detección de cavidades con fpocket. Los resultados de este proceso se plasman sobre una malla tridimensional superpuesta a la estructura de la proteína. La malla puede entonces ser visualizada o analizada en mayor detalle. Lo primero se puede llevar a cabo con programas de visualización molecular tales como PyMOL, VMD o Chimera. Otra funcionalidad dentro de MDpocket es la de seguir la evolución de las propiedades de una cavidad o zona de interés (definida por el usuario) a lo largo del tiempo. Cabe destacar que MDpocket es igualmente capaz de identificar sitios de unión de moléculas tipo fármaco como pequeños canales en la matriz proteica que pueden ser importantes para la migración de pequeños ligandos como gases o moléculas de agua. Las posibles aplicaciones de MDpocket se ejemplifican en tres casos distintos. El primero es la capacidad de identificar la apertura transitoria de cavidades en el sitio de unión de ATP en la proteína HSP90. En el segundo ejemplo, se muestra como MDpocket permite identificar un canal de migración de moléculas biatómicas en mioglobina, un sistema de referencia bien conocido. Aquí se demuestra que MDpocket puede, no tan solo identificar los sitios internos de unión a Xenón, sino también los canales que se abren de forma transitoria para permitir a los ligandos migrar de un sitio a otro. En el último ejemplo, las propiedades del sitio de unión a ATP de la proteína cinasa P38 se analizaron a lo largo de una trayectoria de MD, evaluando la capacidad de MDpocket para identificar aquellas conformaciones que pueden ser particularmente útiles para realizar docking molecular. Uno de los principales problemas en docking de proteína-ligando es que el receptor generalmente se considera rígido, mientras que si se utilizan múltiples conformaciones (cristalográficas o derivadas de MD) para representar al receptor es difícil decidir a priori cuales de ellas pueden dar mejores resultados. Aquí mostramos que MDpocket se puede utilizar para seleccionar conformaciones concretas de una trayectoria de MD para usarlas en procesos de docking. Concretamente, hemos observado que la densidad hidrofóbica promedio (previamente identificada como un descriptor importante para predecir ‘druggability’) correlaciona bien con la probabilidad de que el modo de unión de ligandos pueda ser predicho correctamente. Tal como en el trabajo anterior, MDpocket se incluye dentro del proyecto fpocket y se está accesible como una herramienta libre y de código abierto. Relaciones estructura-cinética de unión El control de los tiempos en interacciones moleculares es una propiedad esencial de los sistemas bioquímicos, pero poco se conoce sobre los factores estructurales que gobiernan la cinética de los procesos de reconocimiento molecular. Partiendo de una observación realizada durante el trabajo de predicción de ‘druggability’, aquí se ha investigado el papel que átomos con poca superficie expuesta a solvente pueden jugar en los sitios de unión de la proteína. En particular, encontramos que los átomos polares en los sitios druggable son minoritarios en comparación con los átomos apolares, pero si bien pueden tener poca superficie accesible, tienden a ser mas protuberantes, lo que los hace más accesibles para establecer interacciones. Hemos establecido que esta propiedad puede estar relacionada con la cinética de unión/disociación de un ligando a su cavidad en el receptor. En diseño de fármacos, la vida media del complejo formado entre el fármaco y su diana terapéutica determina en gran medida sus efectos biológicos, pero en ausencia de relaciones estructura cinética, se hace imposible optimizar esta propiedad de forma racional. Aquí se muestra que átomos polares prácticamente enterrados (ABPAs) – un elemento comúnmente encontrado en los sitios de unión de proteínas – tienden a formar puentes de hidrógeno que están protegidos de las moléculas de agua. La formación y ruptura de este tipo de puentes de hidrógeno implica un estado de transición penalizado energéticamente porque ocurre de modo asincrónico con el proceso de deshidratación/rehidratación. En consecuencia, los puentes de hidrógeno protegidos se intercambian a velocidades lentas. Estas conclusiones se basan en el estudio computacional del proceso de unión de un pequeño ligando a un sitio de unión modelo. El receptor modelo se construyó para permitir modular tanto el grado de exposición del átomo polar como la curvatura del entorno apolar. Mediante el uso de dinámicas moleculares con constricciones y la relación de Jarzinsky, se obtuvieron los perfiles de energía libre de unión para cada cavidad. La presencia de un estado de transición (y por tanto menor velocidad de asociación/disociación) puede anticiparse mediante un simple análisis estructural tal como la medición de la superficie accesible del átomo polar o su grado de protrusión. Esto constituye una nueva y valiosa clave para interpretar y predecir relaciones estructura-actividad, que se ha puesto a prueba investigando sistemas reales. En primer lugar, analizando tanto estructuras cristalográficas depositadas en el PDB como trayectorias de dinámica molecular, se ha demostrado que aquellas moléculas de agua que forman puentes de hidrógeno con ABPAs tienden a tener menor movilidad e intercambios más lentos. Posteriormente, la validez del principio se ha demostrado en dos pares de inhibidores de la proteína Hsp90, una diana terapéutica para cáncer, para los que se han obtenido datos estructurales, termodinámicos y cinéticos mediante distintas técnicas experimentales. El acuerdo entre observables macroscópicas y los resultados de simulaciones moleculares confirma la función de los puentes de hidrógeno protegidos de solvente como trampas cinéticas e ilustra como nuestro hallazgo puede ser usado para facilitar el proceso de diseño de fármacos basado en estructura. Base de datos de cavidades: hacia el ‘pocketoma’ El trabajo presentado en el principio de la tesis perseguía un objetivo muy especifico, que se enmarca en un proyecto mayor del grupo de investigación. La herramienta de predicción de ‘druggability’ se desarrolló con el fin de cribar grandes bases de datos estructurales, tales como el PDB, identificando complejos proteína-proteína no obligados (transitorios) que contengan en su interfase una cavidad potencialmente capaz de unir moléculas de tipo fármaco. Con ello se pretende estabilizar selectivamente dicha interacción y conseguir un efecto biológico que pueda ser terapéutico. Dado que la información sobre cavidades y su druggability asociada va a ser explotadas por otras personas en el grupo en este y otro tipo de proyectos encaminados a facilitar la explotación de nuevos mecanismos de acción, es necesario crear una base de datos que contenga esta información y sea fácilmente navegable. Para empezar, se ejecutó el programa para cada una de las estructuras depositadas en el PDB, identificando todas las cavidades y extrayendo sus descriptores, entre los que se incluye la función de puntuación de druggability. Esta información se guarda de forma organizada en una base de datos relacional (pocketDB), que se relaciona con otras bases de datos tales como Uniprot y Uniref, que contienen información sobre secuencias. Igualmente, se incluyeron información sobre la estructura cuaternaria y otros recursos tales como Kegg, haciendo de pocketDB un potente recurso para filtrar de modo eficiente millones de cavidades, identificando aquellas que tengan mayor interés para cada proyecto. De modo particular, cabe destacar la aplicación de pocketDB a la identificación de cavidades ‘druggable’ situadas en la interfase de complejos transitorios proteína-proteína, resultando en 39 complejos candidatos, entre los que se recobraron 3 casos conocidos previamente, lo que valida la metodología. Además otros tres sistemas identificados, después de una inspección minuciosa, han sido seleccionados en el grupo como candidatos para realizar la prueba de concepto que valide esta nueva estrategia farmacológica. Uno de ellos está actualmente en fase de validación experimental. El ‘pocketoma’ La última sección de mi tesis presenta un proyecto que hace un uso extensivo de la base de datos de cavidades (pocketDB) previamente presentada. Dos cuestiones importantes aún persisten hoy día en el proceso de descubrimiento de fármacos y, de algún modo, contribuyen a la alta tasa de fracasos en las fases tardías del desarrollo, que normalmente se explican por la baja eficacia o el exceso de efectos secundarios (normalmente tóxicos) para el organismo. Ambas situaciones pueden ser explicadas por un fenómeno común: la falta de selectividad. Las fármacos interaccionan en la célula con una diversa variedad de macromoléculas además de con la diana terapéutica, induciendo así efectos secundarios imprevistos. Asimismo, considerar solamente una diana para nuestro fármaco puede resultar menos efectivo de lo esperado, puesto que la pérdida de función de una sola proteína diana puede ser fácilmente reemplazada debido a los mecanismos homeostáticos controlados por robustas redes de interacciones, derivando en una pérdida de eficacia de nuestra molécula. Este trabajo pretende sentar las bases para poder establecer relaciones entre macromoléculas biológicas en base a su potencial para interaccionar con una misma entidad química (fármaco). El trabajo se basa en la asunción de que cavidades similares son capaces de unir ligandos similares. Existen varios métodos que calculan la similitud entre cavidades de unión, sin embargo, hasta la fecha no se ha realizado un análisis relacional profundo de todas las cavidades en el PDB que permita establecer relaciones entre ellos. Con el fin de cumplir con los requerimientos técnicos de unos objetivos tan ambiciosos, se ha desarrollado un novedoso método de comparación de cavidades. En este particular método se considera una representación muy abstracta de la cavidad. Dicha representación reúne información tanto sobre la forma de la cavidad cómo sobre la distribución por pares de los puntos de interacción en la superficie. No obstante, la información sobre la topología exacta de la cavidad es ignorada. Tal abstracción intenta relacionar cavidades que estructuralmente están alejadas, pero que se parecen entre ellas en términos de forma y propiedades fisicoquímicas globales. Usando varios ejemplos de validación en un conjunto de cavidades de referencia, el método resulta capaz de recuperar de un gran set de cavidades aquellas más similares y relacionadas entre sí. Del mismo modo, el método demuestra ser útil para encontrar relaciones entre cavidades previamente no relacionadas y que sin embargo unen los mismos ligandos o moléculas muy similares. Esta nueva implementación se ha utilizado en un experimento de exploración a gran escala para encontrar (i) las mismas cavidades en diferentes estructuras, (ii) cavidades relacionadas y (iii) cavidades con la misma estructura de ligando. Se obtuvieron excelentes resultados para estas tres categorías. Seguidamente, se compararon entre ellas todas las cavidades encontradas en el PDB. Se desarrolló una herramienta computacional novedosa para permitir la navegación en el 'pocketoma' resultante de las comparaciones, que será posible descargar gratuitamente. Los resultados presentados muestran por primera vez un espacio global interrelacionando cavidad-ligando para todas las cavidades del PDB. Finalmente, se señalan a continuación dos aplicaciones que ponen de manifiesto el posible impacto del ‘pocketoma’ y la herramienta de navegación. En el primer ejemplo, una cavidad no caracterizada encontrada en GSK3-β fue comparada contra todas las cavidades del PDB, permitiendo obtener una variedad de cavidades, y sistemas, supuestamente relacionadas. Entre los resultados se encontraban las subunidades de unión a ADP dhaL y dhaM de la PTS dependiente di-hidroacetona cinasa. Se encontró que el sitio de unión a ADP era muy similar a la cavidad investigada en GSK3-β con una sorprendente similitud estructural entre ambos. En el último ejemplo, se navegó por el ‘pocketoma’ utilizando la herramienta visual desarrollada para tal tarea. Durante la exploración se encontró una curiosa e importante relación entre el sitio de unión de la hormona del receptor de estrógenos y una cavidad no caracterizada en la proteína Caspasa-3. Seguidamente, se realizó un estudio de docking con ligandos similares a la hormona y se procedió a realizar una extensiva dinámica molecular con el ligando en la mejor posición para verificar la estabilidad del compuesto en la cavidad de Caspasa-3. El complejo proteína-ligando estudiado resultó ser muy estable. Actualmente, el compuesto identificado se encuentra bajo validación experimental por nuestros colaboradores.

Disulfides are the primary covalent interactions within a protein molecule that connect residues which are sequentially distant. Naturally occurring disulfides enhance the stability of the protein by destabilization of the unfolded state. Previous attempts to introduce disulfide bridges as a means to enhance protein stability have met with mixed results. Tools have been developed to predict potential sites for disulfide introduction. However, it must be noted that engineering disulfides is not a trivial task. The effect of the engineered disulfide on protein stability is difficult to predict. There have been few systematic studies carried out to study disulfides in the context of secondary structures. The work in this thesis is aimed at studying disulfides in two kinds of secondary structures- antiparallel β-sheets and helices. In particular, the focus in this thesis is on cross-strand disulfides in antiparallel β-sheets and intrahelical disulfides. The analysis of naturally occurring disulfides in these structural elements coupled with protein engineering studies in model proteins were used to understand the effects of introducing disulfides in helices and antiparallel β-sheets. Synopsis This thesis also includes studies carried out on molten globules of four periplasmic binding proteins of E.coli- Maltose binding protein (MBP), Leucine, isoleucine, valine binding protein (LIVBP), Leucine binding protein (LBP) and Ribose binding protein (RBP). Work carried out in the lab previously had shown that these molten globules can bind the ligands that the proteins do in their corresponding native states. The analysis of the thermodynamic data obtained for these molten globules by differential scanning calorimetry (DSC) studies and isothermal titration calorimetry (ITC) to characterize stability and ligand binding respectively are described in this thesis. To further study the structural features of molten globules by fluorescence resonance energy transfer (FRET), double cysteine mutants of MBP were constructed and characterized. The rationale behind the construction of these mutants and their characterization is reported. Chapter 1 gives an introduction to disulfides in proteins. Previous attempts at cataloguing and characterizing naturally occurring disulfides are described. An overview of studies carried out to determine the effects of removal of naturally occurring disulfides in proteins and the effect of engineered disulfides in different proteins is given. The various tools developed to predict potential disulfide sites are described. Chapter 1 also briefly discusses various aspects of molten globules and FRET. Chapters 2 and 3 involve studies with cross-strand disulfides occurring in antiparallel β-sheets. A detailed analysis on various stereochemical aspects of naturally occurring cross-strand disulfides is described in Chapter 2. The reasons for these disulfides to almost exclusively occur at non-hydrogen-bonded registered pairs have been explored with conformational analysis, modeling studies and energy calculations. In Chapter 3, the effect of engineering cross-strand disulfides in four model proteins- LBP, LIVBP, MBP and Top7 are described. The ease of formation of the introduced disulfides and their effects on protein stability are described. The proteins with engineered cross-strand disulfides at exposed positions were also examined for redox activity. Our studies have shown that in antiparallel strands, engineered disulfides at exposed NHB registered pairs provide a robust means of increasing protein stability. In Chapters 4 and 5, studies about intrahelical disulfides are described. In Chapter 4, the various conformational aspects of intrahelical disulfides occurring naturally are studied. Analysis of structures of proteins in conjunction with modeling studies show that all naturally occurring intrahelical residues bridge cysteines occurring between the N-Cap and 3rd residue of helices. To further explore conformational requirements for intrahelical disulfides, Cys pairs were introduced at N-terminal and interior of helices in a E.coli thioredoxin mutant lacking its active site disulfide. The ease of formation of the engineered disulfides, and their effects on protein stability were studied. The redox activity of the engineered disulfides was also examined. The studies demonstrated that intrahelical disulfides can only occur at the N-terminus of an α-helix and that the N-terminal CYS residue must adopt a non-helical backbone conformation. Although none of the engineered intrahelical disulfides increased the stability of the protein, they conferred mild redox activity. In Chapter 5, the ability of an engineered CXXC motif to bind Zn(II) is also explored. The effect of Zn(II) on the stability of the reduced and oxidized states of an engineered protein with a N-terminal intrahelical CXXC was ascertained. I have also shown that iminodiacetate (IDA) and nitrilotriacetate (NTA) resins charged with zinc can bind the protein CGPC 95-98 in reduced state. These Synopsis preliminary experiments on metal binding show that this property of CXXC motif could be exploited to develop a protein purification method. In Chapter 6, thermodynamic characterization of molten globules of four periplasmic binding proteins (LBP, LIVBP, MBP and RBP) is described. Studies had been previously carried out in the lab to characterize the stability and ligand binding of these molten globules. All four molten globules were found to bind their corresponding ligands without conversion to the native state. In Chapter 6, the estimation of ΔCp of unfolding and ligand binding from the DSC and ITC data is described. The binding of molten globules to their ligands and the ability to undego cooperative thermal unfolding indicated the presence of native protein-like tertiary contacts. To study the molten globule structure, we decided to construct double cysteine mutants of MBP for FRET studies. We decided to employ a strategy for differential labeling of the two cysteines with two different fluorophores based on the conformational differences between MBP in the ligand bound and free forms. Seven double cysteine mutants of MBP were made. The rationale behind the construction of these mutants and their preliminary characterization is described in the appendix to Chapter 6. The optimization of the differential labeling procedure of the MBP double mutants needs to be fine-tuned before further studies through FRET. The work described in this thesis has resulted in the following publications: 1.Prajapati RS, Indu S, Varadarajan R. Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins. Biochemistry. 2007 (46):10339-52. 1 Indu S, Kumar ST, Thakurela S, Gupta M, Bhaskara RM, Ramakrishnan C, Varadarajan R. Disulfide conformation and design at helix N-termini. Proteins.2010 (78):1228-42. 2 Indu S, Kochat V, Thakurela S, Ramakrishnan C, Varadarajan R. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. (Manuscript submitted)

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.