Halogen bond is an important non-covalent interaction which is receiving a growing attention in the study of protein-ligand complexes. Many drugs are halogenated molecules and it has been recently shown that many halogenated ligands establish halogen bonds with biomolecules. As the halogen bond nature is due to an anisotropy of the electrostatic potential around halogen atoms, it is not possible to use traditional force fields based on a set of atom-centred charges to study halogen bonds in biomolecules. We show that the introduction of pseudo-atoms on halogens permits us to correctly describe the anisotropy of the electrostatic potential and to perform molecular dynamics simulations on complexes of proteins with halogenated ligands that reproduce experimental values. The results are compared with crystallographic data and with hybrid quantum mechanics/molecular mechanics calculations.

Spike protein (S protein) is the virus “key” to infect cells and is able to strongly bind to the human angiotensin-converting enzyme2 (ACE2), as has been reported. In fact, Spike structure and function is known to be highly important for cell infection as well as for entering the brain. Growing evidence indicates that different types of coronaviruses not only affect the respiratory system, but they might also invade the central nervous system (CNS). However, very little evidence has been so far reported on the presence of COVID-19 in the brain, and the potential exploitation, by this virus, of the lung to brain axis to reach neurons has not been completely understood. In this Article, we assessed the SARS-CoV and SARS-CoV-2 Spike protein sequence, structure, and electrostatic potential using computational approaches. Our results showed that the S proteins of SARS-CoV-2 and SARS-CoV are highly similar, sharing a sequence identity of 77%. In addition, we found that the SARS-CoV-2 S protein is slightly more positively charged than that of SARS-CoV since it contains four more positively charged residues and five less negatively charged residues which may lead to an increased affinity to bind to negatively charged regions of other molecules through nonspecific and specific interactions. Analysis the S protein binding to the host ACE2 receptor showed a 30% higher binding energy for SARS-CoV-2 than for the SARS-CoV S protein. These results might be useful for understanding the mechanism of cell entry, blood-brain barrier crossing, and clinical features related to the CNS infection by SARS-CoV-2.

α-Synuclein is a presynaptic protein associated to Parkinson’s disease, which is unstructured when free in the cytoplasm and adopts α helical conformation when bound to vesicles. After decades of intense studies, α-Synuclein physiology is still difficult to clear up due to its interaction with multiple partners and its involvement in a pletora of neuronal functions. Here, we looked at the remarkably neglected interplay between α-Synuclein and microtubules, which potentially impacts on synaptic functionality. In order to identify the mechanisms underlying these actions, we investigated the interaction between purified α-Synuclein and tubulin. We demonstrated that α-Synuclein binds to microtubules and tubulin α2β2 tetramer; the latter interaction inducing the formation of helical segment(s) in the α-Synuclein polypeptide. This structural change seems to enable α-Synuclein to promote microtubule nucleation and to enhance microtubule growth rate and catastrophe frequency, both in vitro and in cell. We also showed that Parkinson’s disease-linked α-Synuclein variants do not undergo tubulin-induced folding and cause tubulin aggregation rather than polymerization. Our data enable us to propose α-Synuclein as a novel, foldable, microtubule-dynamase, which influences microtubule organisation through its binding to tubulin and its regulating effects on microtubule nucleation and dynamics.

Halogen bonding is a noncovalent interaction between a halogen atom and a nucleophilic site. Interactions involving the π electrons of aromatic rings have received, up to now, little attention, despite the large number of systems in which they are present. We report binding energies of the interaction between either NCX or PhX (X = F, Cl, Br, I) and the aromatic benzene system as determined with the coupled cluster with perturbative triple excitations method [CCSD(T)] extrapolated at the complete basis set limit. Results are compared with those obtained by Møller-Plesset perturbation theory to second order (MP2) and density functional theory (DFT) calculations by using some of the most common functionals. Results show the important role of DFT in studying this interaction.

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes.

Aims. Metis is the first solar coronagraph designed for a space mission and is capable of performing simultaneous imaging of the off-limb solar corona in both visible and UV light. The observations obtained with Metis aboard the Solar Orbiter ESA-NASA observatory will enable us to diagnose, with unprecedented temporal coverage and spatial resolution, the structures and dynamics of the full corona in a square field of view (FoV) of ±2.9 • in width, with an inner circular FoV at 1.6 • , thus spanning the solar atmosphere from 1.7 R to about 9 R , owing to the eccentricity of the spacecraft orbit. Due to the uniqueness of the Solar Orbiter mission profile, Metis will be able to observe the solar corona from a close (0.28 AU, at the closest perihelion) vantage point, achieving increasing out-of-ecliptic views with the increase of the orbit inclination over time. Moreover, observations near perihelion, during the phase of lower rotational velocity of the solar surface relative to the spacecraft, allow longer-term studies of the off-limb coronal features, thus finally disentangling their intrinsic evolution from effects due to solar rotation. Methods. Thanks to a novel occultation design and a combination of a UV interference coating of the mirrors and a spectral bandpass filter, Metis images the solar corona simultaneously in the visible light band, between 580 and 640 nm, and in the UV H i Lyman-α line at 121.6 nm. The visible light channel also includes a broadband polarimeter able to observe the linearly polarised component of the K corona. The coronal images in both the UV H i Lyman-α and polarised visible light are obtained at high spatial resolution with a spatial scale down to about 2000 km and 15000 km at perihelion, in the cases of the visible and UV light, respectively. A temporal resolution down to 1 second can be achieved when observing coronal fluctuations in visible light. Results. The Metis measurements, obtained from different latitudes, will allow for complete characterisation of the main physical parameters and dynamics of the electron and neutral hydrogen/proton plasma components of the corona in the region where the solar wind undergoes the acceleration process and where the onset and initial propagation of coronal mass ejections (CMEs) take place. The near-Sun multi-wavelength coronal imaging performed with Metis, combined with the unique opportunities offered by the Solar Orbiter mission, can effectively address crucial issues of solar physics such as: the origin and heating/acceleration of the fast and slow solar wind streams; the origin, acceleration, and transport of the solar energetic particles; and the transient ejection of coronal mass and its evolution in the inner heliosphere, thus significantly improving our understanding of the region connecting the Sun to the heliosphere and of the processes generating and driving the solar wind and coronal mass ejections. Conclusions. This paper presents the scientific objectives and requirements, the overall optical design of the Metis instrument, t...

Microtubules are polymeric structures formed by the self-assembly of tubulin dimers. The growth and shrinkage of these dynamic arrays have a key role during the cell-proliferation process. This makes tubulin the molecular target of many anticancer drugs currently in use or under clinical trial. Their impressive success is limited by the onset of resistant tumour cells during the treatment, so new resistance-proof molecules need to be developed. Here we use molecular dynamics and free-energy calculations to study the network of interactions that allow microtubule formation. Modelling the protein-protein interface allows us to identify the amino acids responsible for tubulin-tubulin binding and thus to design peptides, which correspond to tubulin subsequences, that interfere with microtubule formation. We show that the application of molecular modelling techniques leads to the identification of peptides that exhibit antitubulin activity both in vitro and in cultured cells.

A number of N2-alkyl and N2-acyl derivatives of guanosine 5'-phosphate (GMP) have been synthesized and tested for their synergistic effect with monosodium L-glutamate (MSG), the prototypical substance imparting umami taste to savory-based foods. Capacities to enhance the taste intensity of MSG (gamma values) were estimated through subjective comparisons of MSG/nucleotide mixtures in water with appropriate solutions of MSG alone. Assuming beta = gamma[nucleotide]/gamma[IMP], beta values of the N2-substituted GMPs were found in the range 1.2-5.7. Such values appear to be related to the chain length of the substituent in the 2-position of the purine nucleus and dependent on the replacement of a CH 2 group with an S atom and/or with an alpha-CO group. These findings indicate that the exocyclic NHR group of the guanine moiety is actively implicated in the synergism between GMP derivatives and MSG. Theoretical calculations suggest that an anti conformation is probably assumed by ribonucleotide molecules interacting with umami receptors.