University, Diss., 2006--Frankfurt (Main). / Zsfassung in engl. und dt. Sprache.

University, Diss., 2006--Frankfurt (Main). / Erscheinungsjahr an der Haupttitelstelle: 2005.

Frankfurt (Main), Univ., Diss., 2009 / Erscheinungsjahr an der Haupttitelstelle: 2008

Univ., Diss., 2006--Frankfurt (Main)

Streptococcus pneumoniae, le pneumocoque, est un pathogène majeur causant plus d'un million de morts par an dans le monde. De plus en plus de souches de pneumocoques sont résistants aux antibiotiques, en faisant un problème majeur de santé publique dans le monde. Une partie des ces antibiotiques sont les peptides anti-microbiens (AMP), qui sont produit aussi bien par l'hôte que des bactéries pathogènes en tant que premier système de défense. On trouve dans le pneumocoque un transporteur ABC (ATP-Binding Cassette) lié à un système de deux composants (TCS) – la kinase d'histidine (HK) et le régulateur de réponse (RR), qui cible les AMP. Récemment, il a été démontré, que l'absence du transporteur ABC augmente la sensibilité à la bacitracine. Dans ce projet, nous avons essayé à comprendre le mécanisme fonctionnel entre le transporteur ABC et TCS en utilisant des outils in vivo et in vitro. / Streptococcus pneumoniae, the pneumococcus, is a major human pathogen causing over a million deaths each year. Many pneumococcal strains display resistance towards antibiotics causing world-wide health concern. Some of these antibiotics are antimicrobial peptides (AMP), which are produced as a primary defense by hosts as well as pathogens. The pneumococcus harbors a system comprised of an ATP-binding cassette (ABC) transporter and a two-component system (TCS) composed of a histidine kinase (HK) and a response regulator (RR), which targets these molecules. It has been shown recently that the removal of this ABC transporter increases the sensitivity of the bacteria towards bacitracin. In this project, we tried to understand the functioning mechanism of the ABC transporter and the co-operation with the TCS using both in vivo and in vitro techniques.

ABCB10, or ATP binding cassette sub-family B member 10, is a protein localized in the mitochondrial inner membrane. It belongs to the ABC transporter family whose members are proteins that facilitate substrate transport across various biological membranes. It has been found that ABCB10 is required for normal heme biosynthesis during erythroid differentiation and also plays a role in protection against the damage caused by reactive oxygen species (ROS) production. This protective effect exists both in the erythrocyte development and in the heart recovery after the ischemia-reperfusion injury. However, as an ABC transporter, its transported substrates are not known, neither is the mechanism by which ABCB10 plays a role in protection against ROS damage. In this dissertation an 8-azido-ATP photolabeling system is established to study the ATP binding and hydrolysis properties of ABCB10. Using this approach, it is found that the conserved amino acid residues Gly497 and Lys498 in the Walker A motif of the nucleotide binding domain of ABCB10 are required for ATP binding. On the other hand, Gly602 in the C-loop motif and Glu624 in the end of the Walker B motif are necessary for ATP hydrolysis. In addition, most ABC transporters increase ATP hydrolysis in the presence of their substrates. Therefore, the 8-azido-ATP photolabeling system can be utilized to test potential substrates of ABCB10. Substances related to the heme biosynthesis such as δ-aminolevulinic acid (dALA) and the mitochondrial redox state such as oxidized glutathione (GSSG) and reduced glutathione (GSH) are tested for this purpose. The 8-azido-ATP photolabeling system shows that GSSG stimulates ATP hydrolysis without affecting ATP binding, whereas GSH decreases ATP binding. Further study shows that the nucleotide binding domain of ABCB10 is glutathionylated at the cysteine residue on the position 547 (Cys547), suggesting that GSH may modulate ABCB10 activity via the glutathionylation-regulated ATP binding. This is a first insight into the molecular mechanism by which the mitochondrial redox state, through the regulation by GSH and GSSG, can modulate ABCB10 activity. / 2016-09-01T00:00:00Z

Haemophilus ducreyi is a gram-negative and heme-dependent bactreia. H. ducreyi is the responsible of causing chancroid, a sexually transmitted infection forming genital ulcers. Infection with H. ducreyi is associated with an increased risk of acquiring HIV-1 as well as increasing the risk of the HIV-1 transmission. Heme acquisition in H. ducreyi occur through a receptor mediated process in which it start with binding of hemoglobin and heme to their cognate outer membrane receptors, HgbA and TdhA, respectively. The receptors are energized by the TonB complex. Following that the deposition of heme into the periplasmic area is unclear. Profiling of the periplasmic proteome of the H. ducreyi resulted in the identification of a periplasmic- binding protein that highly expressed in heme limitation conditions, and it has been called hHbp. This protein is encoded by a gene resides in a locus of four genes displaying genetic features of an ABC transporter. The gene cluster is organized as an operon comprising an internal membrane protein (IntPro), a sulphate reductase gamma subunit (dsvC), a heme dependant periplasmic bind-ing protein (hHBP), and an ATPase. The purified periplasmic binding protein, hHbp, bind heme in a dose-dependent and saturable manner. Moreover, the binding between heme and hHbp was specifically competitively inhibited by heme. The proposal planned to cre-ate an isogenic hhbp mutant by insertional inactivation using a kanamycin cassette, to genotypically and phenotypically characterize the mutant and thereby to confirm the cru-cial role of the hhbp gene in heme transport in H. ducreyi. Several attempts to ligate a kanamycin resistance cassette into hhbp to construct such a mutant were unsuccessful de-spite the systematic alteration of the ligation conditions and the use of kanamycin re-sistant genes derived from a variety of different plasmids. The explanations for this fail-ure are uncertain. In future work, two other approaches to construct an hhbp mutant in-clude the FRT-FLP recombinase technology and the use of overlapping extension PCR with a chloramphenicol cassette.

Benznidazol (BZ), fármaco utilizado para o tratamento da doença de Chagas, apresenta eficácia limitada na fase crônica da doença. Falhas terapêuticas foram atribuídas majoritariamente a diferenças na suscetibilidade a BZ entre as cepas do T. cruzi. Resultados prévios de nosso grupo indicam que o gene de um transportador ABC da subfamília G, TcABCG1, encontra-se super-expresso em cepas resistentes a BZ. Transportadores ABCG foram associados a resistência a drogas em vários organismos. O objetivo central do presente estudo foi caracterizar o gene TcABCG1 em cepas de diferentes linhagens e cuja suscetibilidade a BZ foi definida. A sequência do gene TcABCG1 (1.998 pb) de 14 cepas foi determinada. Observamos algumas variações de aminoácidos na proteína ABC entre as cepas. Análises genealógicas de TcABCG1 definiram quatro clados (TcI, TcII, TcIII e Tcbat). Os dois haplótipos das cepas híbridas TcV e TcVI agruparam com os clados TcII e TcIII. Dados de imunofluorescência indireta em epimastigotas indicam que TcABCG1 está localizado em vesículas intracelulares. / Benznidazole (BZ), drug employed for Chagas disease treatment, has limited efficacy in the chronic phase of the disease. Treatment failures have been attributed mostly to differences in BZ susceptibility among T. cruzi strains. Previous data from our group indicate that one ABC transporter gene of the G subfamily, named TcABCG1, is overexpressed in BZ-resistant strains. ABCG transporters have been associated to drug resistance in several organisms. The central goal of the present study was to characterize TcABCG1 gene in strains belonging to different lineages and of defined BZ susceptibility. TcABCG1 gene sequence (1,998 bp) of 14 strains was determined. Few amino acid substitutions were detected in the ABC transporter protein among the strains. Genealogic analyses of TcABCG1 showed four distinct clades (TcI, TcII, TcIII and Tcbat). The two haplotypes of TcV and TcVI hybrid strains clustered with TcII and TcIII clades. Indirect immunofluorescence analysis in epimastigote forms indicated that TcABCG1 is localized to intracellular vesicles.

Background The Breast Cancer Resistance Protein (BCRP) drug transporter is important for drug disposition and plays a critical role in regulating drug entry into the brain. Its substrate spectrum overlaps with substrates of Multi Drug Resistance Protein 1 (MDR1, P-gp), which influences and complicates the interpretation of data on drug distribution into tissues (e.g. brain). Distinguishing BCRP mediated transport from the transport by the MDR1 is often problematic. However, with new in vitro tools, this is now possible. In this project, two drug compounds, i.e. Dantrolene and Ritonavir, were investigated using these new in vitro models. The results from the experimental in vitro assay were matched with molecular dynamics (MD) simulations. Using coarse-grained (CG) simulations, a model of the BCRP transporter in a lipid bilayer was built, this model is based on the human BCRP structure revealed by Taylor et al (2017). Simulations were run for Dantrolene (a known substrate of BCRP) independently three times, and another with Ritonavir (a non-substrate) three times. Aim To determine substrate specificity for the BCRP transporter for two compounds, and to construct a CG model of BCRP transporter to see whether in silico methods can be used as an alternative for assessing substrate specificity.  Methods Madin-Darby canine kidney (MDCK) II cell line with no endogenous canine MDR1 (cMDR1) expression (MDCKcMDR1-KO), overexpressing human MDR1 (hMDR1) (MDCK-hMDR1cMDR1-KO) and stable expression of human BCRP (hBCRP) (MDCK-hBCRPcMDR1-KO) cells were cultured and used in Transwell experiments. Samples were analyzed using LC-MS/MS to determine the substrate concentrations. Apparent permeability and efflux ratio was calculated and evaluated.  MD simulations used the Martini 3 CG force field, and were run with Gromacs (version 2020.4). Tools including MODELLER, INSANE and others were used to construct the initial model (Webster, 2000; Wassenaar et al., 2015), for parameterization of substrate and non-substrate molecules. And visual inspection was done with the visual molecular dynamics (VMD) program and PyMOL. Results In vitro transport experiment confirmed that Dantrolene is a BCRP specific substrate, and Ritonavir is MDR1 specific substrate. Following simulations of these two compounds, Dantrolene is observed to stay in the transmembrane domains (TMD) for a certain period (on average several hundreds of nanoseconds), while Ritonavir is not found to bind in the TMD, which provides a proof of concept for future studies.

In this work two overall subjects were addressed. 1. In recent years high pressure perturbance has become a tool to investigate the folding energy landscape, the volumetric properties and the conformational equilibria of proteins. Conformational states which are not populated at ambient conditions thus become accessible to spectroscopic characterization. In this work a high pressure application was combined with EPR spectroscopy to investigate three spin labeled proteins, BSA from Bos taurus, HisJ from Salmonella enterica serovar Typhimurium and α-synuclein from Homo sapiens. The goal of these studies was to comprehend the influence of pressure on the respective EPR spectra and to identify changes in conformational equilibria and volumetric properties of the investigated proteins. Studies on BSA revealed a negative activation volume for rotational diffusion of the spin labeled site. Moreover, a rotameric equilibrium was derived from the pressure-dependent side chain dynamics and a correlating negative partial molar volume was observed, indicating a shift of the rotameric equilibrium to lesser order. In this regard it was also shown that a chaotropic medium (guanidine hydrochloride) supports the pressure-dependent effect. Spin labeled sites in the substrate binding protein HisJ revealed to be highly influenceable by low pressures between ambient conditions and 200 bar. Pressurization induced oligomerization and precipitation of the protein. Substrate binding revealed differences in pressure-dependence with regard to a decreased precipitation effect but not in relation to oligomerization. The natively unfolded protein α-synuclein plays a key role in Parkinson´s disease and is known for forming β-sheet rich aggregates, so called amyloid fibrils. The experimental data of this work revealed that hydrostatic pressure can induce a non-amyloid aggregation of monomeric α-synuclein which produces an unspecific oligomer. Furthermore, it was shown that α-synuclein amyloid fibrils can be dissolved by hydrostatic pressure. From the pressure dependent conformational equilibrium between the monomer and the fibril form the change of the partial molar volume of the investigated site was determined. 2. The second subject of this work was focused on different import systems, ATP-binding cassette (ABC) transporters and Energy-Coupling-Factor (ECF) transporters, for amino acids, vitamins and metal ions in prokaryotes. Studies on one bacterial ABC and two ECF transporter systems from two different organisms, the histidine ABC-type transporter HisQMP2 from Salmonella enterica serovar Typhimurium, the biotin ECF-type importer BioMNY from Rhodobacter capsulatus and the cobalt-specific ECF-type transporter CbiMNQO from Rhodobacter capsulatus, were performed using DEER and cw EPR spectroscopy. The goal of the studies on HisQMP2 and BioMNY was to shed light on conformations and dynamics connected to their transporter function. Studies on CbiMNQO aimed at the detection of the substrate in the transporter´s substrate binding unit. For HisQMP2 transport cycle dependent conformational changes and interactions with the substrate binding protein HisJ were revealed. Three different distance values between sites H101R1 and H101’R1 in the transporter´s nucleotide binding domains were assigned to the apo-, the ATP-bound and the posthydrolysis state. It was shown that the closed conformation of the nucleotide binding domains is achieved only in the presence of the ligand-bound HisJ which indicates a transmembrane communication of the association of HisJ to the transporter. Furthermore, interspin distances were determined between sites D86R1-A96R1, C197R1-C104R1 and A118R1-G123R1 in the transmembrane domains HisQ and HisM revealing distinguishable conformational states which correlate to the different states of the nucleotide binding sites during the hydrolysis cycle. Measured interspin distances between HisJ and HisM in the HisQMP2 complex showed that interaction only occurred in the closed state of the HisP2 dimer, the nucleotide bound state. Two different, substrate-dependent interactions between site G24R1 in HisJ and site A96R1 in HisQMP2 were observed, revealing that the substrate-free and substrate-bound form of HisJ both associate with HisQMP2. Distance measurements between sites G24R1 and T151R1 in HisJ in the presence and absence of its substrate revealed interspin distance changes that correlate with the proteins open and closed conformation. Investigations on the ECF transporter BioMNY, reconstituted into nanodiscs, revealed a closure and reopening of the nucleotide binding domains between sites H87R1 and H87’R1 using DEER spectroscopy which delivered interspin distance values that correlate with the apo-, the ATP-bound and the posthydrolysis state of the transporter. Further experiments were aimed to shed light on the transporters substrate-translocation mechanism with regard to the so called toppling over mechanism. Unfortunately, the experiments of this work were not able to give a distinct answer with respect to the proposed model because of the transmembrane domains tendency to oligomerize when reconstituted into nanodiscs. In this work we showed that substrate uptake by the substrate binding unit CbiM of the cobalt-specific ECF transporter CbiMNQO depends on the presence of the small transmembrane protein CbiN. Measurements of spin labeled CbiMN in detergent showed oligomerization of CbiM.