The effect of ionic liquid on the structure of active site pocket and catalytic activity of a β-glucosidase from Halothermothrix orenii

Impact of surface-active ionic solutions on the structure and function of laccase from trametes versicolor: Insights from molecular dynamics simulations

Many protein-ionic liquid investigations have examined laccase interactions. Laccases are a class of poly-copper oxidoreductases that retain significant biotechnological relevance owing to their notable oxidative capabilities and their application in the elimination of synthetic dyes, phenolic compounds, insecticides, and various other substances. This study investigates the impact of surface active ionic liquids (SAILs), namely, decyltrimethylammonium bromide [N10111][Br] and 1-decyl-3-methylimidazolium chloride [C10mim][Cl] as cationic surfactant ionic liquids and cholinium decanoate [Chl][Dec], an anionic surfactant ionic liquid, on the structure and function of laccase from the fungus Trametes versicolor (TvL) by the molecular dynamics (MD) simulation method. In summary, this study showed that laccase solvent-accessible surface area increased in the ionic liquid [Chl][Dec] while it decreased in the other two ionic liquids. Interestingly, [Chl][Dec] ionic liquid components formed hydrogen bonds with laccase, while [N10111][Br] and [C10mim][Cl] components were unable to form hydrogen bonds with laccase. The quantity of hydrogen bonds formed between water molecules and the enzyme was also diminished in the presence of [Chl][Dec] in comparison to the other two ionic liquids. especially at a concentration of 250 mM. In 250 mM concentrations of [N10111][Br] and [C10mim][Cl], clusters of long-chain cations are likely to form near the copper T1 site. However, even at low [Chl][Dec] concentrations, long [Dec]- chains were observed to penetrate the enzyme near the copper T1 site, and at 250 mM [Chl][Dec], a large cluster of anions occupied the opening of the active site. The results of the analysis also show that the interaction between the [Dec]- anion and the enzyme is stronger than the interaction between [N10111]+ and [C10mim]+ with laccase; in addition, the [Dec]- anion, compared to [Br]- and [Cl]- has a much greater tendency to bind with the enzyme residues.

Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation

Small molecules as ligands target multifunctional ribonucleic acids (RNA) for therapeutic engagement. This study explores how the anticancer DNA intercalator harmine interacts various motifs of RNAs, including the single-stranded A-form poly (rA), the clover leaf tRNAphe, and the double-stranded A-form poly (rC)-poly (rG). Harmine showed the affinity to the polynucleotides in the order, poly (rA) > tRNAphe > poly (rC)·poly (rG). While no induced circular dichroism change was detected with poly (rC)poly (rG), significant structural alterations of poly (rA) followed by tRNAphe and occurrence of concurrent initiation of optical activity in the attached achiral molecule of alkaloid was reported. At 25 °C, the affinity further showed exothermic and entropy-driven binding. The interaction also highlighted heat capacity (ΔC o p ) and Gibbs energy contribution from the hydrophobic transfer (ΔG hyd) of binding with harmine. Molecular docking calculations indicated that harmine exhibits higher affinity for poly (rA) compared to tRNAphe and poly (rC)·poly (rG). Subsequent molecular dynamics simulations were conducted to investigate the binding mode and stability of harmine with poly(A), tRNAphe, and poly (rC)·poly (rG). The results revealed that harmine adopts a partial intercalative binding with poly (rA) and tRNAphe, characterized by pronounced stacking forces and stronger binding free energy observed with poly (rA), while a comparatively weaker binding free energy was observed with tRNAphe. In contrast, the stacking forces with poly (rC)·poly (rG) were comparatively less pronounced and adopts a groove binding mode. It was also supported by ferrocyanide quenching analysis. All these findings univocally provide detailed insight into the binding specificity of harmine, to single stranded poly (rA) over other RNA motifs, probably suggesting a self-structure formation in poly (rA) with harmine and its potential as a lead compound for RNA based drug targeting.

Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models

For quickly predicting the rational arrangement of catalysts and substrates, we previously proposed a method to calculate the interacted volumes of molecules over their 3D point cloud models. However, the nonuniform density in molecular point clouds may lead to incomplete contours in some slices, reducing the accuracy of the previous method. In this paper, we propose a two-step method for more accurately computing molecular interacted volumes. First, by employing a prematched mesh slicing method, we layer the 3D triangular mesh models of the electrostatic potential isosurfaces of two molecules globally, transforming the volume calculation into finding the intersecting areas in each layer. Next, by subdividing polygonal edges, we accurately identify intersecting parts within each layer, ensuring precise calculation of interacted volumes. In addition, we present a concise overview for computing intersecting areas in cases of multiple contour intersections and for improving computational efficiency by incorporating bounding boxes at three stages. Experimental results demonstrate that our method maintains high accuracy in different experimental data sets, with an average relative error of 0.16%. On the same experimental setup, our average relative error is 0.07%, which is lower than the previous algorithm's 1.73%, improving the accuracy and stability in calculating interacted volumes.

MD simulation to comprehend polygalacturonase inactivation mechanism during thermal and non-thermal effects of infrared processing

Food quality is greatly impacted by traditional heat methods for polygalacturonase (PG) inactivation; therefore, it's imperative to develop a novel infrared (IR) inactivation approach and identify its mechanism. Utilizing molecular dynamics (MD) simulation, this study verified the PG's activity, structure, active sites, and substrate channel under the single thermal and non-thermal effects of IR. PG activity was significantly reduced by IR, and structure was unfolded by increasing random coils (65.62 %) and decreasing β-sheets (29.11 %). MD data indicated that the relative locations of PG's active sites were altered by both IR effects, and the enzyme-substrate channel was shortened (10.53 % at 18 μm and 15.79 % at 80 °C). The thermal effect of IR on the inactivation of PG was significantly more pronounced than its non-thermal effect. This study unveiled the mechanism by which the infrared disrupted PG's activity, active sites, and substrate channels; thus, it expanded the infrared technique's efficacy in enzyme control.

Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications

Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics-Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.

Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods

Tea, a widely consumed aromatic beverage, is often adulterated with dyes such as Bismarck brown Y (C.I. 21000) (BBY), Prussian blue, and Plumbago, which pose potential health risks. The objective of this study is to analyze how the food dye BBY interacts with serum protein, bovine serum albumin (BSA). This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl ring due to increased hydrophobic interaction. The energetics of gas phase optimized and stable MD structures of BBY indicated similar values which further confirmed that the conformational changes were minor, and it also exhibited a moderate binding with BSA as shown by the MM/PBSA results. This study enhances our understanding of the molecular-level interactions between BBY and BSA, emphasizing the critical role of hydrophobic interactions.

Computer-aided accurate calculation of interacted volumes for 3D isosurface point clouds of molecular electrostatic potential

The quality of chiral environment (i.e. catalytic pocket) is directly related to the performance of chiral catalysts. The existing methods need super computing power and time, i.e., it is difficult to quickly judge the interaction between chiral catalysts and substrates for accurately evaluating the effects of chiral catalytic pockets. In this paper, for the 3D isosurface point clouds of molecular electrostatic potential, by using computer simulations, we propose a robust method to detect interacted points, and then accurately have the corresponding interacted volumes. First, by using the existing marching cubes algorithm, we construct the 3D models with triangular surface for isosurface point clouds of molecular electrostatic potentials. Second, by using our improved hierarchical bounding boxes algorithm, we significantly filter out most redundant non-collision points. Third, by using the normal vectors of the remaining points and related triangles, we robustly determine the interacted points to construct interacted sets. And finally, by combining the classical slicing with our multi-contour segmenting, we accurately calculate the interacted volumes. Over three groups of the point clouds of the chemical molecules, experimental results show that our method effectively removes the non-interacted points at average rates of 71.65%, 77.76%, and 71.82%, and calculates the interacted volumes with the average relative errors of 1.7%, 1.6%, and 1.9%, respectively.

Thermal Sensitivity of the Enzymatic Activity of β-Glucosidase: Simulations Lend Mechanistic Insights into Experimental Observations

A crucial prerequisite for industrial applications of enzymes is the maintenance of specific activity across wide thermal ranges. β-Glucosidase (EC 3.2.1.21) is an essential enzyme for converting cellulose in biomass to glucose. While the reaction mechanisms of β-glucosidases from various thermal ranges (hyperthermophilic, thermophilic, and mesophilic) are similar, the factors underlying their thermal sensitivity remain obscure. The work presented here aims to unravel the molecular mechanisms underlying the thermal sensitivity of the enzymatic activity of the β-glucosidase BglB from the bacterium Paenibacillus polymyxa. Experiments reveal a maximum enzymatic activity at 315 K, with a marked decrease in the activity below and above this temperature. Employing in silico simulations, we identified the crucial role of the active site tunnel residues in the thermal sensitivity. Specific tunnel residues were identified via energetic decomposition and protein-substrate hydrogen bond analyses. The experimentally observed trends in specific activity with temperature coincide with variations in overall binding free energy changes, showcasing a predominantly electrostatic effect that is consistent with enhanced catalytic pocket-substrate hydrogen bonding (HB) at Topt. The entropic advantage owing to the HB substate reorganization was found to facilitate better substrate binding at 315 K. This study elicits molecular-level insights into the associative mechanisms between thermally enabled fluctuations and enzymatic activity. Crucial differences emerge between molecular mechanisms involving the actual substrate (cellobiose) and a commonly employed chemical analogue. We posit that leveraging the role of fluctuations may reveal unexpected insights into enzyme behavior and offer novel paradigms for enzyme engineering.

Elucidating the Ionic Liquid-Induced Mixed Inhibition of GH1 β-Glucosidase H0HC94

Deciphering the ionic liquid (IL) tolerance of glycoside hydrolases (GHs) to improve their hydrolysis efficiency for fermentable sugar synthesis in the "one-pot" process has long been a hurdle for researchers. In this work, we employed experimental and theoretical approaches to investigate the 1-ethyl-3-methylimidazolium acetate ([C2C1im][MeCO2])-induced inhibition of GH1 β-glucosidase (H0HC94) from Agrobacterium tumefaciens 5A. At 10-15% [C2C1im][MeCO2] concentration, H0HC94 experiences competitive inhibition (R2 = 0.97, alpha = 2.8). As the IL content increased to 20-25%, the inhibition pattern shifted to mixed-type inhibition (R2 = 0.98, alpha = 3.4). These findings were further confirmed through characteristic inhibition plots using Lineweaver-Burk plots. Atomistic molecular dynamics simulations conducted with 0% [C2C1im][MeCO2], 10% [C2C1im][MeCO2], and 25% [C2C1im][MeCO2] revealed the accumulation of [C2C1im]+ at the negatively charged active site of H0HC94 in 10% [C2C1im][MeCO2], supporting the occurrence of competitive inhibition at lower IL concentrations. At higher IL concentrations, the cations and anions bound to the secondary binding sites (SBSs) of H0HC94, leading to a tertiary conformational change, as captured by the principal component analysis based on the free-energy landscape and protein structure networks. The altered conformation of H0HC94 affected the interaction with [C2C1im][MeCO2], which could possibly shift the inhibition from competitive to more mixed-type (competitive + noncompetitive) inhibition, as observed in the experiments. For the first time, we report a combined experimental and theoretical insight behind the mixed inhibition of a GH1 β-glucosidase. Our findings indicated the role of SBS in IL-induced inhibition, which could aid in developing more IL-tolerant β-glucosidases for biorefinery applications.

Structural studies and molecular dynamic simulations of polyphenol oxidase treated by high pressure processing

High pressure processing (HPP) exhibited different effect on polyphenol oxidase (PPO), but the conformational changes was not clear yet. In this study, molecular dynamics simulation combined with spectroscopic experiments were used to explore PPO conformational changes under high pressure at the molecular level. The simulation results showed that high pressure decreased volume and hydrogen bonds, induced changes in active center and movement of loop. Especially, the conformational changes under 200 and above 400 MPa were different. Under 200 MPa, the distance between His 61 and Cu decreased by 0.4 Å, active pocket was exposed, substrate channel became larger. However, the distance increased by 6.1 Å under 600 MPa, active pocket moved inward, substrate channel became narrower. Docking results of 200 and 600 MPa had the highest and lowest binding affinity, whose T-score was 4.657 and 4.130, respectively. These results were consistent with spectroscopic experiments of PPO after HHP.