Molecular interactions: metal ions and protein chaperones in the urease system from Helicobacter pylori

Although nickel is a toxic metal for living organisms in its soluble form, its importance in many biological processes recently emerged. In this view, the investigation of the nickel-dependent enzymes urease and [NiFe]-hydrogenase, especially the mechanism of nickel insertion into their active sites, represent two intriguing case studies to understand other analogous systems and therefore to lead to a comprehension of the nickel trafficking inside the cell. Moreover, these two enzymes have been demonstrated to ensure survival and colonization of the human pathogen H. pylori, the only known microorganism able to proliferate in the gastric niche. The right nickel delivering into the urease active site requires the presence of at least four accessory proteins, UreD, UreE, UreF and UreG. Similarly, analogous process is principally mediated by HypA and HypB proteins in the [NiFe]-hydrogenase system. Indeed, HpHypA and HpHypB also have been proposed to act in the activation of the urease enzyme from H. pylori, probably mobilizing nickel ions from HpHypA to the HpUreE-HpUreG complex. A complete comprehension of the interaction mechanism between the accessory proteins and the crosstalk between urease and hydrogenase accessory systems requires the determination of the role of each protein chaperone that strictly depends on their structural and biochemical properties. The availability of HpUreE, HpUreG and HpHypA proteins in a pure form is a pre-requisite to perform all the subsequent protein characterizations, thus their purification was the first aim of this work. Subsequently, the structural and biochemical properties of HpUreE were investigated using multi-angle and quasi-elastic light scattering, as well as NMR and circular dichroism spectroscopy. The thermodynamic parameters of Ni2+ and Zn2+ binding to HpUreE were principally established using isothermal titration calorimetry and the importance of key histidine residues in the process of binding metal ions was studied using site-directed mutagenesis. The molecular details of the HpUreE-HpUreG and HpUreE-HpHypA protein-protein assemblies were also elucidated. The interaction between HpUreE and HpUreG was investigated using ITC and NMR spectroscopy, and the influence of Ni2+ and Zn2+ metal ions on the stabilization of this association was established using native gel electrophoresis, light scattering and thermal denaturation scanning followed by CD spectroscopy. Preliminary HpUreE-HpHypA interaction studies were conducted using ITC. Finally, the possible structural architectures of the two protein-protein assemblies were rationalized using homology modeling and docking computational approaches. All the obtained data were interpreted in order to achieve a more exhaustive picture of the urease activation process, and the correlation with the accessory system of the hydrogenase enzyme, considering the specific role and activity of the involved protein players. A possible function for Zn2+ in the chaperone network involved in Ni2+ trafficking and urease activation is also envisaged.

Bioconjugation and synthetic approach towards enantioenriched gem-difluoromethylene compounds through carbenium ions

Bioconjugation of peptides and asymmetric synthesis of gem-difluoromethylene compounds are areas of the modern organic chemistry for which mild and selective methods continue to be developed. This thesis reports new methodologies for these two areas based on the use of stabilized carbenium ions. The reaction that makes the bioconjugation of peptides possible takes place via the direct nucleophilic substitution of alcohols and is driven by the spontaneous formation of stabilized carbenium ions in water. By reacting with the thiol group of cysteine in very mild conditions and with a high selectivity, these carbenium ions allow the site-specific ligation of polypeptides containing cysteine and their covalent derivatization with functionalized probes. The ligation of the indole ring of tryptophan, an emerging target in bioconjugation, is also shown and takes place in the same conditions. The second area investigated is the challenging access to optically active gem-difluoromethylene compounds. We describe a methodology relying on the synthesis of enantioenriched 1,3-benzodithioles intermediates that are shown to be precursors of the corresponding gem-difluoromethylene analogues by oxidative desulfurization-fluorination. This synthesis takes advantage of the highly enantioselective organocatalytic α-alkylation of aldehydes with the benzodithiolylium ion and of the wide possibilities of synthetic transformations offered by the 1,3-benzodithiole group. This approach allows the asymmetric access to complex gem-difluoromethylene compounds through a late-stage fluorination step, thus avoiding the use of fluorinated building blocks.

Ions and Small Molecules as Modulators of F1FO-ATPase, Mitochondrial Bioenergetics and Cell Metabolism

The properties of the mitochondrial F1FO-ATPase activated by the natural cofactor Mg2+ or by Ca2+, were studied, mainly on heart mitochondria from swine, widely used in translational medicine. The Ca2+ driven conformational changes in the F1FO-ATPase form the mitochondrial permeability transition pore (mPTP), which triggers regulated cell death and is involved in severe pathologies. The Ca2+-activated F1FO-ATPase hydrolyzes ATP with kinetics slightly different from those of the Mg2+-ATPase. Known F1-ATPase inhibitors inhibit both the Ca2+-activated F1FO-ATPase and the mPTP formation strengthening the molecular link between them. The different Gd3+ effects on the Ca2+- and Mg2+-activated F1FO-ATPases confirm their difference as also phenylglyoxal which preferentially inhibits the Ca2+-activated F1FO-ATPase. The effects of phenylarsine and dibromobimane, which interact with differently distant Cys thiols, show that mPTP opening is ruled by nearby or distant dithiols. Bergamot polyphenols and melatonin inhibit the mPTP and ROS formation. H2S, a known cardiovascular protector, unaffects the F1FO-ATPase, but inhibits Ca2+ absorption and indirectly the mPTP, both in swine heart and mussel midgut gland mitochondria. New generation triazoles inhibit the Ca2+-activated F1FO-ATPase and the mPTP, but unaffect the Mg2+-activated F1FOATPase. In parallel, the energy metabolism was investigated in mammalian cells. In boar sperm ATP is mainly produced by mitochondrial oxidative phosphorylation (OXPHOS), even if it decreases over time because of less active mitochondria. Insufficient ATP may induce sperm dysfunction. Also, canine mesenchymal stem cells rely on OXPHOS; those from umbilical cord which produce more ATP than those from adipose tissue, seem preferable for transplant studies. The intestinal porcine enterocyte cell line IPEC-J2, used for human gut research, responds to different fetal bovine serum concentrations by remodeling OXPHOS without altering the bioenergetic parameters. The IPEC-J2 bioenergetics is modulated by Vitamin K vitamers. These data shoulder cell bioenergetics as precious tool for medical research.

Hybrid lead-halide perovskites as novel materials for thin film direct and flexible ionizing radiation detectors

Ionizing radiations are important tools employed every day in the modern society. For example, in medicine they are routinely used for diagnostic and therapy. The large variety of applications leads to the need of novel, more efficient, low-cost ionizing radiation detectors with new functionalities. Personal dosimetry would benefit from wearable detectors able to conform to the body surfaces. Traditional semiconductors used for ionizing radiation direct detectors offer high performance but they are intrinsically stiff, brittle and require high voltages to operate. Hybrid lead-halide perovskites emerged recently as a novel class of materials for ionizing radiation detection. They combine high absorption coefficient, solution processability and high charge transport capability, enabling efficient and low-cost detection. The deposition from solution allows the fabrication of thin-film flexible devices. In this thesis, I studied the detection properties of different types of hybrid perovskites, deposited from solution in thin-film form, and tested under X-rays, gamma-rays and protons beams. I developed the first ultraflexible X-ray detector with exceptional conformability. The effect of coupling organic layers with perovskites was studied at the nanoscale giving a direct demonstration of trap passivation effect at the grain boundaries. Different perovskite formulations were deposited and tested to improve the film stability. I report about the longest aging studies on perovskite X-ray detectors showing that the addition of starch in the precursors’ solution can improve the stability in time with only a 7% decrease in sensitivity after 630 days of storage in ambient conditions. 2D perovskites were also explored as direct detector for X-rays and gamma-rays. Detection of 511 keV photons by a thin-film device is here demonstrated and was validated for monitoring a radiotracer injection. At last, a new approach has been used: a 2D/3Dmixed perovskite thin-film demonstrated to reliably detect 5 MeV protons, envisioning wearable dose monitoring during proton/hadron therapy treatments.

Optoelectronic investigation of defects in hybrid metal halide perovskites

The growing demand for flexible and low-cost electronics has driven research towards the study of novel semiconducting materials to replace traditional semiconductors like silicon and germanium, which are limited by mechanical rigidity and high production cost. Some of the most promising semiconductors in this sense are metal halide perovskites (MHPs), which combine low-cost fabrication and solution processability with exceptional optoelectronic properties like high absorption coefficient, long charge carrier lifetime, and high mobility. These properties, combined with an impressive effort by many research groups around the world, have enabled the fabrication of solar cells with record-breaking efficiencies, and photodetectors with better performance than commercial ones. However, MHP devices are still affected by issues that are hindering their commercialization, such as degradation under humidity and illumination, ion migration, electronic defects, and limited resistance to mechanical stress. The aim of this thesis work is the experimental characterization of these phenomena. We investigated the effects of several factors, such as X-ray irradiation, exposure to environmental gases, and atmosphere during synthesis, on the optoelectronic properties of MHP single crystals. We achieved this by means of optical spectroscopy, electrical measurements, and chemical analyses. We identified the cause of mechanical delamination in MHP/silicon tandem solar cells by atomic force microscopy measurements. We characterized electronic defects and ion migration in MHP single crystals by applying for the first time the photo-induced current transient spectroscopy technique to this class of materials. This research allowed to gain insight into both intrinsic defects, like ion migration and electron trapping, and extrinsic defects, induced by X-ray irradiation, mechanical stress, and exposure to humidity. This research paves the way to the development of methods that heal and passivate these defects, enabling improved performance and stability of MHP optoelectronic devices.