Browsing by Author "Guzzi, Rita"

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    Molecular simulation of transport proteins in interaction with physiological and pharmacological ligands
    (2014-11-13) Evoli, Stefania; Bartolino, Roberto; Carbone, Vincenzo; Guzzi, Rita; Rizzuti, Bruno
    Molecular complexes of transport proteins with small compounds have been studied by using docking techniques and molecular dynamics simulations. The macromolecules considered are β- lactoglobulin and albumin, i.e. the most abundant proteins in bovine milk and human blood serum, respectively. The ligands are long-chain fatty acids of different length and ibuprofen, a molecule of pharmaceutical interest. Simulations of β-lactoglobulin with fatty acids, ranging from caprylic to stearic acid, revealed the key protein residues that contribute to the binding process. In particular, a rationale was found for the high binding affinity of both stearic and palmitic acid compared to shorter lipids. Moreover, the location of two low-affinity external binding sites was predicted for palmitic acid, by comparing docking results with those obtained for vitamin D3, for which an external site has already been identified in crystallography. For human serum albumin, docking results suggest different candidate binding locations for both charged and neutral ibuprofen. An alchemical free energy approach has been used to estimate the binding affinity for each pose. The results show that charged ibuprofen has a greater affinity for albumin compared to the ligand in the neutral form, suggesting that the former corresponds to the physiological binding state. The simulation findings were compared to experimental results and show an overall good agreement, predicting details of the protein-ligand interaction that include binding geometries and contacts with specific amino acid residues. The overall findings reveal significant features of the binding of well-known ligands to two extensively investigated transport proteins, and show how computational tools can be used to support experimental techniques in a variety of cases.
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    Non-destructive material investigation: advanced techniques across disciplines
    (Università della Calabria, 2025-01-03) Crocco, Maria Caterina; Cipparrone, Gabriella; Agostino, Raffaele Giuseppe; Guzzi, Rita
    The advancement of experimental physical techniques has significantly improved the study of materials across a range of scales, from micro to macro, and has allowed for probing various material characteristics with remarkable precision. Among these techniques, X-ray microtomography and Fourier transform infrared (FTIR) spectroscopy stand out as powerful tools that provide critical insights into the structural and molecular properties of materials. This thesis investigates the complementary applications of these techniques across multiple scientific disciplines, including biology, engineering, and photonics. X-ray microtomography offers high-resolution, non-destructive imaging capabilities, enabling the detailed visualization of internal structures of materials. In contrast, FTIR spectroscopy provides molecular-level information through the identification of vibrational modes, offering a deeper understanding of chemical composition and bonding environments. By combining these techniques, it is possible to bridge the gap between structural and chemical analysis, thus achieving a more holistic characterization of complex systems. This thesis presents a detailed exploration of how the integration of X-ray microtomography, FTIR spectroscopy, and other experimental methods can lead to a more comprehensive understanding of diverse classes of materials. Through case studies in biological sample analysis, defect analysis in engineering materials, and the characterization of optical fibers, this work demonstrates the synergistic potential of these techniques. The overall findings underscore that a multidisciplinary and integrated approach, utilizing advanced physical techniques, not only enriches scientific understanding but also fosters technological innovation across various fields. Keywords: X-ray microtomography, Fourier transform infrared spectroscopy, biological systems, engineering, photonics research, multiple sclerosis, hearts, cells.