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.

Functional photoactive and electroactive nanodevices

Most of current ultra-miniaturized devices are obtained by the top-down approach, in which nanoscale components are fabricated by cutting down larger precursors. Since this physical-engineering method is reaching its limits, especially for components below 30 nm in size, alternative strategies are necessary. Of particular appeal to chemists is the supramolecular bottom-up approach to nanotechnology, a methodology that utilizes the principles of molecular recognition to build materials and devices from molecular components. The subject of this thesis is the photophysical and electrochemical investigation of nanodevices obtained harnessing the principles of supramolecular chemistry. These systems operate in solution-based environments and are investigated at the ensemble level. The majority of the chemical systems discussed here are based on pseudorotaxanes and catenanes. Such supramolecular systems represent prototypes of molecular machines since they are capable of performing simple controlled mechanical movements. Their properties and operation are strictly related to the supramolecular interactions between molecular components (generally photoactive or electroactive molecules) and to the possibility of modulating such interactions by means of external stimuli. The main issues addressed throughout the thesis are: (i) the analysis of the factors that can affect the architecture and perturb the stability of supramolecular systems; (ii) the possibility of controlling the direction of supramolecular motions exploiting the molecular information content; (iii) the development of switchable supramolecular polymers starting from simple host-guest complexes; (iv) the capability of some molecular machines to process information at molecular level, thus behaving as logic devices; (v) the behaviour of molecular machine components in a biological-type environment; (vi) the study of chemically functionalized metal nanoparticles by second harmonic generation spectroscopy.

Structural and biochemical studies of Sporosarcina pasteurii UreE: a nickel-chaperone involved in the urease activation process

Urease is a nickel-dependent enzyme that catalyzes hydrolysis of urea in the last step of organic nitrogen mineralization. Its active site contains a dinuclear center for Ni(II) ions that must be inserted into the apo-enzyme through the action of four accessory proteins (UreD, UreE, UreF, UreG) leading to activation of urease. UreE, acting as a metallo-chaperone, delivers Ni(II) to the preformed complex of apo-urease-UreDFG and has the capability to enhance the GTPase activity of UreG. This study, focused on characterization of UreE from Sporosarcina pasteurii (SpUreE), represents a piece of information on the structure/mobility-function relationships that control nickel binding by SpUreE and its interaction with SpUreG. A calorimetric analysis revealed the occurrence of a binding event between these proteins with positive cooperativity and a stoichiometry consistent with the formation of the (UreE)2-(UreG)2 hetero-oligomer complex. Chemical Shift Perturbations induced by the protein-protein interaction were analyzed using high-resolution NMR spectroscopy, which allowed to characterize the molecular details of the protein surface of SpUreE involved in the complex formation with SpUreG. Moreover, backbone dynamic properties of SpUreE, determined using 15N relaxation analysis, revealed a general mobility in the nanoseconds time-scale, with the fastest motions observed at the C-termini. The latter analysis made it possible for the first time to characterize of the C-terminal portions, known to contain key residues for metal ion binding, that were not observed in the crystal structure of UreE because of disorder. The residues belonging to this portion of SpUreE feature large CSPs upon addition of SpUreG, showing that their chemical environment is directly affected by protein-protein interaction. Metal ion selectivity and affinity of SpUreE for cognate Ni(II) and non cognate Zn(II) metal ions were determined, and the ability of the protein to select Ni(II) over Zn(II), in consistency with the proposed role in Ni(II) cations transport, was established.

Development of Core Design Methods and Tools for Gen-IV Heavy Liquid Metal Cooled Reactors

Heavy Liquid Metal Cooled Reactors are among the concepts, fostered by the GIF, as potentially able to comply with stringent safety, economical, sustainability, proliferation resistance and physical protection requirements. The increasing interest around these innovative systems has highlighted the lack of tools specifically dedicated to their core design stage. The present PhD thesis summarizes the three years effort of, partially, closing the mentioned gap, by rationally defining the role of codes in core design and by creating a development methodology for core design-oriented codes (DOCs) and its subsequent application to the most needed design areas. The covered fields are, in particular, the fuel assembly thermal-hydraulics and the fuel pin thermo-mechanics. Regarding the former, following the established methodology, the sub-channel code ANTEO+ has been conceived. Initially restricted to the forced convection regime and subsequently extended to the mixed one, ANTEO+, via a thorough validation campaign, has been demonstrated a reliable tool for design applications. Concerning the fuel pin thermo-mechanics, the will to include safety-related considerations at the outset of the pin dimensioning process, has given birth to the safety-informed DOC TEMIDE. The proposed DOC development methodology has also been applied to TEMIDE; given the complex interdependence patterns among the numerous phenomena involved in an irradiated fuel pin, to optimize the code final structure, a sensitivity analysis has been performed, in the anticipated application domain. The development methodology has also been tested in the verification and validation phases; the latter, due to the low availability of experiments truly representative of TEMIDE's application domain, has only been a preliminary attempt to test TEMIDE's capabilities in fulfilling the DOC requirements upon which it has been built. In general, the capability of the proposed development methodology for DOCs in delivering tools helping the core designer in preliminary setting the system configuration has been proven.

Additive Manufacturing by LPBF and WAAM of metals: correlation between production process, microstructure and mechanical properties

In the most recent years, Additive Manufacturing (AM) has drawn the attention of both academic research and industry, as it might deeply change and improve several industrial sectors. From the material point of view, AM results in a peculiar microstructure that strictly depends on the conditions of the additive process and directly affects mechanical properties. The present PhD research project aimed at investigating the process-microstructure-properties relationship of additively manufactured metal components. Two technologies belonging to the AM family were considered: Laser-based Powder Bed Fusion (LPBF) and Wire-and-Arc Additive Manufacturing (WAAM). The experimental activity was carried out on different metals of industrial interest: a CoCrMo biomedical alloy and an AlSi7Mg0.6 alloy processed by LPBF, an AlMg4.5Mn alloy and an AISI 304L austenitic stainless steel processed by WAAM. In case of LPBF, great attention was paid to the influence that feedstock material and process parameters exert on hardness, morphological and microstructural features of the produced samples. The analyses, targeted at minimizing microstructural defects, lead to process optimization. For heat-treatable LPBF alloys, innovative post-process heat treatments, tailored on the peculiar hierarchical microstructure induced by LPBF, were developed and deeply investigated. Main mechanical properties of as-built and heat-treated alloys were assessed and they were well-correlated to the specific LPBF microstructure. Results showed that, if properly optimized, samples exhibit a good trade-off between strength and ductility yet in the as-built condition. However, tailored heat treatments succeeded in improving the overall performance of the LPBF alloys. Characterization of WAAM alloys, instead, evidenced the microstructural and mechanical anisotropy typical of AM metals. Experiments revealed also an outstanding anisotropy in the elastic modulus of the austenitic stainless-steel that, along with other mechanical properties, was explained on the basis of microstructural analyses.

Metal additive manufacturing of soft magnetic material for electric machines

This research work concerns the application of additive manufacturing (AM) technologies in new electric mobility sectors. The unmatched freedom that AM offers can potentially change the way electric motors are designed and manufactured. The thesis investigates the possibility of creating optimized electric machines that exploit AM technologies, with potential in various industrial sectors, including automotive and aerospace. In particular, we will evaluate how the design of electric motors can be improved by producing the rotor core using Laser Powder Bed Fusion (LPBF) and how the resulting design choices affect component performance. First, the metallurgical and soft magnetic properties of the pure iron and silicon iron alloy parts (Fe-3% wt.Si) produced by LPBF will be defined and discussed, considering the process parameters and the type of heat treatment. This research shows that using LPBF, both pure iron and iron silicon, the parts have mechanical and magnetic properties different from the laminated ones. Hence, FEM-based modeling will be employed to design the rotor core of an SYN RM machine to minimize torque ripple while maintaining structural integrity. Finally, we suggest that further research should extend the field of applicability to other electrical devices.

Theoretical and experimental study of novel hybrid composite and metal-composites interfaces

The growing demand for lightweight solutions in every field of engineering is driving the industry to seek new technological solutions to exploit the full potential of different materials. The combination of dissimilar materials with distinct property ranges embodies a transparent allocation of component functions while allowing an optimal mix of their characteristics. From both technological and design perspectives, the interaction between dissimilar materials can lead to severe defects that compromise a multi-material hybrid component's performance and its structural integrity. This thesis aims to develop methodologies for designing, manufacturing, and monitoring of hybrid metal-composite joints and hybrid composite components. In Chapter 1, a methodology for designing and manufacturing hybrid aluminum/composite co-cured tubes is assessed. In Chapter 2, a full-field methodology for fiber misalignment detection and stiffness prediction for hybrid, long fiber reinforced composite systems is shown and demonstrated. Chapter 3 reports the development of a novel technology for joining short fiber systems and metals in a one-step co-curing process using lattice structures. Chapter 4 is dedicated to a novel analytical framework for the design optimization of two lattice architectures.

Design of luminescent metal complexes for polymer science

The program of my PhD studies has been dealing with the investigation of the research outcomes that may result from the use of luminescent Iridium(III) cyclometalated complexes in the field of polymer science. In particular, my activity has been focused on exploring two main applicative contexts, i.e. Ir(III) complexes for preparing polymers and in combination with polymers. In the first part, a new set of luminescent Ir(III) complexes was exploited as photocatalysts for light-assisted atom transfer radical polymerization of methyl methacrylate. The decoration of both cyclometalated and ancillary ligands with sp3 hybridized nitrogen substituents together with the use of specific counterions, imparted suitable photophysical and redox properties for an efficient photocatalyzed process. The second part has been focused on the employment of Ir(III) tetrazole complexes as phosphorescent dyes in polymeric materials. Colourless luminescent solar concentrators were prepared blending two Ir(III) cyclometalates with acrylate polymers. Their performances were investigated, leading to promising outcomes comparable, or superior, to those obtained from colourless LSCs based on organic fluorophores. As a complementary approach, Ir(III) complexes were covalently linked to polymers in the side chain, to obtain a new class of metallopolymers. To this extent, a bifunctional tetrazolate molecule, equipped with a coordination site and a polymerizable unit, was designed. The photophysical properties of the resultant luminescent polymeric films were discussed. In the end, an additional project involving both polymers and metal compounds was carried out during my experience as a visiting PhD student at Humboldt – University of Berlin. Polystyrene and polyethylene glycol -based ion-exchange resins were functionalized with peptides through a ligation pathway, for the selective chelation of Copper(II) in aqueous solutions. The coordinating capability of the materials towards Cu2+ ions was tested by ICP-MS analysis. The resins strategically modified with ion-selective peptides, may be exploited in the preparation of water-processing devices.