Chapter 1gives a general introduction to the CXXC motif found in natural proteins. It then reviews the studies where disulphides were engineered in various proteins. The various strategies developed to engineer metal binding activity and redox activity are described. The objectives behind engineering the CXXC motif into a protein, such as imparting it novel metal-binding and redox activities, are discussed next. Alternative strategies which achieve the same objectives are described as well. This chapter then introduces the model proteins used in the course of this thesis: maltose-binding protein (MBP) and E. coli. Thioredoxin (Trx). This chapter also briefly discusses the role of signal peptide in protein export. Chapter 2describes the experimental studies and their results in which we introduced the widely occurring cysteine motif CXXC into the maltose binding protein (one-at-a-time, in five alpha-helices, at the N-termini) to test three hypotheses: 1) Does a disulphide bond form at the N-terminus? 2) Does the protein acquire any oxido-reductase activity? 3) Does it acquire new metal-binding properties? The results confirmed: 1) Each cysteine pair forms a stable intrahelical disulphide bond under non-reducing conditions. 2) The five mutant proteins acquire considerable oxidoreductase activity, tested by the insulin aggregation assay. 3) The mutants acquire novel metal-binding properties for Ni2+, Cd2+, and Zn2+ upon reduction. Further, introducing the CXXC motif neither destabilizes the protein nor affects its global structure. Our results demonstrated that introduction of CXXC motifs can be used to probe alpha-helix start sites and to introduce oxidoreductase and metal binding functionality into proteins. Chapter 3describes further experimentson a few of the metal ion binding mutants discussed in the previous chapter. We explore the effect and usefulness of reducing agents (DTT and TCEP) on the binding of metal salts to the CXXC mutants. We also studied the explore of metal salts on the thermal stability of the mutants and show that metal ions bind to the CXXC motif even when the protein is in the unfolded state. The chapter describes the use of an immobilized metal affinity chromatography (IMAC) based method for the purification of MBP mutants.Yields ranging from 60-85% were obtained for thethree MBP mutants. The cysteines were located at different positions in thesethree MBP mutants (MBP 42-45 Cys, MBP 128-131 Cys, and MBP 359-359 Cys mutants). The yields for wild-type MBP, a single cysteine mutant (MBP S211C), a double cysteine mutant (MBP 230, 30) were all below 15%. Chapter 3 also reports a new crystal structure of the MBP356-359 mutant in ligand bound form:it crystallizes as an intermolecular dimer, bonded by two disulfides formed by the cysteines of the CXXC motif. Chapter 4describes the effects of inserting signal peptide sequences on protein folding and expression. We fused the malE and pelB signal sequences at the N-terminus of the model protein thioredoxin and observed that the wild-type and pelB fusion constructs are soluble when expressed, but the malE construct was targeted to inclusion bodies. Nonetheless, it could be refolded in vitro to yield a monomeric product with a secondary structure identical to the wild-type thioredoxin. This chapter also details the thermodynamic stability, aggregation propensity and activity of the purified recombinant proteins in comparison with the wild-type thioredoxin. The presence of the signal sequences reduces the thermodynamic stability and activity of the recombinants and increases their aggregation propensity, with malE having much larger effects than pelB. These studies show that besides acting as address labels, different signal sequences affect protein stability and aggregation differently. Chapter 5describes three different strategies to label a protein at different sites with cysteine-specific fluorophores using MBP as the model. The first strategy exploits the differential accessibility of residues within MBP in its maltose-bound and maltose-free states. The second strategy involves insertion of a 14-amino-acid loop called V3 from the HIV gp120 protein into MBP; anti-V3 antibodies shield the cysteine residue present inside the inserted loop, while we label another cysteine present outside the loop. In the third strategy, we introduce a third cysteine residue onto the background of the MBP mutant already containing a disulphide bridge at the N-terminus of one of its helices (discussed in Chapter 2). We label the third, free cysteine while the cysteines involved in the disulphide bridge remain protected. We observed successful differential labelling using the first strategy and also observed FRET between the fluorophore labels. Similarly, after trying the second strategy we could individually label all the mutants except one. The third strategy based on the triple-cysteine mutant was not successful because the fluorophore we chose (DBM) did not show site specificity and instead labelled all three cysteines. In addition, the triple-cysteine mutant did not even show disulphide-bridge formation.We showed that indeed the V3 loop inserted in MBP binds anti-V3 antibodies and we could individually label all the mutants expect D41C. The third strategy was not successful because unfortunately in the triple cysteine mutant, the fluorophore we chose (DBM) did not show site specificity and labeled all three cysteines. In addition, the disulfide bridge was not found to be present in the triple cysteine mutant. Chapter 6discusses the synthesis, characterization and binding of various maltolipids, (and their corresponding maltose-free controls) to MBP. The maltolipids were synthesised with varying linker lengths and anchor- & head-groups and then used to prepare liposomes and micelles. Although both liposomal and micellar forms could bind to MBP, only the micelles were screened subsequently for their ability to bind to MBP. The binding was assessed using various techniques such as fluorescence spectroscopy, gel filtration and thermal stability assay. We screened the maltolipids and determined how their anchor group, linker length and charge on the head group influences the binding of MBP to micelles formed by these maltolipids.

Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2018-08-14T14:53:58Z No. of bitstreams: 2 Dissertação - Jéssika Vieira dos Reis - 2018.pdf: 3710658 bytes, checksum: de2614771619ec9c58bbd1e7d57942c3 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-08-16T11:28:50Z (GMT) No. of bitstreams: 2 Dissertação - Jéssika Vieira dos Reis - 2018.pdf: 3710658 bytes, checksum: de2614771619ec9c58bbd1e7d57942c3 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-08-16T11:28:50Z (GMT). No. of bitstreams: 2 Dissertação - Jéssika Vieira dos Reis - 2018.pdf: 3710658 bytes, checksum: de2614771619ec9c58bbd1e7d57942c3 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-07-24 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / With the increasing resistance of microrganisms to available drugs, mainly in hospital environments, the pharmaceutical industries have concentrated efforts in the research of new versatility of their molecular structures and their biological effects achieved. The hydrazones belong to an important class as they present a broad pharmacological profile whose properties have been extensively studied in medicinal chemistry because of their chelating capacity and the role of coordination in their biochemical mechanism of action. In this work a chemical ligand called J3 was synthesized which was complexed with copper nitrate (II), nickel nitrate, cadmium nitrate, cobalt perchlorate and diphenyltin dichloride, being called: J3Cu, J3Ni, J3Cd, J3Co and J3Sn, respectively. From the formation of the crystals, they were subjected to spectroscopic analysis of single crystal X-ray diffraction and infrared spectroscopy, which confirmed the chemical structures obtained from the ligand and its complexes. The biological activity of the six synthesized compounds was evaluated through the microdilution method on 96 wells plates, and the determination of the minimum inhibitory concentration (MIC) was determined by the density measurement in ELISA reader after incubations of 24, 48, 72 and 96 hours in bacteria of the species Escherichia coli and Staphylococcus aureus. The J3Cu, J3Cd and J3Sn compounds presented moderate activity for the tested bacteria, whereas the J3 ligand and its J3Co and J3Ni complexes did not inhibit 100% of the microrganisms in the tested concentrations. Through the tests of determination of the minimum bactericidal concentration (MBC), it was concluded that the complexes J3Sn and J3Cd presented bacteriostatic and bactericidal activity and J3Cu complex presented activity bacteriostatic. / Com o crescente aumento da resistência de microrganismos aos fármacos disponíveis, principalmente em ambiente hospitalar, as indústrias farmacêuticas têm concentrado esforços na pesquisa de novos fármacos. Diversas classes de compostos orgânicos despertam o interesse de pesquisadores devido à versatilidade de suas estruturas moleculares e seus efeitos biológicos alcançados. As hidrazonas pertencem a uma classe importante pois apresentam um amplo perfil farmacológico cujas propriedades têm sido extensivamente estudadas na Química Medicinal em razão de sua capacidade quelante e do papel da coordenação no seu mecanismo bioquímico de ação. Neste trabalho foi sintetizado um ligante químico denominado J3 o qual foi complexado com Nitrato de Cobre (II), Nitrato de Níquel, Nitrato de Cádmio, Perclorato de Cobalto e Dicloreto de difenilestanho, sendo denominados de: J3Cu, J3Ni, J3Cd, J3Co e J3Sn, respectivamente. A partir da formação dos cristais, os mesmos foram submetidos a análises espectroscópicas de difração de raios x em monocristal e espectroscopia na região do infravermelho, que confirmaram as estruturas químicas obtidas do ligante e seus complexos. Foi avaliada a atividade biológica dos seis compostos sintetizados através do método de microdiluição em placas de 96 poços, e a determinação da concentração inibitória mínima (CIM) foi determinada através da medida de densidade em leitor de ELISA após incubações de 24, 48, 72 e 96 horas em bactérias das espécies Escherichia coli e Staphylococcus aureus. Foi determinada a concentração bactericida mínima para os compostos que apresentaram CIM contra as bactérias testadas. Os compostos J3Cu, J3Cd e J3Sn apresentaram atividade moderada para as bactérias testadas, ao passo que o ligante J3 e seus complexos J3Co e J3Ni não inibiram 100% dos microrganismos nas concentrações testadas. Através dos testes de determinação da concentração bactericida mínima, concluiu-se que os complexos J3Sn e J3Cd apresentaram atividade bacteriostática e bactericida, o complexo J3Cu apresentou atividade bacteriostática.

Les systèmes toxine-antitoxines (TA) sont abondants dans la majorité des génomes bactériens séquencés à ce jour. Ces systèmes codent une toxine stable qui inhibe soit la transcription, soit la traduction, et une antitoxine qui contrecarre l’effet de la toxine par formation d’un complexe avec celle-ci. L’antitoxine est instable suite à sa dégradation continue par les protéases ATP-dépendantes. Afin de maintenir un ratio antitoxine :toxine constant en condition normale de croissance, l’expression des systèmes TA est régulée négativement au niveau transcriptionnel par le complexe toxine-antitoxine.<p><p>Au début de notre travail, cinq systèmes TA étaient identifiés dans le chromosome d’E. coli. Il avait été montré par notre laboratoire que parmi ces systèmes, seul yefM-yoeB était activé en condition de surproduction de la protéase ATP-dépendante Lon. Ce résultat était surprenant puisque Lon était connue pour dégrader également l’antitoxine RelB du système chromosomique relBE. Un des objectifs de notre travail était de comprendre les mécanismes sous-jacents à cette spécificité. Nous avons montré que l’antitoxine YefM était dégradée à la fois par Lon et les protéases ClpAP et ClpXP. Nous avons également montré qu’en condition de surproduction de Lon, YefM était fortement instable (t1/2~ 10 min. vs 60 min en condition normale). Cette instabilité accrue permet donc l’activation du système yefM-yoeB, c’est-à-dire la libération de la toxine YoeB du complexe qu’elle forme avec YefM. Nous avons également avons montré que le t1/2 de RelB n’était pas affecté par la surproduction de Lon, ce qui explique pourquoi le système relBE n’est pas activé dans ces conditions. Notre hypothèse était qu’un cofacteur soit nécessaire à la dégradation de RelB par Lon et que celui-ci serait limitant dans nos conditions expérimentales. Le crible génétique que nous avons réalisé n’a cependant pas permis d’identifier de cofacteur de dégradation ni de régulateur transcriptionnel en trans du système relBE. <p><p>Un deuxième volet de notre travail de thèse a consisté en l’étude de la fonction des systèmes TA chromosomiques. L’hypothèse prévalente au début de notre travail était que les systèmes TA soient intégrés dans les voies adaptatives de réponses au stress. Cependant, le résultat de leur activation était controversé. L’hypothèse du groupe de Gerdes était que leur activation mène à un état bactériostatique réversible alors que le groupe d’Engelberg-Kulka montrait que le système mazEF était un système de mort programmée. Afin d’éclaircir le rôle des cinq systèmes TA dans la physiologie d’E. coli, nous avons testé l’effet de nombreux stress sur la croissance et la viabilité de souches sauvages et de souches délétées de ces systèmes. Aucune des conditions que nous avons testées n’a entraîné une diminution de la viabilité excluant de manière définitive l’hypothèse de la mort programmée. De plus, l’inhibition de croissance causée par ces différents stress s’est avérée être indépendante des cinq systèmes, de même que la phase de récupération suivant les différents stress. Enfin, nos expériences de compétition ont clairement démontré que les cinq systèmes ne procuraient aucun avantage sélectif aux bactéries dans des conditions de compétition en carence nutritive. Les systèmes TA étudiés dans ce travail ne jouent donc aucun rôle dans l’adaptation aux stress que nous avons testé puisqu’ils n’améliorent ni l’aptitude (fitness), ni la compétitivité des bactéries dans ces conditions. <p><p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Micromachined biosensors are used in chemical and biological applications. A biosensor which uses mass based transduction is called a mass sensor. Mass sensors are used to detect extremely small mass of biomolecules such as proteins, viruses or even parts of DNA in the range of femtograms (10-15 gm) to zeptograms (10−21 gm). Highly effective and reliable microcantilevers are used for detecting the mass of biomolecules using either static deflection or dynamic resonant peak shifts. The main objective of our work is to investigate the effect of elasticity of the attached mass on the shift in the resonant frequency and examine the validity of the rigid mass assumption used in the literature. The natural frequencies of a resonator are either found by solving the governing differential equation or approximately using Rayleigh-Ritz method. The mass of a body, attached to a resonator beam is determined using resonant frequency shift method. In our study, we derive an analytical expression for ‘δm’ based on the shift in frequency ‘δf’ that accounts for the elasticity of the added mass and the location of the mass on the beam. We study the simplest model to incorporate these effects where the added mass is itself modeled as a single degree of freedom spring-mass system. The entire system is represented as a 2-DOF lumped model of cantilever and the attached elastic mass. The natural frequencies are obtained using eigenvalue analysis. We study the mass estimation of Escherichia Coli (E. Coli), a food borne pathogen, using experimental results reported in the literature. We treat E.Coli as an elastic mass and model it as a single degree of freedom system to account for its elasticity. We use the elastic model as well as the rigid mass model to check the results available in the literature and point out the difference that results in mass estimation using the two models. To demonstrate the effect of elasticity on mass sensing using the resonant peak shift technique, we conduct mesoscale experiments. Since the fundamental principle does not depend on any phenomenon exclusively dependent on micro scales, the mesoscale experiments are justified. For this purpose, an experimental set-up with metallic cantilevers and flexible rubber strands as attached masses are used. We also use our experimental set-up to study the effect of positional inaccuracy of the added mass (rigid) in the computation of its mass from the shift in the resonance frequency. The results obtained show that elasticity of the added mass as well as its position on the resonator affect the computed mass but this effect is dependent on the relative stiffness and mass of the resonator and the added mass. We also observe the limitations of the experiments in carrying out studies over the desired range of parameters. We also create a computational model of the system and carry out simulations to explore a larger range of parameter values. In particular, we create an FEM model of our system in ANSYS, and carry out modal analysis for the cantilever beam resonator with and without the added mass, varying the relative stiffness and mass of the two components (the cantilever beam and the added mass). We compare the results of shift in the resonant frequency with those obtained from the rigid mass model. The results show the effect of elasticity clearly in certain ranges of relative stiffness and mass.

Listeria monocytogenes continues to challenge the dairy industry in causing post-process contamination of cheeses. To reduce risk of contamination, it is crucial to understand the growth and survival of pathogenic bacteria in cheese products and to develop post-process mitigation strategies. This study evaluated the fate of pathogens in reduced and regular sodium Mozzarella cheese, and the potential of Supercritical Fluid Extraction with CO2 (SFE) to reduce Listeria innocua on Mozzarella and Queso Fresco. The survival of L. monocytogenes, Salmonella, and E.coli O157:H7 (2-3 log CFU/g) in reduced sodium Mozzarella (1.62%), compared to regular sodium Mozzarella cheese (2.15%) at 4ºC and 12ºC for 90 and 30 days, respectively, was evaluated. Salmonella and E. coli O157:H7 populations decreased over incubation time at both temperatures and no difference (pListeria monocytogenes population also decreased during incubation time at 4°C regardless of the sodium concentration in Mozzarella cheese. However, there was a difference in the population of L. monocytogenes for regular and reduced sodium incubated 12°C, and its populations increased 1 log CFU/g in reduced sodium Mozzarella cheese. Additionally, this study determined the bactericidal effect of SFE on the population of L. innocua, a surrogate for L. monocytogenes, in Mozzarella and Queso Fresco cheese (6 log CFU/g) treated with SFE at two pressures and temperatures (120 bar at 40°C and 150 bar at 50°C) for 30 min. SFE treatment at 120 bar, 40°C for 30 min decreased L. innocua by approximately 3.0 and 3.5 log CFU/g in Mozzarella and Queso Fresco cheeses, respectively. SFE at 150 bar and 50°C reduced L. innocua by approximately 3.78 and 5.2 log CFU/g in Mozzarella and Queso Fresco cheeses, respectively. Since SFE had a minimal effect on the physico-chemical characteristics of the cheeses assayed, the results suggest SFE might be used to reduce L. monocytogenes in cheeses without negatively impacting product quality.

The diploma thesis "Media terrorism via bacteria E.coli" puts the so-called cucumber affair from Summer 2011 into wider context and aims to discover the main attributes of contemporary risks and define the way they are presented in the media. Misguiding media releases and the inability to identify the source of the bloody diarrhea outbreak in Germany caused by E.coli bacteria have collectively had a significant impact on consumer behavior and economic stability on a global level. Most people are dependent on government and expert authorities due to the fact that they cannot recognize what represents a realistic threat and what serves as a basis for media sensation. This is why this thesis studies the social constructionist theory, basic media routines and practices as well as theoretical concepts that support the production of pseudo-events. A content analysis of selected Czech dailies and weeklies was executed in order to enable a comparison of the language that has been common for all "pandemics" in the 21st century.

Die chronisch-entzündlichen Darmerkrankungen Morbus Crohn und Colitis ulzerosa sind wiederkehrende, nicht heilbare, immunvermittelte Krankheiten unklarer Ursache. Genetische Prädisposition und Umweltfaktoren können die Barrierefunktion der Darmmukosa stören, so dass eine überschiessende Entzündungsreaktion folgt, die durch kommensale Bakterien der normalen Darmflora verstärkt wird. Die Infektion mit H. pylori im Magen kann zu Gastritis, Ulkuskrankheit und der Entstehung von MALT-Lymphomen und Magenkarzinomen führen. An der Erkennung von bakteriellen Bestandteilen im Gastrointestinaltrakt sind Toll-like-Rezeptoren (TLR), als Komponenten des angeborenen Immunsystems maßgeblich beteiligt. In der vorliegenden Arbeit wurden Veränderungen der Bakterienflora bei Ileitis, Colitis und bei Vorliegen einer H. pylori-Infektion im Mausmodell untersucht. Durch eine globale Florenanalyse mit klassischen mikrobiologischen und molekularbiologischen Techniken konnte gezeigt werden, dass die Konzentrationen an Gram-negativen Stäbchenbakterien während der Entzündung in Ileum und Colon anstiegen. Die bakteriellen Faktoren, die eine Ileitis induzierten, wurden durch den Einsatz von gnotobiotischen TLR-defizienten Mäusen mit definierter bakterieller Rekolonisierung ermittelt. Hierbei zeigte sich, dass eine Ileitis durch das LPS von akkumulierenden E. coli über die TLR4-vermittelte Signaltransduktion verstärkt wurde. Die Entzündungsreaktionen konnten durch Behandlung mit Antibiotika oder dem LPS-Antagonisten Polymyxin B gebessert werden. In Folge einer H. pylori-Infektion kam es im Mausmagen zu einer erhöhten Diversität der Bakterienflora durch die Besiedelung mit Bakterienarten, die normalerweise das Colon kolonisieren. Eine derartige Florenverschiebung konnte durch eine Vakzinierung gegen H. pylori verhindert werden. Die Tiermodelle zur T. gondii-induzierten Ileitis und DSS-Colitis erlauben eine reproduzierbare Analyse entzündungsrelevanter Komponenten und damit die Möglichkeit, therapeutische Ansatzpunkte, wie z.B. den Einsatz von Lipopolysaccharid-Inhibitoren, die Blockade von TLR4 oder dem LPS-Bindeprotein oder den Einsatz von Probiotika, unter definierten Bedingungen zu analysieren. / Inflammatory bowel diseases like Crohn´s disease and ulcerative colitis are chronic, relapsing, immunologically mediated disorders with uncertain etiology. Genetic abnormalities and environmental factors may have negative influences on the physiologic barrier function of the intestinal mucosa with inflamamtion coming up after immune response which is aggravated by commensal intestinal bacteria. The infection of H. pylori can cause gastritis and ulcus disease and contribute to the occurence of MALT lymphoma and gastric cancer. Bacterial ligands in the intestine are recognized by toll-like receptors (TLR) which are one component of the innate immune system. This study observed variations of the bacterial flora in mice with ileitis, colitis or H. pylori-infection. Performing a global survey of the intestinal flora combining culture based techniques with molecular methods, it was observed, that the concentration of gram-negative rods is elevated during ileitis or colitis. The bacterial factors, which are capable of inducing ileitis, could be confirmed using gnotobiotic TLR-deficient mice with a defined bacterial recolonization. It was clearly shown that ileitis was aggravated by LPS of accumulating E. coli through a TLR4-mediated signal transduction. The inflammation was ameliorated through antibiotic treatment or after application of the LPS-scavenger polymyxin B. H. pylori infection of mice leads to an increase of bacterial diversity in the stomach and bacterial species which are normally colonize the colon were detected after infection. Vaccination against H. pylori could prevent this diversity shift. The animal models for the T. gondii-induced ileitis and DSS-colitis used in this study offering the reproducible analysis of inflammation relevant components so that new approaches of treatment like inhibition of lipopolysaccharide, blockage of TLR4 or LPS binding protein or application of probiotics could be studied under well defined conditions.

This PhD thesis showed the applicability of a gel-based proteomic separation tool, 2-D electrophoresis in three independent projects. Supplemented with results obtained using different techniques the proteomic studies enabled a global imaging of proteoms in the studied biological systems. Comparing total proteoms of E. coli 61 protein changes were identified and connected with the development of the bacterial population in the presence of an antibiotic compound, erythromycin. This classic proteomic approach included sample extraction, optimization of its 2D separation followed by 2D gel analysis and protein identification by MS methods. A disadvantage of this work was an enourmously large amount of data to be analyzed by computer analysis. For the study of membrane proteom of B. subtilis during a pH induced stress, on the other hand, a modification of isolation techniques for membrane and membrane associated proteins was required first to improve the subsequent protein separation by 2-D electrophoresis. The optimalization of protein extraction included changes in detergents used for protein solubilization and a prolongation of time periods in the protein solubilization protocol. 5 relevant protein changes were then described that play a role in the bacterial response to pH stress. The proteins were...

Pantothenate synthetase (PS), which catalyzes the last step in the pantothenate (vitamin B5) biosynthesis, is a dimeric enzyme present in bacteria, fungi and plants. The enzymatic properties of PS from Escherichia Coli, Mycobacterium tuberculosi, Fusarium Oxysporum, Lotus japonicus, Oryza sativum, Brassica napus and Arabidopsis thaliana have been characterized. The chemical reaction and the proposed mechanism of reaction are identical for PS, irrespective of the source. However, from an enzyme mechanistic point of view, plant PS’s are dissimilar to their bacterial counterparts, in that they exhibit “allosteric behavior”, a property that has not been observed in the bacterial enzyme. The behavior is quite remarkable when one takes into consideration the fact that plant PS’s share a high degree of sequence identity (~ 40%) with the bacterial enzymes. Even more intriguing is the structural mechanism proposed to explain the observed differences in structure between the PS’s from E.Coli and M.tb, which share a 42% sequence identity. Till date there is no structural information available on the plant PS’s and of the substrate bound conformation of E.coli PS. This thesis aims to provide an understanding on some aspects of the structure – function relationship of this physiologically important enzyme. Specifically, the solution properties of E. coli PS have been examined using high-resolution multinuclear, multidimensional NMR methods. Given the large size of the full-length protein (~ 63 KDa), the structurally distinct N and C-terminal domains were cloned and expressed as individual proteins and their properties investigated. Towards this end, the tertiary fold of the 40 kDa dimeric amino-terminal domain of E. coli pantothenate synthetase has been determined using multidimensional multinuclear nuclear magnetic resonance (NMR) methods (PDB entry 2k6c). Sequence specific resonance assignments for backbone HN, 15N, 13Cα, 13C', sidechain 13Cβ and aliphatic 13CH3 (of isoleucine, leucine and valine residues) were obtained using perdeuterated ILV-methyl protonated samples (BMRB entry 6940). Secondary structure of nPS was determined from 13C secondary chemical shifts and from short and medium range NOEs. Global fold of the 40 kDa homo-dimeric nPS has been determined using a total of 1012 NOEs, 696 dihedral angles, 260 RDCs, 155 hydrogen bonds, radius of gyration potential, non-crystallographic symmetry potential and database derived potential based upon the Ramachandran map. The calculated structures, which show that the N-terminal domain forms a homo-dimer in solution, is of high stereochemical quality as judged by the Ramachandran statistics (70% of the residues have backbone dihedral angles in the allowed region, 25.5% in the additionally allowed region, 4.0% in generously allowed region, and only 0.5% in disallowed region). Dynamics of nPS, which has rotational correlation time τc of 17.3 ns, was investigated by 15N relaxometry measurements. Results of these studies indicate that the E. coli protein exhibits dynamic nature at the dimer interface. These structural and dynamic features of the protein were found to be of interest when correlated with NMR based substrate binding studies. Interaction of homo-dimeric amino-terminal domain (nPS) of E. coli pantothenate synthetase (PS; encoded by the gene panC; E.C. 6.3.2.1) with the substrates pantoate, β-alanine, ATP and the product pantothenate has been studied using isotopically edited solution NMR methods. Addition of pantoate prior to ATP has led to the interesting observation that pantoate binds each monomer of nPS at two sites. ATP displaces a molecule of pantoate from the ATP binding site. β-alanine and pantothenate do not bind the protein under the condition studied. Binding of pantoate and ATP also manifests as changes in residual dipolar couplings (RDCs) of backbone 1H-15N pairs in nPS when compared to the free form of the protein. Structures of homo-dimeric nPS bound to two molecules of pantoate (PDB entry 2k6e) as well as to pantoate + ATP (PDB entry 2k6f) were calculated by inclusion of hydrogen bonds between the ligands and backbone 1H-15N pairs of nPS in addition to other NMR derived restraints. The ligand bound structures have been compared to the similar forms of the M. tb PS. Structure of each monomer of nPS bound to pantoate and ATP shows the substrates in a favorable orientation for the intermediate pantoyl adenylate to form. Moreover, at all stages of substrate binding the symmetry of the dimer was preserved. A single set of resonances was observed for all protein-ligand complexes implying symmetric binding with full-occupancy of the ligands bound to the protein. In an effort to understand the structural basis of the observed enzymatic properties of plant PS’s, a structural model of the Arabidopsis PS was constructed. The results of these structural and substrate binding studies strongly suggest that 1 Substrate binding to PS occurs only at the active site. 2 There are no additional substrate binding sites which could potentially participate as regulatory sites. 3 Pantoate does not bind at the dimer interface to induce the observed homotropic effects. 4 The structural results presented on the substrate bound forms of nPS have direct implication for the development of novel antibacterial and herbicidal agents. Recently a great deal of interest has been evinced on the effects of molecular crowding on protein folding / unfolding pathways. Nuclear magnetic resonance is the only method by which high resolution structural information can be obtained on partially denatured states of a protein under equilibrium condition. Recent methodological advances have enabled the determination of high resolution structures using information embedded in the residual dipolar couplings. Molecular crowding using confinement may thus reveal important details about chaperone mediated protein folding. We have attempted to develop a protocol to study the effects of molecular confinement by sequestering proteins in poly-acrylamide gels and then subjecting these protein molecules to denaturation and then characterize these states by nuclear magnetic resonance. The preliminary results of these studies are described here.

Nous nous proposons d'étudier la gestion du bruit stochastique d'expression génique. On s'intéresse plus particulièrement à la dynamique du bruit lors de la réponse cellulaire. Comment évolue le bruit? Quels sont les mécanismes en jeux? Quelle est l'importance du bruit dans le fonctionnement cellulaire? Pour répondre à ces questions, nous nous appuyons sur le réseau de régulation génétique qui gère la réponse au stress nutritionnel chez E. Coli. L'étude du comportement dynamique de ce réseau, au niveau d'une population de bactéries, a été initiée et est portée par la forte collaboration de deux équipes de la région : une de bio-informaticiens (l'équipe de Hidde de Jong de l'INRIA Rhône-Alpes) et la deuxième de biologistes (l'équipe de Hans Geiselmann, Laboratoire d'Adaptation et Pathogénie des Micro-organismes). En profitant donc de l'expérience et de la compréhension acquise par ces équipes, nous étudions les réponses individuelles de chaque bactérie lors de la transition entre état de stress nutritionnel, et état de croissance exponentielle. Le bruit d'expression génique est quantifié dans des nœuds clés du réseau de régulation. Pour ce faire, les bactéries sont suivies individuellement par microscopie de fluorescence sur plusieurs générations. Les données de fluorescence collectées sur cellules uniques permettent d'étudier la variabilité inter-cellulaire. Cette variabilité est quantifiée tout le long de la réponse: à chaque instant, on connaît la distribution des densités de fluorescence cellulaire dans la population de cellules. Et le suivi des lignées individuelles permet de travailler sur une population de cellules saines: les individus malades ou morts qui ne se divisent pas, sont écartés. En réduisant ainsi les phénomènes cellulaires en jeux, on réduit le nombre de paramètres. Les sources de bruit sont moins nombreuses, et il est plus facile de comprendre les mécanismes en jeux. Les informations de lignage cellulaire permettent aussi d'étudier la variabilité introduite par la phase du cycle cellulaire: les événements de division cellulaire peut être artificiellement synchronisés. Le bruit est alors étudié sur une population en phase lors de la division. Cette étude montre que le bruit sondé n'est pas dominé par les différences dans la phase du cycle cellulaire. On peut donc modéliser nos cellules sans tenir compte des différences introduites par le cycle cellulaire. Le modèle testé est simplifié aux étapes de transcription-traduction-maturation. Les paramètres du modèle sont inférés de nos données expérimentales, et le modèle est testé à travers des simulations.