Protein Stability Depends Critically on the Surface Hydrogen-Bonding Network: A Case Study of Bid Protein

Novel Immobilized Enzyme System Using Hydrophobic Dendritic Mesoporous Silica Nanospheres for Efficient Flavor Ester Production

Enzymatic synthesis of flavor esters is widely used in the food and flavor industries, but challenges remain in improving the catalytic efficiency and stability of biocatalysts. This study evaluates the performance of a novel biocatalyst, CALB@DMSN-C8, formed by immobilizing Candida antarctica lipase B (CALB) on hydrophobic dendritic mesoporous silica nanospheres (DMSN-C8), for synthesizing flavor esters. The CALB@DMSN-C8 catalyst achieves a caproic acid conversion rate of 98.5 ± 0.5% in just 30 min and demonstrates outstanding thermal stability, retaining a high conversion efficiency over 20 reuse cycles. To our knowledge, this study represents the most efficient synthesis of flavor esters, including ethyl valerate, ethyl caproate, ethyl heptanoate, and ethyl caprylate, compared to studies in the existing literature. Analysis of aroma characteristics and molecular docking simulations revealed the typical flavor profiles and synthesis mechanisms of various mellow esters. This study develops an innovative strategy by using self-made immobilized lipases to catalyze the production of flavor esters with potential applications in food and cosmetics.

Molecular docking simulation reveals the lipase-substrate binding mechanism in the enzymatic synthesis of diacylglycerol-enriched vegetable oils

Diacylglycerol (DAG) is a functional lipid that is naturally present in vegetable oils in limited concentrations (1 %-5 %). This study proposed an enzymatic method to afford high-content-DAG vegetable oils via a reaction catalyzed by an immobilized lipase, PS@OMS-C8, using high-speed homogenization and molecular distillation. Results indicated that 48.6 % DAG was initially obtained through the enzymatic glycerolysis of rapeseed oil with glycerol, of which 90.2 % was sn-1,3-DAG. PS@OMS-C8 maintained 35.5 % DAG content after 10 reuse cycles, confirming its catalytic stability; this was attributed to lipase immobilization on the ordered mesoporous silica that significantly improve the secondary protein structures, including α-helix and β-sheet, thereby strengthening the rigidity of PS@OMS-C8. In addition to producing DAG-enriched rapeseed oil, other edible oils with 39.4 %-50.2 % DAG content were obtained, as revealed via molecular docking simulation. This study offers new strategies for the sustainable synthesis of vegetable oils with a high content of functional lipids high-content functional lipids.

Ultrasonication-assisted lipase-catalyzed esterification of chlorogenic acid: A comparative study using fatty alcohol and acids in solvent and solvent-free conditions

Chlorogenic acid, a well-known antioxidant, has potential applications in health care, food, and cosmetic sectors. However, its low solubility hinders its application at the industrial scale. The primary goal of the present study was to increase the lipophilic property of chlorogenic acid through esterification using an ultrasonication approach and Novozym® 435 as the catalyst. The esterification was executed in two ways. In the first method, chlorogenic acid was converted to chlorogenic acid ester using octanol in a solvent-free reaction. Catalytic factors such as reaction time (12 h ∼ 36 h), enzyme dosage (10 ∼ 50 mg), and ultrasonication power (90 ∼ 150 W) were optimized using Box-Behnken design (BBD) while temperature (60 ℃) and molar ration (chlorogenic acid/octanol, 1:500) were kept constant. A maximum conversion rate of 95.3 % was achieved when the esterification was performed for 12 h at 120 W ultrasonication power and 50 mg enzyme dosage. Contrary to the first method, when esterification was done using caprylic acid in the presence of 2-methyl-2-butanol as a solvent, the conversion rate was relatively low. Despite optimization of factors including molar ratio, enzyme dosage, and reaction time, the highest conversion rate achieved was of only 36.8 %. Moreover, molecular docking results revealed that the lowest binding energy was between lipase and octanol. The finding of the study clearly stated that the esterification of chlorogenic acid was more effective in a solvent-free condition as compared to in the presence of solvent.

Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches

β-glucosidases play a pivotal role in second-generation biofuel (2G-biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable β-glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 β-glucosidase by two-point mutations E96K (TR1) and M416I (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson-Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization; (ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap; (iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid co-evolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed here can be helpful for future rational approaches to the engineering of optimized β-glucosidases for 2G-biofuel production for industry, biotechnology, and science.

Nanodisc Lipids Exhibit Singular Behaviors Implying Critical Phenomena

Nanodiscs are broadly used for characterization of membrane proteins as they are generally assumed to provide a near-native environment. In fact, it is an open question whether the physical properties of lipids in nanodiscs and membrane vesicles of the same lipid composition are identical. Here, we investigate the properties of lipids (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dilauroyl-sn-glycero-3-phosphocholine, and their mixtures) in two different sample types, nanodiscs and multilamellar vesicles, by means of spin-label electron spin resonance techniques. Our results provide a quantitative description of lipid dynamics and ordering, elucidating the molecular details of how lipids in the two sample types behave differently in response to temperature and lipid composition. We show that the properties of lipids are altered in nanodiscs such that the dissimilarity of the fluid and gel lipid phases is reduced, and the first-order phase transitions are largely abolished in nanodiscs. We unveil that the ensemble of lipids in the middle of a nanodisc bilayer, as probed by the end-chain spin-label 16-PC, is promoted to a state close to a miscibility critical point, thereby rendering the phase transitions continuous. Critical phenomena have recently been proposed to explain features of the heterogeneity in native cell membranes. Our results lay the groundwork for how to establish a near-native environment in nanodiscs with simple organization of lipid components.

Protein Design: From the Aspect of Water Solubility and Stability

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.

Simple Cryoprotectant-Free Method to Advance Pulsed Dipolar ESR Spectroscopy for Capturing Protein Conformational Ensembles

Double electron-electron resonance (DEER) is a powerful technique for studying protein conformations. To preserve the room-temperature ensemble, proteins are usually shock-frozen in liquid nitrogen prior to DEER measurements. The use of cryoprotectant additives is, therefore, necessary to ensure the formation of a vitrified state. Here, we present a simple modification of the freezing process using a flexible fused silica microcapillary, which increases the freezing rates and thus enables DEER measurement without the use of cryoprotectants. The Bid protein, which is highly sensitive to cryoprotectant additives, is used as a model. We show that DEER with the simple modification can successfully reveal the cold denaturation of Bid, which was not possible with the conventional DEER preparations. The DEER result reveals the nature of Bid folding. Our method advances DEER for capturing the chemically and thermally induced conformational changes of a protein in a cryoprotectant-free medium.