Residue Specific Interaction of an Unfolded Protein with Solvents in Mixed Water–Ethanol Solutions: A Combined Molecular Dynamics and ONIOM Study

Investigation of protective effect of ethanol on the natural structure of protein with infrared spectroscopy

The stability of biological drugs with protein as an active substance depends heavily on the retention of natural protein structure during freeze-drying. Stabilizers have become important substances in the process of protein freeze-drying. In order to further understand the mechanism of the interaction between protein and stabilizers, human serum albumin (HSA) and simple hydroxyl compound ethanol were used as models. Infrared (IR) spectroscopy combined with chemometrics was implemented to investigate the changes of secondary structure and hydration of HSA when different concentrations of ethanol were considered as interference. Through the analysis of the protein secondary structure and hydrated layer, we found that the addition of ethanol-d6 increased the α-helix of HSA and reduced the disordered structure. The hydrogen bond structure around HSA was enhanced and intermolecular aggregation was reduced through the action of the water molecules. The hypothesis was verified by circular dichroism (CD) and transmission electron microscopy (TEM) observation by adding different concentrations of ethanol-d6. It was found that a small amount of ethanol could protect the native conformation of HSA. In conclusion, this study revealed the mechanism of ethanol as a protein protector, provided a new idea for protein purification process and a theoretical basis for biomolecular interaction.

Unraveling the origin of interactions of hydroxychloroquine with the receptor-binding domain of SARS-CoV-2 in aqueous medium

Interactions of hydroxychloroquin (HCQ) with the receptor binding domain (RBD) of SARS-CoV-2 were studied from atomistic simulation and ONIOM techniques. The key-residues of RBD responsible for the human transmission are recognized to be blocked in a heterogeneous manner with the favorable formation of key-residue:HCQ (1:1) complex. Such heterogeneity in binding was identified to be governed by the differential life-time of the hydrogen bonded water network anchoring HCQ and the key-residues. The intermolecular proton transfer facilitates the most favorable Lys417:HCQ complexation. The study demonstrates that off-target bindings of HCQ need to be minimized to efficiently prevent the transmission of SARS-CoV-2.

Self-regenerated silk fibroin with controlled crystallinity for the reinforcement of silk

HYPOTHESIS

Silk artifacts constitute a fundamental cultural and historical heritage, yet they are affected by degradation that alters the secondary structure of fibroin and weakens the mechanical properties of textiles, hindering their conservation. Feasible and compatible consolidants for silk are still widely needed.

EXPERIMENTS

Here, we propose a robust and reliable method to restore the mechanical properties of fragile, aged silk fibers, based on the adhesion of self-regenerated silk fibroin (SRSF) with controlled crystallinity, prepared from waste silk, to the aged fibers. By varying the concentration of fibroin dispersions, the content of crystalline and amorphous domains in SRSF films can be tuned, as demonstrated by 2D micro-Fourier transform infrared spectroscopy Imaging and thermal analysis.

FINDINGS

The presence of amorphous fibroin domains, distributed between the aged silk fibers, completely recovered their mechanical properties. Instead, the presence of domains with high content of ordered structures, distributed between the fibers, reduced their tensile strength and elongation length. The different mechanical behavior is likely due to the fact that adhesion of crystalline layers produces a brittle material, while amorphous layers with higher fibroin chain mobility increase ductility. The tunability of this treatment allows easy control of desired mechanical properties of degraded silk fibers, simply controlling the crystallinity Vs amorphousness of SRSF; these findings open up new perspectives in textile conservation, in the engineering of biomaterials and materials, and in the preparation of composite materials with enhanced properties.

Can 2,2,2-trifluoroethanol be an efficient protein denaturant than methanol and ethanol under thermal stress?

We report the heterogeneous unfolding phenomenon of a small protein Chymotrypsin Inhibitor 2 in various concentrations of methanol, ethanol and TFE solutions by performing atomistic molecular dynamics simulation studies. Our study reveals that the unfolding phenomenon of CI2 under thermal stress majorly depends on the concentration and the nature of the alcohol.