1,721,025 research outputs found
Theoretical Study of Vibrational Properties of Peptides: Force Fields in Comparison and Ab Initio Investigation
No full textInfrared (IR) spectroscopy is a valuable tool to obtain information about protein secondary structure. The far-infrared (FIR) spectrum is characterized by a complex combination of different molecular contributions which, for small molecules, may be interpreted with the help of quantum-mechanical (QM) calculations. Unfortunately, the high computational cost of QM calculations makes them inapplicable to larger molecules, such as proteins and peptides. In this work, we present a theoretical study on the secondary structure, molecular properties, and vibrational spectra of different peptides, using both a classical and a QM approach. Our results show that the amide I main peak value, and related quantities, such as dipole strength (DS) and transition dipole moment (TDM), depends on protein secondary structure; in particular, from QM calculations arises that α-rich molecular systems present lower intensities than β-rich ones. Furthermore, it is possible to decouple and identify the intensity of the different contributions of the inter- and intra-molecular motions which characterize the FIR spectrum, starting from the results obtained with QM calculations
The Discovery of Naringenin as Endolysosomal Two-Pore Channel Inhibitor and Its Emerging Role in SARS-CoV-2 Infection
No full textThe flavonoid naringenin (Nar), present in citrus fruits and tomatoes, has been identified as a blocker of an emerging class of human intracellular channels, namely the two-pore channel (TPC) family, whose role has been established in several diseases. Indeed, Nar was shown to be effective against neoangiogenesis, a process essential for solid tumor progression, by specifically impairing TPC activity. The goal of the present review is to illustrate the rationale that links TPC channels to the mechanism of coronavirus infection, and how their inhibition by Nar could be an efficient pharmacological strategy to fight the current pandemic plague COVID-19
The role of metals in protein conformational disorders - The case of prion protein and Aβ -peptide
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Tuning force-field parameters by pressure measurements in micro-canonical simulations
No full textWe show that the dramatic dependence of pressure on the parameters of the intermolecular potential can be exploited to tune them to their best values. We support the viability of this strategy by a careful study of a fully diffusive Lennard-Jones fluid, showing that Lennard-Jones parameters can be easily optimized to better than a 1% accuracy
Designing effective anticancer-radiopeptides. A Molecular Dynamics study of their interaction with model tumor and healthy cell membranes
No full textOne of the greatest merit of the use of radiopeptides in oncology is their selectivity which, however, brings about the drawback that each radiopeptide is specific for a given tumor type. To overcome this problem the direction currently taken in drug design is that of radiolabelling peptide hormones (or their analogues), relying on their intrinsic ability to bind to specific receptors in precise areas of the human body, at the cost, however, of a poor selectivity against healthy cells. We present here an extensive Molecular Dynamics study of a promising alternative inspired by the mechanism through which antimicrobial peptides interact with the negatively charged bacterial membranes. Appropriately modifying the human antimicrobial peptide, LL-37, we designed a functionalized radionuclide carrier capable of binding more strongly to the negatively charged (model) tumor membranes than to the neutral healthy ones. The mechanism behind this behaviour relies on the fact that at the slight acidic pH surrounding tumor tissues the histidines belonging to the peptide get protonated thus making it positively charged. We have investigated by an extended numerical study the way in which this artificial peptide interacts with models of tumor and healthy cell membranes, proving by Potential Mean Force calculations that the affinity of the peptide to model tumor membranes is significantly larger than to healthy ones. These features (high affinity and generic tumor selectivity) recommend antimicrobial derived customized carriers as promising theranostic constructs in cancer diagnostic and therapy
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
The Role of Metals in Misfolding and Aggregation Processes: X-ray Spectroscopy and Numerical Simulations
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