Οι νικοτινικοί υποδοχείς της ακετυλοχολίνης (nAChRs) ανήκουν στην υπερ-οικογένεια των ιοντικών καναλιών που ενεργοποιούνται από τη δέσμευση ενός προσδέτη (LGICs) και αποτελούνται από πέντε ομόλογες υπομονάδες. Κάθε μονομερής υπομονάδα αποτελείται από μία Ν-τελική εξωκυττάρια περιοχή (ΕΚΠ), από τέσσερεις διαμεμβρανικές α-έλικες και από μία κυτταροπλασματική περιοχή. Στην ΕΚΠ βρίσκεται η χαρακτηριστική Cys-θηλιά της υπερ-οικογένειας, καθώς και οι θέσεις πρόσδεσης αγωνιστών και ανταγωνιστών του υποδοχέα. Οι γνώσεις μας γύρω από τη δομή των nAChRs προέρχονται κυρίως από κρυσταλλογραφικές δομές ομολόγων πρωτεϊνών δέσμευσης της ACh (AChBP) μαλακίων, από μια δομή του nAChR από ιχθείς του γένους Torpedo που προέρχεται από ηλεκτρονική μικροσκοπία, από την κρυσταλλογραφική δομή της α1-ΕΚΠ ποντικού σε σύμπλοκο με α-μπουγκαροτοξίνη (α-Btx) και από κρυσταλλογραφικές δομές δύο προκαρυωτικών LGICs. Παρά τη μεγάλη πρόοδο που πραγματοποιήθηκε με τα παραπάνω επιτεύγματα, ακόμη δεν έχει επιλυθεί πειραματικά η δομή ανθρώπινου υποδοχέα. Επίσης λίγα είναι γνωστά για την επίδραση της γλυκοζυλίωσης των ΕΚΠ στη λειτουργία του nAChR. Χρησιμοποιώντας ως εκμαγείο την κρυσταλλογραφική δομή του συμπλόκου α1-ΕΚΠ ποντικού/α-Btx δημιουργήθηκαν υπολογιστικά μοντέλα της ανθρώπινης α1-ΕΚΠ προσδεμένης στις τοξίνες α-μπουγκαροτοξίνη (α-Btx), α-κομπρατοξίνη (α-Cbtx), α-κωνοτοξίνη (α-Ctx) ImI και α-κωνοτοξίνη GI. Στα σύμπλοκα με α-Btx και α-Cbtx προστέθηκε η υδατανθρακική αλυσίδα, συνδεδεμένη με το κατάλοιπο Asn141, που συγκρυσταλλώθηκε μαζί με την α1-ΕΚΠ ποντικού. Για να μελετηθεί η δυναμική συμπεριφορά της αλληλεπίδρασης υποδοχέα-τοξίνης καθώς και η συνεισφορά των σακχάρων σε αυτήν πραγματοποιήθηκαν προσομοιώσεις Μοριακής Δυναμικής σε υδατικό περιβάλλον. Με τη χρήση υπολογιστικών εργαλείων για τη μελέτη των συμπλόκων προσδιορίστηκαν σε ατομικό επίπεδο οι αλληλεπιδράσεις που καθοδηγούν την πρόσδεση τοξινών στην α1-ΕΚΠ. Βρέθηκε ότι η υδατανθρακική αλυσίδα συμμετέχει δυναμικά στη δέσμευση της τοξίνης στον υποδοχέα. Τα σάκχαρα συγκλίνουν προς την προσδεμένη τοξίνη στηριζόμενα στα κατάλοιπα Ser187 και Trp184 της α1 υπομονάδας. Η τοξίνη επίσης μετακινείται φέρνοντας τη θηλιά Ι σε επαφή με τα σάκχαρα. Αναγνωρίστηκαν σημαντικές αλληλεπιδράσεις των σακχάρων με τα τοξινικά κατάλοιπα Thr6, Ser9, και Th15 της α-Btx και Thr6 και Pro7 της α-Cbtx. Επίσης επιβεβαιώθηκε η ύπαρξη μιας υδρόφιλης κοιλότητας στο εσωτερικό του υδρόφοβου πυρήνα της α1-ΕΚΠ, η οποία πιθανόν εμπλέκεται στο άνοιγμα του ιοντικού καναλιού του nAChR. Τα αποτελέσματα αυτά παρέχουν σημαντικά δεδομένα για την κατανόηση της επίδρασης της υδατανθρακικής αλυσίδας στη λειτουργία του υποδοχέα, η οποία μπορεί να αξιοποιηθεί στην αντιμετώπιση των πολλών παθολογικών καταστάσεων στις οποίες εμπλέκονται οι nAChRs. / Nicotinic acetylcholine receptors (nAChRs) belong to the superfamily of ligand-gated ion channels (LGICs). LGICs form homo- or hetero-pentamers of related subunits, and each of them consists of a N-terminal extracellular ligand-binding domain (ECD), four transmembrane α-helixes and an intracellular region. The characteristic Cys-loop of the superfamily is found in the ECD of each subunit. The ECD also contains binding sites for agonists and competitive antagonists. Our knowledge regarding the nAChR structure mainly derives from the X-ray crystal structures of the molluscan ACh-binding proteins (AChBPs), the electron microscopy structure of the Torpedo nAChR, the X-ray crystal structure of the mouse nAChR α1-ECD bound to α-bungarotoxin (α-Btx), and the X-ray crystal structures of two prokaryotic LGICs. Despite the progress made by these achievements, the determination of any human nAChR structure has not yet been accomplished. Furthermore, the effect of glycosylation on nAChR function has not yet been explored. Based on the crystal structure of the extracellular domain of the mouse nAChR α1 subunit bound to α-Btx we have generated in silico models of the human nAChR α1-ECD bound to the toxins α-bungarotoxin (α-Btx), α-cobratoxin (α-Cbtx), α-conotoxin (α-Ctx) ImI and α-conotoxin GI. In the case of the α1-ECD/α-Btx and α-Cbtx complexes, a Asn141-linked carbohydrate chain was modeled, its coordinates taken from the crystal structure of the mouse α1-ECD. To gain further insight into the structural role of glycosylation molecular dynamics (MD) simulations were carried out in explicit solvent so as to compare the conformational dynamics of the binding interface between nAChR α1 and the two toxins. The use of computational methods allowed the monitoring of the interactions that govern toxin binding. The MD simulations revealed the strengthening of the receptor-toxin interaction in the presence of the carbohydrate chain. A shift in the position of the sugars towards the bound toxin was observed. Residues Ser187 and Trp184 of nAChR act as critical anchor points for the stabilization of the sugar chain in a close position to the toxin. Toxin Finger I shifts closer to the mannoses, forming important toxin-sugar interactions that implicate residues Thr6, Ser9, and Thr15 of α-Btx, as well as Thr6 and Pro7 of α-Cbtx. Additionally the MD simulations of the human α1 ECD–toxin complexes confirmed the possible accommodation of two water molecules into a hydration cavity inside the hydrophobic core of the subunit, which may contribute to the gating mechanism of the receptor. These findings provide additional structural data that are intended to inspire biophysical studies on the functional role of glycosylation in the gating mechanism of nAChR and also guide the development of novel therapeutic agents for the treatment of nAChR-associated diseases.

Les norovirus sont l'une des causes principales de gastroentérite. Depuis 2002, des variants de norovirus GII.4 successifs ont circulé dans la population par cycle de 2-3 ans, ce qui suscite des interrogations quant au rôle de leurs ligands, les antigènes tissulaires de groupes sanguins (HBGA), dans leur évolution. Nous avons analysé l'interaction entre des variants de GII.4 représentatifs et des HBGA, et déterminé le rôle d’acides aminés (aa) clés. Par mutagénèse dirigée, nous avons montré qu’une configuration stricte des aa directement impliqués dans l’accroche est indispensable. La suppression de la thréonine 395, caractéristique des variants après 2002, confère la capacité de se lier à Lex et Si-Lex, démontrant que les aa en dehors du site de liaison peuvent modifier les propriétés d’attachement. L'analyse de l'accroche de VLP de 6 variants isolés de 1987 à 2007 à des échantillons de salive phénotypés et des HBGA synthétiques montre que tous les variants sont capables de s’attacher à la salive des sécréteurs indépendamment du phénotype ABO et aux oligosaccharides propres au phénotype sécréteur. Deux variants récents ont pu également s’accrocher aux sucres présents dans la salive des nonsécréteurs Le(+). Nos données suggèrent que la capacité de se lier à Lex et Si-Lex serait une conséquence de la variation génétique des aa situés à proximité du site de liaison. L'analyse des propriétés d’attachement par résonance plasmonique de surface a montré que seuls les variants après 2002 présentent une affinité forte pour les antigènes A et B, suggérant que l’accélération évolutive des GII.4 pourrait être liée à une affinité accrue des variants pour les HBGA après 2002. / Noroviruses are one of the leading causes of gastroenteritis worldwide. Since 2002 successive GII.4 variants have circulated in the population before being replaced every 2-3 years, which raises questions about the role of their histo-blood group antigen (HBGAs) receptors in their evolution. We analyzed the interaction between representative GII.4 variants and HBGAs and determined the role of selected amino acids (aa) in the binding profiles. By mutagenesis, we showed that there was a strict structural requirement for the aa directly implicated in HBGA bindings. The ablation of the threonine 395 residue, an epidemiological feature of the post 2002 variants, allowed to gain the capacity to bind to the Lewis x and sialyl-Lewis x antigens, demonstrating that aa residues outside the HBGA binding site can modify the binding properties. The analysis of the attachment of VLPs from 6 variants isolated from 1987 to 2007 to phenotyped saliva samples and synthetic HBGAs shows that all variants could attach to saliva of secretors irrespective of the ABO phenotype and to oligosaccharides characteristic of the secretor phenotype. Interestingly, two recent variants additionally bound to carbohydrates present in the saliva of Lewis-positive non-secretors. Our data suggest that GII.4 binding to Lex and Si-Lex antigens might be a by-product of the genetic variation of the aa located in the vicinity of the binding site. Analysis of the binding properties by surface plasmon resonance showed that only post 2002 variants presented a strong affinity for A and B antigens, suggesting that the GII.4 evolution could be related to an increased affinity for HBGAs for the post 2002 variants.

Macromolecular assemblies such as the ribosome, spliceosome, polymerases are imperative for cellular functions. The current understanding of these important machineries and many other assemblies at the molecular level is poor. The lack of structural data for many macromolecular assemblies further causes a bottleneck in understanding the cellular processes and the various disease manifestations. Hence, it is essential to characterize the structures and molecular architectures of these macromolecular assemblies. Though the number of 3-D structures for individual proteins structures or domains in the Protein Data Bank (PDB) is growing, the number of structures deposited for macromolecular assemblies is relatively poor. Hence, apart from the use of experimental techniques for characterizing macromolecular assembly structures, the use of computational techniques would help in supplementing the growth of macromolecular assembly structures. This thesis deals with the use of integrative approaches where computational methods are combined with experimental data to model and understand the mechanistic features of macromolecular assemblies with a special focus on a sub-complex of the spliceosome machinery. Chapter 1 of this thesis provides an introduction to protein-protein interactions and macromolecular assemblies. Further, the modelling of macromolecular assemblies using integrative methods are discussed, with a subsequent introduction to the spliceosome machinery. In chapter 2, modelling studies were performed on the proteins involved in the general amino acid control mechanism, which is triggered in yeast under amino acid starvation conditions. The proteins involved in the study were Gcn1, a ribosome binding protein and the RWD-domain containing proteins Gcn2, Yih1, Gir2 and Mtc5. From laboratory experiments it is known that in order for Gcn2 activation, an eIF2α kinase, its RWD-domain has to bind to Gcn1 and the residue Arg-2259 is important for this interaction. As the 3-D structure for the Gcn1 region containing Arg-2259 is not currently available, its 3-D structure was inferred using fold recognition and comparative modelling techniques. Further, in order to understand the Gcn2 RWD domain-Gcn1 molecular interaction, a complex structure was inferred by using a restrained protein-protein docking procedure. As the proteins, Yih1 and Gir2 are known to bind to Gcn1 using their RWD-domains, first the structures of the RWD-domain containing proteins including Mtc5 were inferred using a Gcn2 RWD domain NMR structure. Additionally, the Gcn1-Gcn2 complex was used to build a set of complexes to explain the binding of other RWD domain containing proteins Yih1, Gir2 and Mtc5. The important molecular interactions were obtained on analysing the interacting residues in these complexes. Thus, the Gcn1-Gcn2 interaction at the molecular level has been proposed for the first time. Future experiments guided by the protein-protein complex models and the proposed set of mutations should provide an understanding about the critical molecular interactions involved in the general amino acid control mechanism. Chapter 3 describes an integrative approach that was used to decipher a pseudo-atomic model of the closed form of human SF3b complex. SF3b is a multi-protein complex containing seven components – p14, SF3b49, SF3b155, SF3b145, SF3b130, SF3b14b and SF3b10. It recognizes the branch point adenosine in the pre-mRNA as part of U2 snRNP or U11/U12 di-snRNP in the spliceosome. Although, the cryo-EM map for human SF3b complex has been available for more than a decade, the structure and relative spatial arrangement of all components in the complex are not yet known. The integrative modelling approach used here involved utilizing structural data in the form of available X-ray and NMR structures, fold recognition and comparative modelling as well as currently available experimental datasets, along with the available cryo-EM density map to provide a model with high structural coverage. Hence, the molecular architecture of closed form human SF3b complex was derived that can now provide insights into the functioning of SF3b in splicing. This might also help the future high resolution structure determination efforts of the entire human spliceosome machinery In chapter 4, the molecular architecture of the closed form of SF3b complex obtained from the use of integrative modelling approach (Chapter 3) is extensively discussed. The structure-function relationships for some of the SF3b components based on the pseudo-atomic model has also been provided. In addition, the extreme flexibility associated with some of the SF3b components based on dynamics analysis has also been examined. Further, using an existing U11/U12 di-snRNP cryo-EM map and the closed form SF3b complex pseudo-atomic model, an open form of the SF3b complex was modelled and the component structures were fit into it. Hence, it was found that the transition between closed and open forms is primarily caused by a flap containing the HEAT repeat protein, SF3b155. This Protein is also known to harbour cancer causing mutations and has the potential to affect the Closed to open transition as well as SF3b complex structure and stability. Thus, this provides a framework for the future understanding of the closed to open transition in SF3b functioning within the spliceosome. Chapter 5 builds upon the integrative modelling approach (Chapter 3) that proposed the molecular architecture of the closed form of human SF3b complex and an open form of SF3b that was derived due to a flap opening of the closed form and which might help in accommodating RNA and other trans-acting factors within the U11/U12 di-snRNP (Chapter 4). In the current chapter, the SF3b open form and its interaction with the RNA elements is studied. The 5' end of U12 snRNA and its interaction with pre-mRNA in branch point duplex was modelled guided by the open form of SF3b that provided the necessary structural constraints and the RNA model is topologically consistent with the existing biochemical data. Further, utilizing the SF3b opens form-RNA model and the existing experimental knowledge, an extensive discussion has been provided on how the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation as well as its potential implications for branch point adenosine recognition fidelity. Moreover, the reasons for SF3b to be defined as a “fuzzy” complex - a complex with highly flexible folded regions along with intrinsically disordered regions is also discussed. Hence, the current work adds to the excellent developments made previously and deepens the understanding of the structure-function relationship of the human SF3b complex in the context of the spliceosome machinery. In chapter 6, a methodology has been proposed for the use of evolutionary conservation of protein-protein interfacial residues in multiple protein cryo-EM density based fitting of the protein components in the low-resolution density maps of multi-protein assemblies. First, the methodology was tested on a dataset of simulated density maps generated at four different resolutions -10, 15, 20 and 25 Å. On utilizing the evolutionary conservation scores obtained from multiple sequence alignments to score the fitted complexes, it was found that there was a decrease in the conservation scores when compared to that of the crystal structures, which were used to generate the simulated density maps. Further, the assessment of the multiple protein density fitting technique to align the actual protein-protein interface residues correctly using a performance metric called F-measure showed there was a decrease in performance as the resolutions became poorer. Hence, based on evolutionary conservations scores as well as F-measure the decrease in conservation scores or performance was found to be mainly due to the errors associated with the fitting process. Subsequently, a refinement methodology was designed involving the use of conservation scores, which improved the accuracy of the fitted models and the same, was observed in an experimental cryo-EM density test case of RyR1-FKBP12 complex. Hence, the conservation information acts as an effective filter to distinguish the incorrectly fitted structures and improves the accuracy of the fitting of the protein structures in the density maps. Thus, one can incorporate the conserved surface residues information in the current density fitting tools to reduce ambiguity and improve the accuracy of the macromolecular assembly structures determined using cryo-EM. In the concluding chapter 7, the learnings on the structural and mechanistic features of protein assemblies obtained from the use of computational techniques and integration of experimental datasets is discussed. In chapter 2, the modelling of a binary macromolecular complex such as the Gcn1-Gcn2 complex was performed using computational structure prediction strategies to understand the molecular basis of its interaction. Due to the potential inaccuracies which can exist in computational modelling, the chapters 3 to 5 dealt with the use of integrative approaches, primarily guided by the cryo-EM map, in order to decipher the molecular architecture of the human SF3b complex in the closed and open forms as well as its contribution for branch point adenosine recognition. Based on the extensive experience gained in modelling of assemblies using cryo-EM data in the previous chapters, a new method has been proposed on the use of evolutionary conservation information to improve the accuracy of cryo-EM density based fitting. Hence, these studies have provided strategies for modelling macromolecular assemblies as well as a deeper understanding of its mechanistic features.

The aim of this master thesis is to consider appropriate solutions of entering the foreign market. After introducing of the company follow the external and internal analysis. The thesis proves a suitability of the target market, deals with a choice of the product portfolio. It also mentions and checks the expectations of new market’s behaviour. In the final part of the thesis we can find a proper suggestions for entering the target market, steps and measures, which the monitored company shouldn’t leave out.

Le criblage virtuel est utilisé dans la recherche de médicaments et la construction de modèle de prédiction de toxicité. L’application d’un protocole de criblage est précédée par une étape d’évaluation sur une banque de données de référence. La composition des banques d’évaluation est un point critique ; celles-ci opposent généralement des molécules actives à des molécules supposées inactives, faute de publication des données d’inactivité. Les molécules inactives sont néanmoins porteuses d’information. Nous avons donc créé la banque NR-DBIND composée uniquement de molécules actives et inactives expérimentalement validées et dédiées aux récepteurs nucléaires. L’exploitation de la NR-DBIND nous a permis d’étudier l’importance des molécules inactives dans l’évaluation de modèles de docking et dans la construction de modèles de pharmacophores. L’application de protocoles de criblage a permis d’élucider des modes de liaison potentiels de petites molécules sur FXR, NRP-1 et TNF⍺. / Virtual screening is widely used in early stages of drug discovery and to build toxicity prediction models. Commonly used protocols include an evaluation of the performances of different tools on benchmarking databases before applying them for prospective studies. The content of benchmarking tools is a critical point; most benchmarking databases oppose active data to putative inactive due to the scarcity of published inactive data in the literature. Nonetheless, experimentally validated inactive data also bring information. Therefore, we constructed the NR-DBIND, a database dedicated to nuclear receptors that contains solely experimentally validated active and inactive data. The importance of the integration of inactive data in docking and pharmacophore models construction was evaluated using the NR-DBIND data. Virtual screening protocols were used to resolve the potential binding mode of small molecules on FXR, NRP-1 et TNF⍺.

Present doctoral thesis contributed to understanding of mechanistic principles of two enzymes participating in the process of carcinogenesis; DNA polymerase  (pol ) and cytochromes P450 (CYP). Pol  is part of the DNA base-excision repair mechanism (BER). The primary role of pol  in, the BER mechanism, is inserting a new nucleotide into a DNA strand according to Watson-Crick base pairing rules. Pol  plays an important role in the process of carcinogenesis, approximately 30 % of human tumors express pol  mutants. The ability of pol  to discriminate between "right" and "wrong" nucleotide during the insertion process is called fidelity. We employed computational methods to elucidate molecular basis of the fidelity of pol . First, the relative free energy calculation method LRA was employed to compare differences in free energies between the "right" and "wrong" nucleotide during its insertion into DNA. The results indicated a better stabilization of transition-state of the nucleophilic substitution catalyzed by pol  in the case of the "right" versus "wrong" nucleotide. This difference resulted in an 80-fold contribution to its fidelity. Further, computational methods FEP and LIE were used to examine how mutations effect fidelity of pol . Results were than correlated with experimental data...

The deleterious effects of MPO make it a new target for medicinal research. The aim of our study is to find promising inhibitors of MPO for using them as starting point of new anti-inflammatory drugs. Depending on previous researches on MPO inhibitors, we selected 5-fluorotryptamine as starting compounds. Using docking experiments, we designed a series of compounds derived from 5-fluorotryptamine. Two modifications were proposed: <p>& / Doctorat en Sciences biomédicales et pharmaceutiques / info:eu-repo/semantics/nonPublished

Indiana University-Purdue University Indianapolis (IUPUI) / Recent work has shown that specific ALDH isoenzymes can contribute to the underlying pathology of different diseases. Many ALDH isozymes are important in oxidizing reactive aldehydes resulting from lipid peroxidation, and, thus, help maintain cellular homeostasis. Increased expression and activity of ALDH isozymes are found in many human cancers and are often associated with poor prognosis. Therefore, the development of inhibitors of the different ALDH enzymes is of interest as means to treat some of these disease states. Here I describe the results of assays designed to characterize the site of interaction and the mode of inhibition for the unique compounds that function as inhibitors of aldehyde dehydrogenase 2 and determine their respective IC50 values with intent to develop structure-activity relationships for future development.

For three decades, the ongoing HIV pandemic has taken the lives of tens of millions of people. Still, more tens of millions are fighting this incurable disease today. Current failures in combating this global problem are caused mainly by the virus's extreme ability of mutation, its very effective molecular shield which repels the immune system's attacks, and its immense variability. A breakthrough, achieved relatively recently, is the discovery of the so-called broadly neutralizing antibodies against HIV-1, which carry a very efficient and broad neutralizing response. So far, it's not known how to elucidate the production of these antibodies in the infected hosts to quell or altogether eliminate the virus. This work deals with experimental results, which led to both in vivo and in vitro proof-of-concept of the so-called protein mimetics, the ability to imitate viral surface epitopes, and therefore stimulate an efficient immune response carried by targeted broadly neutralizing antibodies. This effect is mediated by recombinant binding proteins, based on the Myomedin scaffold. This work describes the selection and characterization of these binding proteins mimicking the epitopes of one of the most effective broadly neutralizing antibodies, 10E8. It shows that the binding affinities of selected...

This dissertation develops the visual pursuit method for air-to-air tracking and rendezvous of unmanned aircraft systems. It also shows the development of vector-field and proportional-integral methods for controlling UAS flight in formation with other aircraft. The visual pursuit method is a nonlinear guidance method that uses vision-based line of sight angles as inputs to the algorithm that produces pitch rate, bank angle and airspeed commands for the autopilot to use in aircraft control. The method is shown to be convergent about the center of the camera image frame and to be stable in the sense of Lyapunov. In the lateral direction, the guidance method is optimized to balance the pursuit heading with respect to the prevailing wind and the location of the target on the image plane to improve tracking performance in high winds and reduce bank angle effort. In both simulation and flight experimentation, visual pursuit is shown to be effective in providing flight guidance in strong winds. Visual pursuit is also shown to be effective in guiding the seeker while performing aerial docking with a towed aerial drogue. Flight trials demonstrated the ability to guide to within a few meters of the drogue. Further research developed a method to improve docking performance by artificially increasing the length of the line of sight vector at close range to the target to prevent flight control saturation. This improvement to visual pursuit was shown to be an effective method for providing guidance during aerial docking simulations. An analysis of the visual pursuit method is provided using the method of adjoints to evaluate the effects of airspeed, closing velocity, system time constant, sensor delay and target motion on docking performance. A method for predicting docking accuracy is developed and shown to be useful for predicting docking performance for small and large unmanned aircraft systems.