Binding proteins are present both in gram-negative and gram-positive bacteria. They are the recognition components of the ABC transport systems that transport different nutrients into the cell, and are in some cases also involved in chemotaxis. In gram-negative bacteria, they are present in the periplasm between the inner and the porous outer membrane. Here, these highly specific proteins can bind to a certain ligand such as ions, sugars and amino acids. The protein-ligand complex can then interact with permeases bound to the inner membrane that transport the nutrient into the cell. Gram-positive bacteria lack an outer membrane and the binding protein must therefore be anchored to the cell membrane. In this thesis different aspects of three members of the super-family of the periplasmic binding proteins have been studied. In the case of the allose-binding protein (ALBP) from E. coli we focused on the movement of the protein when ligand is bound and released. This protein was also compared with the ribose-binding protein (RBP) which belongs to the same structural cluster and from which both open and closed structures are available. The leucine-binding protein (LBP) from E. coli was studied with regards to the structural basis of its specificity for different ligands as well as its conformational changes. The leucine-isoleucine-valine protein has 80% sequence identity with LBP but still exhibits a different preference for ligands. The structure of the maltose-binding protein (MBP) was obtained from a gram-positive thermoacidophile, A. acidocaldarius. Here, our goal was to study acid-stability of proteins. Since little is known about this and structures of the mesophilic counterpart in E. coli are available, as well as structures from two hyperthermophiles, we had an opportunity to study differences in their structural properties that could explain their differing stabilities.

AcrA is the periplasmic component of an efflux system AcrA-AcrB-TolC, which can expel different classes of antibiotics. AcrB is the inner membrane (IM) pump that utilizes proton-motive force for the active transport, TolC is the outer membrane (OM) channel, and AcrA coordinates the actions of AcrB and TolC, so that substrates are expelled across the two membranes, bypassing the periplasm. It has been proposed that AcrA either provides a static seamless link between AcrB and TolC, or acts like its analogous viral membrane fusion protein (MFP) and actively brings the IM and OM closer for substrate transfer. To better understand the role of AcrA in the efflux mechanism, site-directed spin labeling (SDSL)/EPR (electron paramagnetic resonance) spectroscopy is used to investigate the structure and dynamics of AcrA in solution. My results demonstrated that AcrA is a dynamic protein that undergoes pH-dependent and reversible conformational changes. AcrA contains an interrupted alpha-helical, coiled-coil domain flanked by a pair of beta-stranded lipoyl motifs, and my SDSL/EPR analysis revealed that the pH-induced conformation change mainly involves the coiled-coil and the lipoyl domains. In addition, I found that each AcrA monomer folds into an intra-molecular hairpin and AcrA monomers oligomerize with their coiled-coil hairpins aligned in parallel. Unlike the pH-induced conformational rearrangement of a viral MFP, change in pH alters both intra- and inter-molecular interaction along the coiled-coil of AcrA without rearranging the hairpin fold. The organization of AcrA protomers and its pH-induced conformational switching are, however, congruent with the TolC coiled-coil hairpins in the iris-like opening of the TolC channel. Together, my studies suggest that rather than being a passive structural linkage between AcrB and TolC, AcrA plays an active role mediating the drug efflux. The reported AcrA dynamics provides new insights into the AcrA-TolC interactions for the channel opening during the efflux process.

AcrA is the periplasmic component of an efflux system AcrA-AcrB-TolC, which can expel different classes of antibiotics. AcrB is the inner membrane (IM) pump that utilizes proton-motive force for the active transport, TolC is the outer membrane (OM) channel, and AcrA coordinates the actions of AcrB and TolC, so that substrates are expelled across the two membranes, bypassing the periplasm. It has been proposed that AcrA either provides a static seamless link between AcrB and TolC, or acts like its analogous viral membrane fusion protein (MFP) and actively brings the IM and OM closer for substrate transfer. To better understand the role of AcrA in the efflux mechanism, site-directed spin labeling (SDSL)/EPR (electron paramagnetic resonance) spectroscopy is used to investigate the structure and dynamics of AcrA in solution. My results demonstrated that AcrA is a dynamic protein that undergoes pH-dependent and reversible conformational changes. AcrA contains an interrupted alpha-helical, coiled-coil domain flanked by a pair of beta-stranded lipoyl motifs, and my SDSL/EPR analysis revealed that the pH-induced conformation change mainly involves the coiled-coil and the lipoyl domains. In addition, I found that each AcrA monomer folds into an intra-molecular hairpin and AcrA monomers oligomerize with their coiled-coil hairpins aligned in parallel. Unlike the pH-induced conformational rearrangement of a viral MFP, change in pH alters both intra- and inter-molecular interaction along the coiled-coil of AcrA without rearranging the hairpin fold. The organization of AcrA protomers and its pH-induced conformational switching are, however, congruent with the TolC coiled-coil hairpins in the iris-like opening of the TolC channel. Together, my studies suggest that rather than being a passive structural linkage between AcrB and TolC, AcrA plays an active role mediating the drug efflux. The reported AcrA dynamics provides new insights into the AcrA-TolC interactions for the channel opening during the efflux process.

It has been observed that confusion exists in literature concerning the meaning and use of the term efficacy. Confusion is worsened by the use of the term as a general term describing agonist activity. The meaning of the terms intrinsic activity, efficacy and intrinsic efficacy as used in theoretical models of drug action was investigated. The classical occupation model, the two-state model, the ternary complex model (including conformational change and ideas surrounding G-proteins) and the operational model were studied in order to understand the historical and current usage of these terms. Although efficacy estimates are often reported as a molecular property, it was shown that agonist activity is tissue dependent and cannot be fully portrayed by an efficacy estimate. It was found that efficacy has a different definition in each model. This is not always recognized in literature. It was suggested that the term efficacy should only be used in the context of a specific model / Thesis (M.Sc. (Pharmacology))--North-West University, Potchefstroom Campus, 2007.

Le récepteur A des peptides natriurétiques (NPRA) fait partie de la famille des guanylates cyclases membranaires. L’activation du NPRA par ses agonistes naturels, ANP et BNP, induit une production de GMPc qui est responsable de leur rôle dans l’homéostasie cardiovasculaire, l’inhibition de l’hypertrophie et de la fibrose cardiaques et la régulation de la lipolyse. Le NPRA est un homodimère non covalent composé d’un domaine extracellulaire de liaison du ligand (ECD), d’un unique domaine transmembranaire (TM), d’un domaine d’homologie aux kinases et d’un domaine guanylate cyclase. Bien que le NPRA ait un rôle physiologique important, les mécanismes moléculaires régissant son processus d’activation restent inconnus. Nous avons donc analysé les premières étapes du processus d’activation du NPRA. Nous avons d'abord étudié le rôle de la dimérisation des ECD dans l’activation du récepteur. Nous avons utilisé les techniques de liaison de radioligand, de FRET et de modélisation moléculaire, pour caractériser la liaison à l’ECD des agonistes naturels, d’un superagoniste et d’un antagoniste. L’ANP se lie à un dimère d’ECD préformé et la dimérisation spontanée est l’étape limitante du processus de liaison. De plus, comme le démontrent nos études de FRET, tous les peptides, incluant l’antagoniste, stabilisent le récepteur sous sa forme dimérique. Cependant, l’antagoniste A71915 stabilise le dimère d’ECD dans une conformation différente de celle induite par l’ANP. La dimérisation du NPRA semble donc nécessaire, mais non suffisante à l’activation du récepteur. L’état d’activation du NPRA dépend plutôt de l’orientation des sous unités dans le dimère. Nous avons ensuite étudié le mécanisme moléculaire de transduction du signal à travers la membrane. Plusieurs études ont suggéré que l’activation du NPRA implique un changement de conformation du domaine juxtamembranaire (JM). Cependant, les études de cristallographie de l’ECD soluble de NPRA n’ont pas permis de documenter la structure du JM et le changement de conformation impliqué dans la transduction du signal reste inconnu. Pour analyser ce changement de conformation, nous avons d’abord séquentiellement substitué les neuf acides aminés du JM par une cystéine. En étudiant la capacité des mutants à former des dimères covalents de façon constitutive ou induite par l’ANP, nous avons pu évaluer la proximité relative des résidus du JM, avant et après activation du NPRA. Ces résultats ont démontré la proximité élevée de certains résidus spécifiques et sont en contradiction avec les données cristallographiques. Nous avons également démontré que le domaine intracellulaire impose une contrainte conformationnelle au JM à l’état de base, qui est levée après liaison de l’ANP. En introduisant de 1 à 5 alanines dans l’hélice-α transmembranaire, nous avons montré qu’une rotation des TM de 40° induit une activation constitutive du NPRA. Le signal d’activation pourrait donc être transmis à travers la membrane par un mécanisme de rotation des TM. En utilisant nos données expérimentales, nous avons généré le premier modèle moléculaire illustrant la conformation active du NPRA, où les domaines JM et TM sont représentés. Dans son ensemble, cette étude apporte une meilleure compréhension des mécanismes moléculaires régissant les premières étapes du processus complexe d’activation du NPRA. / Natriuretic peptide receptor-A (NPRA) is a member of the particulate guanylate cyclase family. NPRA activation by natural agonists, ANP and BNP, leads to cGMP production, which is responsible for their role in cardiovascular homeostasis, cardiac hypertrophy and fibrosis inhibition and lipolysis regulation. NPRA is a non covalent dimer composed of an extracellular domain (ECD) with a ligand binding site, a single transmembrane region (TM), a kinase homology domain, and a guanylyl cyclase domain. Although NPRA plays an important physiologic role, molecular mecanisms driving its activation process are yet unknown. We thus analysed the first steps of NPRA’s activation process. First, we studied the role of ECD dimerization in receptor activation and determined the sequential steps of this dimerization process. We used radioligand binding, FRET and molecular modeling to characterize the interaction of ECD with natural agonists, a superagonist and an antagonist. ANP binds to preformed ECD dimers and spontaneous dimerization is the rate-limiting step of the ligand binding process. Furthermore, like demonstrated with fluorescence homoquenching, all the studied peptides, including A71915 antagonist, stabilize a dimeric form of the receptor. However, A71915 stabilizes the ECD dimer in a conformation distinct from those induced by ANP. Thus, ECD dimerization is necessary but not sufficient for NPRA activation. The activation state of NPRA seems to depend on the orientation of the receptor subunits within the dimer. Then, we tried to identify the molecular mechanism of signal transduction through the plasma membrane. Previous studies have shown that activation of NPRA involves a conformational change of the juxtamembrane domain (JM). However, crystallographic study of the soluble ECD of NPRA has failed to document JM structure, and the conformational change involved in transmembrane signal transduction is still unknown. To analyse this conformational change, we first sequentially substituted nine amino acids of JM by a cysteine residue. By studying the mutant’s capacity to form ANP-induced or constitutive covalent disulfide dimers, we evaluated the relative proximity of JM residues, before and after NPRA activation. These results demonstrate a high proximity of specific JM residues and are in disagreement with crystallography data. We also demonstrated that intracellular domain imposes a conformational constraint on JM at basal state, which becomes relaxed upon ANP binding. We finally confirmed, with a full-length receptor, that A71915 stabilizes NPRA in a dimeric form where JM are in a conformation distinct from the basal state. By introducing 1 to 5 alanine residues in the transmembrane α-helix, we showed that a TM rotation of 40° leads to constitutive NPRA activation. Activation signal could thus be transmitted through the membrane by a TM rotation mechanism. We finally studied the role of the TM in NPRA dimerization. By using the ToxR system, we demonstrated that the last JM residues are required to stabilize the TM dimer. Using these experimental data, we generated the first molecular model illustrating the active conformation of NPRA, where JM and TM are depicted. In summary, this study allows a better understanding of molecular mecanisms driving the first steps of NPRA’s complex activation process.

Das Hüllglykoprotein Hämagglutinin (HA) von Influenzavirus ist verantwortlich sowohl für die Bindung als auch für die nachfolgende Fusion der viralen Hülle mit der endosomalen Membran. Eine Analyse der 3D Struktur der HA-Ektodomaine zeigt, dass die Stabilität des Proteins sowohl durch kovalente als auch durch nicht-kovalente Wechselwirkungen bedingt ist. Die Konformationsänderung von HA bei saurem pH-Wert weißt auf eine mögliche Rolle von Protonierungseffekten auf ionisierbare Aminosäuren hin. Untersuchungen zur Bedeutung geladener Aminosäuren und Salzbrücken für die Struktur des HA wurden auf der Grundlage von ‚site directed mutagenesis’ durchgeführt. Der Einfluss der Mutationen auf die Konformationsänderung und die Fusionsaktivität von HA wurden durch einen Proteinase K-Assay bzw. Fluoreszenzmikroskopie erfasst. Die Ergebnisse beider Methoden wurden miteinander korreliert. Abgesehen von der Mutante R109E zeigten Wildtyp-HA und alle anderen Mutanten eine vergleichbare Oberflächenexpression. Die beobachteten Unterschiede in der pH-Abhängigkeit der Konformationumwandlung zwischen Wildtyp-HA und HA-Mutanten zeigen, daß eine Zerstörung von Salzbrücken und ggf. eine Erhöhung der elektrostatischen Abstoßung an den betrachteten Kontakstellen sehr wahrscheinlich eine Herabsetzung der energetischen Barriere der Konformationsumwandlung verursacht. Dieser Ergebnisse erklären die molekularen Grundlagen des erhöhten pH-Schwellwertes der HA-Konformationsumwandlung von Amantadin-resistenten Influenzaviren. Im Gegensatz wurde für Mutanten, die die Stabilität von HA erhöhten, keine Konformationsumwandlung bei einem pH-Wert beobachtet, der typisch für die Konformationumwandlung von Wildtyp-HA war. Aminosäuren, die denen dieser stabiliserenden Mutationen entsprachen, wurden in einer natürlichen Influenzavirusvariante – A/JPN/305/57 – gefunden. Die Bedeutung von Ladungen für die Stabilität der HA-Ektodomaine wird dadurch unterstrichen, dass eine Konservierung einer positiven Ladung und insbesondere eines Argininrestes in der Position 109 (Nummerierung auf der Basis von HA X31) für alle Influenzaviren A und B gefunden wurde. Die Ergebnisse der Arbeit zeigen, dass sehr wahrscheinlich eine komplexe Salzbrücke an der Kontaktfläche zwischen HA1 und HA2 für alle Influenzaviren A evolutionär konserviert ist. / Hemagglutinin (HA), a major envelope glycoprotein is responsible for fusing viral and endosomal membranes during influenza virus entry. The analysis of 3D crystal structure of the HA ectodomain shows that the stability of protein is maintained by both non-covalent and covalent interactions. The conformational change of HA at low pH indicates a role for protonation effects of the ionisable amino acids. Structural investigations were done using “site directed mutagenesis” in order to conceive the importance of charged amino acids and more emphatically the involvement of salt bridges. The effect of mutations on the conformational change and fusion activity was probed by proteinase K assay and fluorescence microscopy respectively. It was observed that HA-wt and all the mutants except R109E showed comparable surface expression. The difference in pH threshold between the HA-wt and the mutants showed that breakage of salt bridge and further incorporation of repulsion at the considered interfaces would lower the energy barrier requirements for the conformational change. The results explain the molecular basis of the higher pH threshold for naturally occurring amantadine resistant mutants. On the other hand, mutants designed to stabilise the HA were resistant to conformational changes at those pH values which typically trigger the conformational change of HA-wt. Coincidentally these mutations were found to be existing in the natural variant of H2 Japan subtype (A/JPN/305/57). Interestingly, the study shows that a positive charge and, more specifically, an Arg residue at position 109 (numbering based on X-31 strain) is conserved in all of the influenza A and B viruses underlining the relevance of electrostatic interactions for the HA stability. Aptly a complex salt bridge at the interface of HA1 and HA2 is probably conserved evolutionarily in all the members of influenza A virus.

Cell adhesion plays an important role in inflammation and immunological responses. Adhesion molecules (e.g., selectins and integrins) are key modulators in mediating these cellular responses, such as leukocyte trafficking under shear stress. In this thesis, we use a bio-membrane force probe (BFP) to study force regulation on kinetics and conformations of selectin and LFA-1 integrin. A new BFP was built up, and a new assay, using thermal fluctuation of the BFP, was developed and used to monitoring selectins and their ligands association and dissociations. The new BFP was also used to investigate the force and force history dependence of selectin-ligand interactions. We found tri-phasic transition of force-dependent off-rates and force-history dependence of selectin/ligaind interactions. The BFP was also used to characterize force-dependent lifetimes of the LFA-1-ICAM-1 interaction. We found that LFA-1/ICAM-1 bonds behaved as catch bond and that LFA-1-ICAM-1's catch bonds were abolished blocking the downward movement of αA domain α7 helix. Finally, the BFP was applied to dynamically probe the global conformational changes of LFA-1 and to characterize force-regulated transitions among different conformational states on a living cell. We observed dynamic transitions of LFA-1 between extended and bent conformations on living cells. The observed average distance change of LFA-1's extensions was about 18nm, while that of the bending was only about 14nm. We also found that forces could facilitate extension but they slow down the bending of LFA-1. The observed transition time of extension was less than 0.1s, while that of contraction was longer than 0.2s. Our observations here are the first in-situ evidence to demonstrate how integrins dynamically transit different conformations and how force regulates these transitions.

Le récepteur A des peptides natriurétiques (NPRA) fait partie de la famille des guanylates cyclases membranaires. L’activation du NPRA par ses agonistes naturels, ANP et BNP, induit une production de GMPc qui est responsable de leur rôle dans l’homéostasie cardiovasculaire, l’inhibition de l’hypertrophie et de la fibrose cardiaques et la régulation de la lipolyse. Le NPRA est un homodimère non covalent composé d’un domaine extracellulaire de liaison du ligand (ECD), d’un unique domaine transmembranaire (TM), d’un domaine d’homologie aux kinases et d’un domaine guanylate cyclase. Bien que le NPRA ait un rôle physiologique important, les mécanismes moléculaires régissant son processus d’activation restent inconnus. Nous avons donc analysé les premières étapes du processus d’activation du NPRA. Nous avons d'abord étudié le rôle de la dimérisation des ECD dans l’activation du récepteur. Nous avons utilisé les techniques de liaison de radioligand, de FRET et de modélisation moléculaire, pour caractériser la liaison à l’ECD des agonistes naturels, d’un superagoniste et d’un antagoniste. L’ANP se lie à un dimère d’ECD préformé et la dimérisation spontanée est l’étape limitante du processus de liaison. De plus, comme le démontrent nos études de FRET, tous les peptides, incluant l’antagoniste, stabilisent le récepteur sous sa forme dimérique. Cependant, l’antagoniste A71915 stabilise le dimère d’ECD dans une conformation différente de celle induite par l’ANP. La dimérisation du NPRA semble donc nécessaire, mais non suffisante à l’activation du récepteur. L’état d’activation du NPRA dépend plutôt de l’orientation des sous unités dans le dimère. Nous avons ensuite étudié le mécanisme moléculaire de transduction du signal à travers la membrane. Plusieurs études ont suggéré que l’activation du NPRA implique un changement de conformation du domaine juxtamembranaire (JM). Cependant, les études de cristallographie de l’ECD soluble de NPRA n’ont pas permis de documenter la structure du JM et le changement de conformation impliqué dans la transduction du signal reste inconnu. Pour analyser ce changement de conformation, nous avons d’abord séquentiellement substitué les neuf acides aminés du JM par une cystéine. En étudiant la capacité des mutants à former des dimères covalents de façon constitutive ou induite par l’ANP, nous avons pu évaluer la proximité relative des résidus du JM, avant et après activation du NPRA. Ces résultats ont démontré la proximité élevée de certains résidus spécifiques et sont en contradiction avec les données cristallographiques. Nous avons également démontré que le domaine intracellulaire impose une contrainte conformationnelle au JM à l’état de base, qui est levée après liaison de l’ANP. En introduisant de 1 à 5 alanines dans l’hélice-α transmembranaire, nous avons montré qu’une rotation des TM de 40° induit une activation constitutive du NPRA. Le signal d’activation pourrait donc être transmis à travers la membrane par un mécanisme de rotation des TM. En utilisant nos données expérimentales, nous avons généré le premier modèle moléculaire illustrant la conformation active du NPRA, où les domaines JM et TM sont représentés. Dans son ensemble, cette étude apporte une meilleure compréhension des mécanismes moléculaires régissant les premières étapes du processus complexe d’activation du NPRA. / Natriuretic peptide receptor-A (NPRA) is a member of the particulate guanylate cyclase family. NPRA activation by natural agonists, ANP and BNP, leads to cGMP production, which is responsible for their role in cardiovascular homeostasis, cardiac hypertrophy and fibrosis inhibition and lipolysis regulation. NPRA is a non covalent dimer composed of an extracellular domain (ECD) with a ligand binding site, a single transmembrane region (TM), a kinase homology domain, and a guanylyl cyclase domain. Although NPRA plays an important physiologic role, molecular mecanisms driving its activation process are yet unknown. We thus analysed the first steps of NPRA’s activation process. First, we studied the role of ECD dimerization in receptor activation and determined the sequential steps of this dimerization process. We used radioligand binding, FRET and molecular modeling to characterize the interaction of ECD with natural agonists, a superagonist and an antagonist. ANP binds to preformed ECD dimers and spontaneous dimerization is the rate-limiting step of the ligand binding process. Furthermore, like demonstrated with fluorescence homoquenching, all the studied peptides, including A71915 antagonist, stabilize a dimeric form of the receptor. However, A71915 stabilizes the ECD dimer in a conformation distinct from those induced by ANP. Thus, ECD dimerization is necessary but not sufficient for NPRA activation. The activation state of NPRA seems to depend on the orientation of the receptor subunits within the dimer. Then, we tried to identify the molecular mechanism of signal transduction through the plasma membrane. Previous studies have shown that activation of NPRA involves a conformational change of the juxtamembrane domain (JM). However, crystallographic study of the soluble ECD of NPRA has failed to document JM structure, and the conformational change involved in transmembrane signal transduction is still unknown. To analyse this conformational change, we first sequentially substituted nine amino acids of JM by a cysteine residue. By studying the mutant’s capacity to form ANP-induced or constitutive covalent disulfide dimers, we evaluated the relative proximity of JM residues, before and after NPRA activation. These results demonstrate a high proximity of specific JM residues and are in disagreement with crystallography data. We also demonstrated that intracellular domain imposes a conformational constraint on JM at basal state, which becomes relaxed upon ANP binding. We finally confirmed, with a full-length receptor, that A71915 stabilizes NPRA in a dimeric form where JM are in a conformation distinct from the basal state. By introducing 1 to 5 alanine residues in the transmembrane α-helix, we showed that a TM rotation of 40° leads to constitutive NPRA activation. Activation signal could thus be transmitted through the membrane by a TM rotation mechanism. We finally studied the role of the TM in NPRA dimerization. By using the ToxR system, we demonstrated that the last JM residues are required to stabilize the TM dimer. Using these experimental data, we generated the first molecular model illustrating the active conformation of NPRA, where JM and TM are depicted. In summary, this study allows a better understanding of molecular mecanisms driving the first steps of NPRA’s complex activation process.

No description available.

It has been observed that confusion exists in literature concerning the meaning and use of the term efficacy. Confusion is worsened by the use of the term as a general term describing agonist activity. The meaning of the terms intrinsic activity, efficacy and intrinsic efficacy as used in theoretical models of drug action was investigated. The classical occupation model, the two-state model, the ternary complex model (including conformational change and ideas surrounding G-proteins) and the operational model were studied in order to understand the historical and current usage of these terms. Although efficacy estimates are often reported as a molecular property, it was shown that agonist activity is tissue dependent and cannot be fully portrayed by an efficacy estimate. It was found that efficacy has a different definition in each model. This is not always recognized in literature. It was suggested that the term efficacy should only be used in the context of a specific model / Thesis (M.Sc. (Pharmacology))--North-West University, Potchefstroom Campus, 2007.