It is explored that ionic liquids can be suitable solvents for nitrile hydratase catalyzed reactions: A gift of the molecular modeling for the industry

Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations

Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.

The effects of mutation and modification on the structure and stability of human lysozyme: A molecular link between carbamylation and atherosclerosis

Amino acid mutations in some proteins such as lysozyme lead to genetically disorder variants and adverse pathogenic consequences. Recently, amino acid modifications were known as a risk factor in many related diseases such as uremia and atherosclerosis, showing the importance of these surface-structure changes. Although the structural consequences of the hereditary proteins have been examined extensively, such effects for the protein modifications are known to a lesser extent. One drawback in the examination of protein modifications is hardness in experimental detection of modifications by techniques such as NMR and crystallography. Molecular modeling and simulation can help to understand such phenomena at the molecular levels. It is more rational that the effects of both mutation and modification can be compared in a single protein model. Here, molecular dynamics simulation is used to compare the effects of a disease-related carbamylation modification and an amyloidogenic mutation (D67H) in human lysozyme as a model protein. The results show that the carbamylation adversely effects on the tertiary structure, leading to the similar unfolding pathway to the hereditary amyloidogenic form. The carbamylation leads to the instability of the overall protein conformation, especially on the β-domain, which is a characteristic of hereditary amyloidosis in human lysozymes. The aggregation behaviors of both modified and mutant lysozyme were examined by molecular docking calculations. The results showed that the partially unfolded lysozyme might form tight protein aggregates upon carbamylation similar to the amyloidogenic variant. Both single and all-residues carbamylations impose serious conformational changes to the tertiary structure of lysozyme. It was obtained that carbamylation of lysozyme strongly effects on the stability of N-terminal β-sheet, which can produce a highly unstable conformation. The results of this study not only show the adverse structural consequences of a disease-associated post-translational modification, but it also may be very helpful to understand the molecular basis for many carbamylation-related diseases such as atherosclerosis in ESRD patients. The results show that non-native post-translational modifications may be as structurally important as hereditary mutations.

Influence of ionic liquid on Novozym 435-catalyzed the transesterification of castor oil and ethyl caffeate

Caffeic acid (CA), one kind of phenolic acids widely occurring in the plant kingdom, can be used as potential UV protective ingredient and antioxidant. However, the application of CA was limited because of its unsatisfactory solubility in hydrophilic and lipophilic media. In this work, BMIMPF₆, one kind of ionic liquids (ILs), was developed as an environmental friendly reaction media for the enzymatic preparation of CA derivatives by the transesterification of castor oil (CO) and ethyl caffeate (EC). Different series of ILs with BF 4 - , TF 2 - , and PF 6 - were screened and compared, and the effects of transesterification variables [temperature (60-100 °C) enzyme concentration (10-90 mg/mL), substrate molar ratio (CO/EC, 1:1-5:1), water load (0-8%), and reaction pressure] were also investigated. Results showed that, in the IL system, hydrophilic and lipophilic products were formed by two competitive reactions [(i) hydrolysis + transesterification and (ii) transesterification]. The maximum hydrophilic caffeoyl lipids yield (26.10 ± 0.28%) and reaction selectivity for hydrophilic caffeoyl lipids (0.4) was achieved in BMIMPF₆ system. The increases of substrate ratio (molar ratio of CO to EC, from 1:1 to 5:1), water load (from 0 to 8%), and enzyme concentration (from 10 to 90 mg/mL) were in favor of hydrophilic caffeoyl lipid formation. However, the vacuum system and high temperature (from 70 to 100 °C) are favorable for lipophilic caffeoyl lipids formation. Under the optimal reaction conditions (90 °C, 75 mg/mL enzyme concentration, substrate ratio 3:1, 60 h, and 10 mmHg vacuum pressures), the maximum EC conversion was 72.48 ± 2.67%. The activation energies of the transesterification, and the selective formations of lipophilic and hydrophilic products were calculated as 44.55, 47.65, and 54.96 kJ/mol, respectively.

How a multimeric macromolecule is affected by divalent salts? Experimental and simulation study

Salts exist in any cell and living organism in contact with biological macromolecules. How these salts affect biomolecules such as enzyme is important from both basic sciences and practical technologies. It was observed that divalent salts can change structure and function of protein at higher concentrations. Here, we investigated the effect of divalent salt on the behavior of a multimeric enzyme. We treated glucose oxidase as dimer-active enzyme in different CaCl₂ concentration and seen that the enzyme become inactive at high concentration of salt. These experimental results are in agreement with recently published researches. To find a possible mechanism, a series of molecular dynamics simulation of the enzyme were performed at different salt concentration. According to the MD simulation, the conformational changes at the active site and FAD-binding site support the hypothesis of enzyme inactivation at high CaCl₂ concentration. MD simulations also showed that enzyme has an unstable conformation at higher salt concentration which is in agreement with our experimental data. Detailed structural properties of the enzyme have been analyzed under different conditions. To the best of our knowledge, this is the first study that bears detailed structural mechanism about the salt effects on multimeric macromolecules.