Characterization of surface binding sites in glycoside hydrolases: A computational study

Advancements in enzymatic biotransformation and bioactivities of rare ginsenosides: A review

Ginsenoside, the principal active constituent of ginseng, exhibits enhanced bioavailability and medicinal efficacy in rare ginsenosides compared to major ginsenosides. Current research is focused on efficiently and selectively removing sugar groups attached to the major ginsenoside sugar chains to convert them into rare ginsenosides that meet the demands of medical industry and functional foods. The methods for preparing rare ginsenosides encompass chemical, microbial, and enzymatic approaches. Among these, the enzyme conversion method is highly favored by researchers due to its exceptional specificity and robust efficiency. This review summarizes the biological activities of different rare ginsenosides, explores the various glycosidases used in the biotransformation of different major ginsenosides as substrates, and elucidates their respective corresponding biotransformation pathways. These findings will provide valuable references for the development, utilization, and industrial production of ginsenosides.

Progress in the Conversion of Ginsenoside Rb1 into Minor Ginsenosides Using β-Glucosidases

In recent years, minor ginsenosides have received increasing attention due to their outstanding biological activities, yet they are of extremely low content in wild ginseng. Ginsenoside Rb1, which accounts for 20% of the total ginsenosides, is commonly used as a precursor to produce minor ginsenosides via β-glucosidases. To date, many research groups have used different approaches to obtain β-glucosidases that can hydrolyze ginsenoside Rb1. This paper provides a compilation and analysis of relevant literature published mainly in the last decade, focusing on enzymatic hydrolysis pathways, enzymatic characteristics and molecular mechanisms of ginsenoside Rb1 hydrolysis by β-glucosidases. Based on this, it can be concluded that: (1) The β-glucosidases that convert ginsenoside Rb1 are mainly derived from bacteria and fungi and are classified as glycoside hydrolase (GH) families 1 and 3, which hydrolyze ginsenoside Rb1 mainly through the six pathways. (2) Almost all of these β-glucosidases are acidic and neutral enzymes with molecular masses ranging from 44-230 kDa. Furthermore, the different enzymes vary widely in terms of their optimal temperature, degradation products and kinetics. (3) In contrast to the GH1 β-glucosidases, the GH3 β-glucosidases that convert Rb1 show close sequence-function relationships. Mutations affecting the substrate binding site might alter the catalytic efficiency of enzymes and yield different prosapogenins. Further studies should focus on elucidating molecular mechanisms and improving overall performances of β-glucosidases for better application in food and pharmaceutical industries.

Innovations in CAZyme gene diversity and its modification for biorefinery applications

For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.

Molecular dynamics study to improve the substrate adsorption of Saccharomycopsis fibuligera R64 alpha-amylase by designing a new surface binding site

Background: Carbohydrate binding module (CBM) and surface binding site (SBS) are two important parts of amylase which respond to the raw starch digestion. They are related to the enzyme ability to adsorb and to catalyze the starch hydrolysis. However, starch processing is still expensive due to the high temperature in the gelatinization step. Therefore, direct starch digestion is more favorable. One of the solutions is to use α-amylase with high starch adsorptivity, which is expected to be capable of digesting starch below the gelatinization temperature. In Indonesia, Saccharomycopsis fibuligera R64 α-amylase (Sfamy R64) is one of the enzymes with the highest activity on starch. However, its raw starch adsorptivity was low. The aim of this study was to propose an in-silico model of Sfamy R64 mutant by introducing a new SBS using molecular dynamics (MD) simulation.

Methods: The structural behavior of Sfamy R64 and positive control were studied using MD simulation. Furthermore, the mutants of Sfamy R64 were designed to have a stable SBS which mimics the positive control. The substrate affinity in all systems was evaluated using the molecular mechanics generalized Born surface area (MM/GBSA) method.

Results: The stability of a new SBS constructed by seven substitutions and a loop insertion was improved throughout MD simulation. The substrate was consistently bound to the SBS over 55 ns of simulation, as compared to 14 ns in wild-type. The structural behavior of SBS in mutant and positive control was similar. The interaction energies of the positive control, wild-type, and mutant were −17.6, −5.2, and −8.2 kcal/mol, respectively.

Conclusion: The enhanced substrate binding in the mutant, due to the existence of a new SBS, suggests the potential of improving starch adsorptivity of Sfamy R64. This result should be useful in developing an enzyme with better substrate adsorption based on the rational computer-aided molecular design approach.

Asp271 is critical for substrate interaction with the surface binding site in β-agarase a from Zobellia galactanivorans

In the marine environment agar degradation is assured by bacteria that contain large agarolytic systems with enzymes acting in various endo- and exo-modes. Agarase A (AgaA) is an endo-glycoside hydrolase of family 16 considered to initiate degradation of agarose. Agaro-oligosaccharide binding at a unique surface binding site (SBS) in AgaA from Zobellia galactanivorans was investigated by computational methods in conjunction with a structure/sequence guided approach of site-directed mutagenesis probed by surface plasmon resonance binding analysis of agaro-oligosaccharides of DP 4-10. The crystal structure has shown that agaro-octaose interacts via H-bonds and aromatic stacking along 7 subsites (L through R) of the SBS in the inactive catalytic nucleophile mutant AgaA-E147S. D271 is centrally located in the extended SBS where it forms H-bonds to galactose and 3,6-anhydrogalactose residues of agaro-octaose at subsites O and P. We propose D271 is a key residue in ligand binding to the SBS. Thus AgaA-E147S/D271A gave slightly decreasing K_D values from 625 ± 118 to 468 ± 13 μM for agaro-hexaose, -octaose, and -decaose, which represent 3- to 4-fold reduced affinity compared with AgaA-E147S. Molecular dynamics simulations and interaction analyses of AgaA-E147S/D271A indicated disruption of an extended H-bond network supporting that D271 is critical for the functional SBS. Notably, neither AgaA-E147S/W87A nor AgaA-E147S/W277A, designed to eliminate stacking with galactose residues at subsites O and Q, respectively, were produced in soluble form. W87 and W277 may thus control correct folding and structural integrity of AgaA.

Interaction mechanism of olaparib binding to human serum albumin investigated with NMR relaxation data and computational methods

The interaction mechanism between olaparib (OLA) and human serum albumin (HSA) has been investigated using experimental and computational techniques. An NMR relaxation approach based on the analysis of proton selective and non-selective spin-lattice relaxation rates at different temperatures can provide quantitative information about the affinity index and the thermodynamic equilibrium constant of the OLA-HSA system. The affinity index and the thermodynamic equilibrium constant decreased as temperature increased, indicating that the interactions between OLA and HSA could be weakened as temperature increased. Molecular docking and dynamics simulations revealed that OLA stably bound to subdomain II (site 1), and OLA could induce the conformational and micro-environmental changes in HSA. CD results suggested that α-helix content decreased after OLA was added, demonstrating that OLA affected the secondary structure of HSA.

Computational Model of the Effect of a Surface-Binding Site on the Saccharomycopsis fibuligera R64 α-Amylase to the Substrate Adsorption

α-Amylase is one of the important enzymes in the starch-processing industry. However, starch processing requires high temperature, thus resulting in high cost. The high adsorptivity of α-amylase to the substrate allows this enzyme to digest the starch at a lower temperature. α-Amylase from Saccharomycopsis fibuligera R64 (Sfamy R64), a locally sourced enzyme from Indonesia, has a high amylolytic activity but low starch adsorptivity. The objective of this study was to design a computational model of Sfamy R64 with increased starch adsorptivity using bioinformatics method. The model structure of Sfamy R64 was compared with the positive control, ie, Aspergillus niger α-amylase. The structural comparison showed that Sfamy R64 lacks the surface-binding site (SBS). An SBS was introduced to the structure of Sfamy R64 by S383Y/S386W mutations. The dynamics and binding affinity of the SBS of mutant to the substrate were also improved and comparable with that of the positive control.