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Abstract: Mycobacterium tuberculosis is responsible for more than 1.6 million deaths each year. One potential antibacterial target in M. tuberculosis is filamentous temperature sensitive protein Z (FtsZ), which is the bacterial homologue of mammalian tubulin, a validated cancer target. M. tuberculosis FtsZ function is essential, with its inhibition leading to arrest of cell division, elongation of the bacterial cell and eventual cell death. However, the development of potent inhibitors against FtsZ has been a challenge owing to the lack of structural information. Here we report multiple crystal structures of M. tuberculosis FtsZ in complex with a coumarin analogue. The 4-hydroxycoumarin binds exclusively to two novel cryptic pockets in nucleotide-free FtsZ, but not to the binary FtsZ-GTP or GDP complexes. Our findings provide a detailed understanding of the molecular basis for cryptic pocket formation, controlled by the conformational flexibility of the H7 helix, and thus reveal an important structural and mechanistic rationale for coumarin antibacterial activity.

Open Access

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Abstract: Biomolecular systems show how host–guest binding can induce changes in molecular behavior, which in turn impact the functions of the system. Here we report an artificial host–guest system where dynamic adaptation during guest binding alters both host conformation and guest dynamics. The self-assembled cage host employed here possesses concave walls and a chirotopic cavity. Complementarity between the curved surfaces of fullerenes and the inner surface of the host cavity leads the host to reconfigure stereochemically in order to bind these guests optimally. The curved molecule corannulene undergoes rapid bowl-to-bowl inversion at room temperature. Its inversion barrier is increased upon binding, however, and increased further upon formation of a ternary complex, where corannulene and a cycloalkane are both bound together. The chiral nature of the host also leads to clear differences in the NMR spectra of ternary complexes involving corannulene and one or the other enantiomer of a chiral guest, which enables the determination of enantiomeric excess by NMR.

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Abstract: The human cell nucleus serves as an important organelle holding the genetic blueprint for life. In this work, X-ray ptychography was applied to assess the masses of human cell nuclei using its unique phase shift information. Measurements were carried out at the I13-1 beamline at the Diamond Light Source that has extremely large transverse coherence properties. The ptychographic diffractive imaging approach allowed imaging of large structures that gave quantitative measurements of the phase shift in 2D projections. In this paper a modified ptychography algorithm that improves the quality of the reconstruction for weak scattering samples is presented. The application of this approach to calculate the mass of several human nuclei is also demonstrated.

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Abstract: The present doctoral thesis examines the properties of carbon-based, porphyrin-based and hybrid carbon-porphyrin nanostructures as promising candidate materials for catalysis (including photocatalysis) applications. I use density functional theory simulations, together with experimental insights from collaborators, to both explain known behaviour and suggest ways in which these materials can be modified for improved catalytic efficiency. Since the catalytic activity of graphitic materials is concentrated on the edges, I investigate their properties in several ways. First, I attempt to understand the properties of folded edges of graphitic nanostructures and quantify their thermodynamic stability, and explain how the application of an electric field leads to their opening. Edge folding can reduce catalytic activity by allowing bond saturation at the edge, but at the same time they provide a way to achieve highly porous carbon-based materials, which could be very useful for catalytic applications. My calculations rationalise the experimental observations about these folded edges. Additionally, I investigate catalysts based on carbon- and iron-based nanostructures, in collaboration with experimentalists. I present models for N-doped graphitic/ferrihydrite nanocatalysts for CO2 reduction, and for Fe-N active sites in graphite-based catalysts. In contrast with carbon nanostructures, porphyrin nanostructures exhibit a welldefined band gap which makes them more useful in photocatalytic applications. In this thesis I explore possible routes to engineer the electronic properties of two types of porphyrin-based materials. The first type consists of fully-organic porphyrin nanostructures with various dimensionalities, and we show how the length of the linkers between porphyrin can be used to engineer their electronic band structures. The second type consists of two-dimensional (2D) porphyrin-based metal-organic frameworks, where we explored different strategies to optimise the photocatalytic behaviour, by changing metal centres, partially reducing the porphyrins or changing the bridges between the porphyrin units. Finally, I consider mixed graphitic/porphyrinic structures, based on the idea that such composites could combine the advantages of both types of structures, leading to superior photocatalytic behaviour. I discuss the adsorption of porphyrins on the surfaces or edges of graphene nanoribbon, and how the interaction affects the electronic properties of the combined structures. Overall, the thesis shows how computer simulation approaches can be used to understand, and also to design and optimise the electronic properties of carbon and porphyrin-based nanostructures to be applied in catalysis and photocatalysis.

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Abstract: Neuronal calcium sensors play a crucial role in different pathways of Ca2+-mediated neurotransmission. Among them guanylate cyclase-activating protein 1 (GCAP1) is expressed only in photoreceptors and activates or inhibits retinal guanylate cyclase 1 (retGC1) depending on cellular Ca2+ concentrations during phototransduction. To date, 22 pathogenic mutations responsible for retinal dystrophy have been associated to GCAP1, but a complete picture of the molecular determinants of the disease is still missing. The only crystal structure available so far is the wt Ca2+-bound monomeric homologue from chicken and no cure exists for retinal dystrophy. In this work I report for the first time that the recombinant human GCAP1 is characterized by a highly dynamic monomer-dimer equilibrium, whose dissociation constant is influenced by salt concentration and by the nature of the divalent ion bound. Surprisingly, I discovered that also the chicken protein shows a similar mechanism, suggesting that this property could be potentially functional for GCAP1 activity and conserved among different species. Despite the large number of crystallization trials, no diffracting crystal of the human GCAP1 was obtained, probably due to the flexible C-terminal tail and the intrinsic dynamicity of the protein. To overcome this issue, I produced a construct lacking the 12 C-term residues and stabilized by a disulfide bridge between the N- and C-term domains which was successfully crystallized. We showed that such engineered construct is able to regulate retGC1 as well as the wt protein. By combining SAXS, protein-protein docking and molecular dynamics simulation we propose two novel three-dimensional models of Ca2+-bound GCAP1 dimer which are stabilized by some of the residues involved in the interaction with the retGC1. We used a biophysical and biochemical approach to thoroughly investigate three pathogenic variants (D100G, E155A and E155G) characterized by mutations in residues directly involved in Ca2+-coordination. All the three variants were able to form oligomers in solutions, showing a decreased affinity for Ca2+ and constitutively activating retGC1 at physiological calcium concentrations. Besides local structural effects, the mutations perturb also the oligomeric state of GCAP1 suggesting that the multimeric assembly of the protein could affect its proper biological function. A recombinant baculovirus for the expression of the cytoplasmic domain of retGC1 in insect cells was produced with the aim to get atomic structural information on the GCAP1/retGC1 5 complex. This will facilitate the identification of drug candidates able to recognize the binding region of the pathogenic GCAP1 mutants with the cyclase and to competitively inhibit the constitutive retGC1 activation, restoring the homeostasis of second messengers which is impaired in retinal degenerative diseases. A preliminary molecular docking based on the crystal structure of the chicken protein was performed and I identified four molecules able to bind the wt human GCAP1 in the millimolar/micromolar range. Together these results shed new light on the quaternary assembly of the wt human GCAP1, showing how the structural changes related to the presence of Ca2+ or Mg2+ are reflected in the different measured dimerization constant. Such conformational changes are in turn likely related to the regulatory mechanism of GCAP1 in the modulation of the retGC1 activity. The differences between the oligomerization state of D100G, E155G and E155A variants suggest a correlation between the altered quaternary assembly of GCAP1 and the aberrant activity of the mutants, representing a step forward to dissect the structural bases of the altered regulatory mechanism of GCAP1 in retinal dystrophies.