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Reactive natural deep eutectic solvents increase selectivity and efficiency of lipase catalyzed esterification of carbohydrate polyols

A novel approach for the enzymatic esterification of carbohydrate polyols with fatty acids was investigated, with reactive natural deep eutectic solvents (R-NADES) as reaction medium and source of reagents. Three binary hydrophilic R-NADES consisting of choline chloride (ChCl) as hydrogen bond acceptor (HBA) and sugar alcohols (D-sorbitol, xylitol, D-arabitol) as hydrogen bond donors (HBD), were prepared and characterized. The carbohydrate polyol-based R-NADES were durable viscous fluids betw...

Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case

Water plays a key role in biomolecular recognition and binding. Despite the development of several computational and experimental approaches, it is still challenging to comprehensively characterize water-mediated effects on the binding process. Here, we investigate how water affects the binding of Src kinase to one of its inhibitors, PP1. Src kinase is a target for treating several diseases, including cancer. We use biased molecular dynamics simulations, where the hydration of predetermined r...

Effects of knot type in the folding of topologically complex lattice proteins

The folding properties of a protein whose native structure contains a 52 knot are investigated by means of extensive Monte Carlo simulations of a simple lattice model and compared with those of a 31 knot. A 52 knot embedded in the native structure enhances the kinetic stability of the carrier lattice protein in a way that is clearly more pronounced than in the case of the 31 knot. However, this happens at the expense of a severe loss in folding efficiency, an observation that is consistent wi...

The Single-Parameter Bragg–Williams Model for Eutectic Solvents

The study of solid–liquid equilibria offers critical insights into the molecular interactions between constituents in binary mixtures. Predicting these equilibria often requires comprehensive thermodynamic models, yet simplified approaches can provide valuable perspectives. In this work, we explore the application of the Bragg–Williams model to solid–liquid equilibria in binary mixtures leading to the formation of eutectic solvents. This model relies on a single parameter—the molar energy cha...

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids

Mutation protocols are a key tool in computational biophysics for modelling unknown side chain conformations. In particular, these protocols are used to generate the starting structures for molecular dynamics simulations. The accuracy of the initial side chain and backbone placement is crucial to obtain a stable and quickly converging simulation. In this work, we assessed the performance of several mutation protocols in predicting the most probable conformer observed in finite temperature mol...

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