Two-dimensional infrared spectroscopic study of cytochrome c peroxidase activity in deep eutectic solvent

Unraveling Hydration Shell Dynamics and Viscosity Effects Around Cyanamide Probes via 2D IR Spectroscopy

Hydration dynamics and solvent viscosity play critical roles in the structure and function of biomolecules. An overwhelming body of evidence suggests that protein and membrane fluctuations are closely linked to solvent fluctuations. While extensive research exists on the use of vibrational probes to detect local interactions and solvent dynamics, fewer studies have explored how the behavior of these reporters changes in response to bulk viscosity. To address this gap, two-dimensional infrared spectroscopy (2D IR) was employed in this study to investigate the ultrafast hydration dynamics around a cyanamide (NCN) probe attached to a nucleoside, deoxycytidine, in aqueous solutions with varying glycerol content. The use of a small vibrational probe on a targeted nucleic acid offers the potential to capture more localized hydration dynamics than alternative methods. The time scales for the frequency correlation decays were found to increase linearly with bulk viscosity, ranging from 0.9 to 11.4 ps over viscosities of 0.96-49.1 cP. Additionally, molecular dynamics (MD) simulations were performed to model the local hydration dynamics around the NCN probe. Interestingly, increasing the glycerol content did not significantly alter the hydration of the deoxycytidine. The MD simulations further suggested that the NCN probe's frequency fluctuations were primarily influenced by the dynamics of water in the second solvation shell. Cage correlation functions, which measure the movement of water molecules in and out of the second solvation shell, exhibited decays that closely matched those of the frequency-fluctuation correlation function (FFCF). These findings offer new insights into hydration dynamics and the impact of viscosity on biological systems.

Can deep eutectic solvents be the best alternatives to ionic liquids and organic solvents: A perspective in enzyme catalytic reactions

As a new generation of green solvents, deep eutectic solvents (DESs) have been considered as a promising alternative to classical organic solvents and ionic liquids (ILs). DESs are normally formed by two or more components via various h-bonds interactions. Up to date, four types of DESs are found, namely, type I DESs (formed by MClx, namely FeCl₂, AlCl₃, ZnCl₂, CuCl₂ and AgCl et al., and quaternary ammonium salts); type II DESs (formed by metal chloride hydrates and quaternary ammonium salts); type III DESs (formed by choline chlorides and different kinds of HBDs) and type IV DESs (formed by salts of transition metals and urea). DESs share many advantages, such as low vapor pressure, good substrate solubility and thermal stability, with ILs, and offering a high potential to be the medium of biocatalysis reactions. In this case, this paper reviews the applications of DESs in enzymatic reactions. Lipases are the most widely used enzyme in DESs systems as their versatile applications in various reactions and robustness. Interestingly, DESs can improve the efficiency of these reactions via enhancing the substrates solubility and the activity and stability of enzymes. Therefore, the directed engineering of DESs for special reactions such as degradation of polymers in high temperature or strong acid-base conditions will be one of the future perspectives of the investigation DESs.

Current understanding and insights towards protein stabilization and activation in deep eutectic solvents as sustainable solvent media

Deep eutectic solvents (DESs) have emerged as a new class of green, designer and biocompatible solvents, an alternative to conventional organic solvents and ionic liquids (ILs) which are comparatively toxic and non-biodegradable. DESs are eutectic mixtures that are formed when a hydrogen bond acceptor (HBA) is mixed with a hydrogen bond donor (HBD) at particular molar ratios by mechanical grinding or under mild heating conditions. Very recently, these solvents have been the center of attention for researchers in biotechnology, biomedicine and various scientific applications. These environmentally benign solvents have a close analogy with ILs; however, they offer certain unique merits over traditional ILs. DESs display remarkable properties such as easy preparation, tunable composition, biodegradability, recyclability, inherently low toxicity, sustainability and biocompatibility; these special features validate DESs as new potential solvents/co-solvents for biomolecules. Mechanistically, the biocompatibility and protein friendly nature of DESs depend on various factors, which include the composition of the DES, viscosity and hydration level. Therefore, it becomes an essential task to bring together all the studies related to protein behaviour in DESs to unlock their biomolecular proficiency. This review specifically highlights recent insights into the biomacromolecular functionality in DESs, including outlines of the solubilization and stabilization of proteins, long term protein packaging, different extraction methods and enzyme activation in the presence of DESs. A literature survey reveals that DESs act as green media in which the protein structure and activity are retained. In some cases, proteins refolded and enzymatic activity was enhanced several fold in the presence of DESs. Furthermore, we have reviewed the possible mechanistic behaviour behind protein stabilization, refolding and activation in DESs. Overall, the main objective of this review is to explicate the advantages of the introduction of DESs for biomolecules and to demonstrate the versatility of these eco-friendly solvents for future bio-based applications.

Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods

Enzymes are dynamic in nature and understanding their activity depends on exploring their overall structural fluctuation as well as transformation at the active site in free state as well as turnover conditions. In this chapter, the application of several different spectroscopy techniques viz. single molecule spectroscopy, ultrafast spectroscopy and Raman spectroscopy in the context of enzyme dynamics and catalysis are discussed. The importance of such studies are significant in the understanding of new discoveries of drugs, cure for some lethal diseases, gene modification as well as in industrial applications.

Mechanism of deep eutectic solvents enhancing catalytic function of cytochrome P450 enzymes in biosynthesis and organic synthesis

Indigo is an insoluble blue dye, which generates serious pollution in its production process. Increasing focus has come to the biosynthesis of indigo that are more environment-preserved and high-efficient. Hence, this study was designed to explore the specific role of various deep eutectic solvents (DESs) on cytochromeP45-BM-3 catalyzing indole to produce indigo. DESs were synthesized by heating and stirring. The structure of the solvent was analyzed by nuclear magnetic resonance (NMR) and fourier transform infrared spectrum (FT-IR), and the relationship between the viscosity, density and refractive index of the solvent, and the water content of the solvent was examined. Circular dichroism spectrometer was used to detect the tertiary structure of the enzyme protein. The effect of solvent type, concentration, pH, temperature, and water content on the catalytic activity and stability of P450 BM-3 was measured using an ultraviolet spectrophotometer. A new solvent biphasic system was established using DESs and buffers, and indigo was prepared using recombinant E. coli-biocatalyzed indole. DESs were low-melting eutectics formed by molecules interaction of components through hydrogen bonding. The physical properties of DESs such as density, viscosity, and refractive index varied with water content and temperature of the solvent. The pH, water content, and temperature of DESs were positively correlated with the catalytic activity of P450 BM-3. To sum up, DESs can improve the catalytic activity and thermal stability of P450 BM-3. Indigo can be efficiently prepared using the DESs-buffer biphasic system.