How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent

Abstract

Deep eutectic solvents (DESs) are utilized as green and inexpensive alternatives to classical ionic liquids. It has been known that some of DESs can be used as solvent in the enzymatic reactions to obtain very green chemical processes. DESs are quite poorly understood at the molecular level. Moreover, we do not know much about the enzyme microstructure in such systems. For example, how some hydrolase can remain active and stable in a deep eutectic solvent including 9 M of urea? In this study, the molecular dynamics of DESs as a liquid was simulated at the molecular level. Urea : choline chloride as a well-known eutectic mixture was chosen as a model DES. The behavior of the lipase as a biocatalyst was studied in this system. For comparison, the enzyme structure was also simulated in 8M urea. The thermal stability of the enzyme was also evaluated in DESs, water, and 8M urea. The enzyme showed very good conformational stability in the urea : choline chloride mixture with about 66% urea (9 M) even at high temperatures. The results are in good agreement with recent experimental observations. In contrast, complete enzyme denaturation occurred in 8M urea with only 12% urea in water. It was found that urea molecules denature the enzyme by interrupting the intra-chain hydrogen bonds in a "direct denaturation mechanism". However, in a urea : choline chloride deep eutectic solvent, as a result of hydrogen bonding with choline and chloride ions, urea molecules have a low diffusion coefficient and cannot reach the protein domains. Interestingly, urea, choline, and chloride ions form hydrogen bonds with the surface residues of the enzyme which, instead of lipase denaturation, leads to greater enzyme stability. To the best of our knowledge, this is the first study in which the microstructural properties of a macromolecule are examined in a deep eutectic solvent.

Chemical modification of biocatalyst for function in supercritical CO2: In silico redesign of stable lipase

“…[62] We found, in our earlier simulation works that one of the initial regions, which decomposed by exposing to scCO 2 and urea 8M is helix5. [63,64] Other researcher have obtained similar result about that and found that modifying helix5 leads to obtaining more active and stable enzymes [62]. Here, we found that carboxylation of Lys 136 can stabilize helix5 from denaturation in scCO 2 .…”

Recent progress on deep eutectic solvents in biocatalysis

“…It is also necessary to consider the ratio of HBA/HBD, which might affect the solvatochromic parameters and the hydrogen bond formation between the reaction mixtures (Kim et al 2016). A molecular dynamics simulation of lipase in ChCl/U firstly proved that the hydrogen bond between DES components could hinder the attack of U to the enzyme function domains, thus resulting in a stabilized enzyme (Monhemi et al 2014). …”

From green chemistry to nature: The versatile role of low transition temperature mixtures

“…with cholinium chloride) whereas its concentration is much more higher [11]. It was found that constituents of the DES form an important non-covalent complex that limit their diffusion to the protein core [12,13]. The DES forms hydrogenbonds with the surface residues of the enzyme which, instead of lipase denaturation, lead to greater enzyme stability.…”