The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.

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Co-processing renewable feedstock in existing refineries could be a prompt and ready-to-use approach to decarbonize the transportation sector, without large modifications to current processing infrastructures. In this study, we explore the possibility of codistilling a blend of fossil crude with hydrothermal liquefaction (HTL) biocrude from primary sewage sludge. HTL biocrude is indeed gaining an increasingly relevant role, because it can be produced from a huge variety of biomass feedstock, including wet byproducts, with no competition with food or feed applications. Despite the highly valuable properties of HTL in comparison with other bio-oils (high heating value, relatively low heteroatoms content, etc.), its introduction in a refinery distillation unit can still be problematic, because of its high acidity and inorganics content. Therefore, partial hydrotreatment was performed prior to blending with a low-sulfur fossil oil, which allowed a blending ratio of 1:4. Codistillation tests were compared with an analogous test with pure fossil oil, in order to assess the contribution of the biomass feed. The obtained distilled cuts were fully analyzed, and a petroleomic approach employing FTICR mass spectrometry was used for a more-detailed characterization at the molecular level. Results showed that biocrude mostly contributes to the high boiling point fractions, especially diesel and residue, although a significant contribution can be also observed to the kerosene range. However, significant amounts of nitrogen were found in the distilled fractions, corresponding to compounds recalcitrant to hydrotreating, resulting in a different carbon number and double-bond equivalent (DBE) distribution. This issue could be controlled by reducing the blending ratio or with specific upgrading treatments. Therefore, codistillation of HTL biocrude with fossil oil is a promising route for the introduction of renewables in the existing refineries.

Bio-oils employed for various industrial purposes, such as biodiesel production, undergo extensive oxidation and degradation during transformation processes. Therefore, it is extremely important to predict their stability at high temperature. We report herein a new procedure based on the optically detected profile of headspace O2 concentration during isotherms at 130 °C for evaluating the oxidation kinetic parameters of several bio-oil feedstocks. The slope of O2 consumption and the induction period duration were related to the oil characteristics (molecular structure, acidity, and presence of intrinsic antioxidants or metals). The increase of the induction time caused by a standardized propyl gallate addition yielded a semiquantitative value of radical generation rate. Investigated oils included used cooking oils; mono-, di-, and triglycerides from natural sources; free fatty acids; transesterified oils; and their blends. With respect to other methods, this characterization presents the advantage of disentangling and evaluating the role of both fatty acids composition and naturally occurring antioxidants, and allows the development of rational strategies for antioxidant protection of oils and of their blends.

SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.