Changes of trypsin in activity and secondary structure induced by complex with trypsin inhibitors and tea polyphenol

Targeting Aminoglycoside Acetyltransferase Activity of Mycobacterium tuberculosis (H37Rv) Derived Eis (Enhanced Intracellular Survival) Protein with Quercetin

Eis (Enhanced intracellular survival) protein is an aminoglycoside acetyltransferase enzyme classified under the family - GNAT (GCN5-related family of N-acetyltransferases) secreted by Mycobacterium tuberculosis (Mtb). The enzymatic activity of Eis results in the acetylation of kanamycin, thereby impairing the drug's action. In this study, we expressed and purified recombinant Eis (rEis) to determine the enzymatic activity of Eis and its potential inhibitor. Glide-enhanced precision docking was used to perform molecular docking with chosen ligands. Quercetin was found to interact Eis with a maximum binding affinity of -8.379 kcal/mol as compared to other ligands. Quercetin shows a specific interaction between the positively charged amino acid arginine in Eis and the aromatic ring of quercetin through π-cation interaction. Further, the effect of rEis was studied on the antibiotic activity of kanamycin A in the presence and absence of quercetin. It was observed that the activity of rEis aminoglycoside acetyltransferase decreased with increasing quercetin concentration. The results from the disk diffusion assay confirmed that increasing the concentration of quercetin inhibits the rEis protein activity. In conclusion, quercetin may act as a potential Eis inhibitor.

Preparation of trypsin-based nanoparticles, colloidal properties and ability to bind bioactive compounds

Nanoparticles (NPs) based on the proteolytic enzyme trypsin (TRY) were prepared by a biocompatible methodology. TRY co-assembled with the anionic polysaccharide chondroitin sulfate (CS) in complexes with well-defined distributions of radii in the range of 100-200 nm by electrostatic complexation at acidic conditions. At pH 7 the complexes were unstable and lost their monomodal size distribution which is potentially related to TRY's weak positive net surface charge and a large negative charge patch that forms at neutral pH. Thermal treatment at conditions which were not expected to interfere with TRY's proteolytic activity was used to stabilize the complexes into NPs that resisted disintegration at pH 7 taking advantage of the ability of the TRY globules to thermally aggregate. The secondary conformation of TRY within the NPs was found fairly unperturbed even after thermal treatment which is crucial for its physiological function. The CS-TRY NPs could bind and encapsulate the bioactive substances curcumin (CUR) and β-carotene (β-C) owing to TRY's hydrophobic domains. The CS-TRY NPs may be considered as a platform for the immobilized active enzyme and multifunctional NPs for hydrophobic bioactive compounds.

Inhibitory effect of lignin from Canna edulis Ker residues on trypsin: kinetics and molecular docking studies

BACKGROUND

Lignin extracted from Canna edulis Ker residues shows a strong inhibitory effect on α-glucosidase and a promoting effect on α-amylase. Protease activity inhibition may play a key role in disease processes, such as metastasis, tumor invasion and bacterial colonization. Hence, in the present study, the inhibitory mechanism of lignin on trypsin was examined, including the interaction type, thermodynamic parameters, structure, reaction site and molecular docking.

RESULTS

The isolated lignin presented an inhibitory effect on trypsin activity with an IC₅₀ value of 1.35 μmol L^-1 . This inhibition was a mixed linear type with a constant K_i of 3.92 μmol L^-1 . The lignin could bind with the key amino acid residue Ser195 on the active site of the trypsin molecule to inhibit its activity, and the phenolic hydroxyl group and -OH on the β-O-4 structure of the lignin molecule were the major groups bound with trypsin.

CONCLUSION

These results illustrate the inhibitory effects of Canna edulis residue lignin on protease, which helps with respect to understanding the possible application of lignin in the food industry in functional foods. © 2020 Society of Chemical Industry.

Electric Field Disruption of Amyloid Aggregation: Potential Noninvasive Therapy for Alzheimer's Disease

The aggregation of β-amyloid peptides is a key event in the formative stages of Alzheimer's disease. Promoting folding and inhibiting aggregation was reported as an effective strategy in reducing Aβ-elicited toxicity. This study experimentally investigates the influence of the external electric field (EF) and magnetic field (MF) of varying strengths on the in vitro fibrillogenesis of hydrophobic core sequence, Aβ_16-22, and its parent peptide, Aβ_1-42. Biophysical methods such as ThT fluorescence, static light scattering, circular dichroism, and infrared spectroscopy suggest that EF has a stabilizing effect on the secondary structure, initiating a conformational switch of Aβ_16-22 and Aβ_1-42 from β to non-β conformation. This observation was further corroborated by dynamic light scattering and transmission electron microscopic studies. To mimic in vivo conditions, we repeated ThT fluorescence assay with Aβ_1-42 in human cerebrospinal fluid to verify EF-mediated modulation. The self-seeding of Aβ_1-42 and cross-seeding with Aβ_1-40 to verify that the autocatalytic amplification of self-assembly as a result of secondary nucleation also yields comparable results in EF-exposed and unexposed samples. Aβ-elicited toxicity of EF-treated samples in two neuroblastoma cell lines (SH-SY5Y and IMR-32) and human embryonic kidney cell line (HEK293) were found to be 15-38% less toxic than the EF untreated ones under identical conditions. Experiments with fluorescent labeled Aβ_1-42 to correlate reduced cytotoxicity and cell internalization suggest a comparatively smaller uptake of the EF-treated peptides. Our results provide a scientific roadmap for future noninvasive, therapeutic solutions for the treatment of Alzheimer's disease.

Inactivation of Soybean Bowman-Birk Inhibitor by Stevioside: Interaction Studies and Application to Soymilk

In this work, the interaction of the soybean Bowman-Birk inhibitor (BBI) with stevioside (STE) was studied by stopped-flow-fluorescence and molecular docking. STE's inactivation of protease-inhibitor activities in soymilk and the influence of STE addition on the sensory character of soymilk were also evaluated. The results indicate that STE binds BBI with a binding constant ( Ka) of 3.38 × 105 L mol-1 to form a 1:1 complex. The docking study reveals that two hydrogen bonds are formed between the side-chain of Lys16 (reactive site 1) of BBI and the glucose-ring hydroxyl groups of STE, which may block BBI from contacting trypsin and thus deactivate the trypsin-inhibitor activity (TIA) of BBI. Moreover, the residual TIA in soymilk could also be inactivated by STE. A mixture of 159 mg/L STE and 60 g/L sucrose could be used for sweetening soymilk without affecting the sensory characteristics when compared to a reference product sweetened with 9% sucrose.

The Role of Dietary Phenolic Compounds in Protein Digestion and Processing Technologies to Improve Their Antinutritive Properties

Digestion is the key step for delivering nutrients and bioactive substances to the body. The way different food components interact with each other and with digestive enzymes can modify the digestion process and affect human health. Understanding how food components interact during digestion is essential for the rational design of functional food products. Plant polyphenols have gained much attention for the bioactive roles they play in the human body. However, their strong beneficial effects on human health have also been associated with a negative impact on the digestion process. Due to the generally low absorption of phenolic compounds after food intake, most of the consumed polyphenols remain in the gastrointestinal tract, where they then can exert inhibitory effects on enzymes involved in the degradation of saccharides, lipids, and proteins. While the inhibitory effects of phenolics on the digestion of energy-rich food components (saccharides and lipids) may be regarded as beneficial, primarily in weight-control diets, their inhibitory effects on the digestion of proteins are not desirable for the reason of reduced utilization of amino acids. The effect of polyphenols on protein digestion is reviewed in this article, with an emphasis on food processing methods to improve the antinutritive properties of polyphenols.

Inactivation of Soybean Trypsin Inhibitor by Epigallocatechin Gallate: Stopped-Flow/Fluorescence, Thermodynamics, and Docking Studies

Tea is one of the most widely daily consumed beverages all over the world, and it is usually consumed with milk and/or soy milk. However, very few researches have studied the interactions between tea polyphenols (TPs) and soy milk proteins as compared with milk proteins. Here, we reported that epigallocatechin gallate (EGCG), a major component of TPs, can effectively inhibit the inhibitory activity of Kunitz trypsin inhibitor (KTI, a major antinutrient in soy milk). The mechanism of inactivation of KTI by EGCG was investigated by stopped-flow/fluorescence, thermodynamics, and docking studies. The results indicated that EGCG binds KTI via both hydrophobic and hydrophilic interactions with an association constant of 6.62 × 105 M-1 to form a 1:1 complex. Molecular docking showed the participation of amino acids includes three amino acid residues (Asn13, Pro72, and Trp117) near the reactive site of KTI, which may prevent KTI from contacting trypsin and hence inactivate KTI.

Small-Angle X-ray Scattering Study of Protein Complexes with Tea Polyphenols

Exploration of the structure of protein complexes, especially the change in conformation and aggregation behavior of proteins upon ligand binding, is crucial to clarify their bioactivities at the molecular level. We applied solution small-angle X-ray scattering (SAXS) to study the complex structure of bovine serum albumin (BSA) and trypsin binding with tea polyphenols, that is, catechin and epigallocatechin gallate (EGCG). We found that tea polyphenols can steadily promote the aggregation of proteins and protein complexes through their bridging effect. The numbers of proteins in the complexes and in the aggregates of complexes are extracted from SAXS intensity profiles, and their dependences as a function of the molar ratio of polyphenol to protein are discussed. EGCG has stronger capability than catechin to promote complex formation and further aggregation, and the aggregates of complexes have a denser core with a relatively smooth surface. The aggregates induced by catechin are loosely packed with a rough surface. BSA shows higher stability than trypsin in the formation of complex with a well-folded conformation. The synergistic unfolding of trypsin results in larger aggregates in the mixtures with more tea polyphenols. The binding affinity and number of tea polyphenols bound to each protein are further determined using fluorescence spectroscopy. The structure of protein complexes explored in this work is referable in the preparation of protein complex-based particles and the understanding of polyphenol-induced formation and further aggregation of protein complexes.

Investigate the binding of catechins to trypsin using docking and molecular dynamics simulation

To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189–195, 214–220 and 225–228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas.

Molecular glues for manipulating enzymes: trypsin inhibition by benzamidine-conjugated molecular glues

Water-soluble bioadhesive polymers bearing multiple guanidinium ion (Gu+) pendants at their side-chain termini (Glue n -BA, n = 10 and 29) that were conjugated with benzamidine (BA) as a trypsin inhibitor were developed. The Glue n -BA molecules are supposed to adhere to oxyanionic regions of the trypsin surface, even in buffer, via a multivalent Gu+/oxyanion salt-bridge interaction, such that their BA group properly blocks the substrate-binding site. In fact, Glue10-BA and Glue29-BA exhibited 35- and 200-fold higher affinities for trypsin, respectively, than a BA derivative without the glue moiety (TEG-BA). Most importantly, Glue10-BA inhibited the protease activity of trypsin 13-fold more than TEG-BA. In sharp contrast, m Glue27-BA, which bears 27 Gu+ units along the main chain and has a 5-fold higher affinity than TEG-BA for trypsin, was inferior even to TEG-BA for trypsin inhibition.

Replica exchange Monte Carlo simulation of human serum albumin-catechin complexes

Replica exchange Monte Carlo simulation equipped with an orientation-enhanced hydrophobic interaction was utilized to study the impacts of molar ratio and ionic strength on the complex formation of human serum albumin (HSA) and catechin. Only a small amount of catechins was found to act as bridges in the formation of HSA-catechin complexes. Selective binding behavior was observed at low catechin to HSA molar ratio (R). Increase of catechin amount can suppress HSA self-aggregation and diminish the selectivity of protein binding sites. Strong saturation binding with short-range interactions was found to level off at around 4.6 catechins per HSA on average, while this number slowly increased with R when long-range interactions were taken into account. Meanwhile, among the three rings of catechin, the 3,4-dihydroxyphenyl (B-ring) shows the strongest preference to bind HSA. Neither the aggregation nor the binding sites of the HSA-catechin complex was sensitive to ionic strength, suggesting that the electrostatic interaction is not a dominant force in such complexes. These results provide a further molecular level understanding of protein-polyphenol binding, and the strategy employed in this work shows a way to bridge phase behaviors at macroscale and the distribution of binding sites at residue level.

Interaction of an amino-functionalized ionic liquid with enzymes: a fluorescence spectroscopy study

The interaction of an amino-functionalized ionic liquid, 1-(2-aminoethyl)-3-butylimidazolium bromide ([NH(2)C(2)C(4)im]Br) with two enzymes, pepsin and papain was investigated using fluorescence spectroscopic technique. It is found that [NH(2)C(2)C(4)im]Br has strong ability to quench the intrinsic fluorescence of pepsin and papain. Quenching mechanisms are considered as static quenching for papain and dynamic quenching for pepsin, respectively. The binding constants and the number of binding sites (n) of [NH(2)C(2)C(4)im]Br to papain were calculated at different temperatures. The thermodynamic parameters such as free energy change (ΔG), enthalpy change (ΔH) and entropy change (ΔS), were calculated by thermodynamic equations. The values of ΔG, ΔH and ΔS suggest that interaction of [NH(2)C(2)C(4)im]Br with the two enzymes is spontaneous. Hydrogen bonding and van der Waals interactions play important roles in the binding process of [NH(2)C(2)C(4)im]Br to papain. However, hydrophobic interaction is the main driving force for the interaction of [NH(2)C(2)C(4)im]Br with pepsin. The results of three-dimensional fluorescence spectra show that [NH(2)C(2)C(4)im]Br has no obvious effects on the polypeptide structures of the two enzymes. Additionally, the [NH(2)C(2)C(4)im]Br-containing system can slightly increase the activities of the two enzymes.

Influence of carbohydrates on the interaction of procyanidin B3 with trypsin

The biological properties of procyanidins, in particular their inhibition of digestive enzymes, have received much attention in the past few years. Dietary carbohydrates are an environmental factor that is known to affect the interaction of procyanidins with proteins. This work aimed at understanding the effect of ionic food carbohydrates (polygalacturonic acid, arabic gum, pectin, and xanthan gum) on the interaction between procyanidins and trypsin. Physical-chemical techniques such as saturation transfer difference-NMR (STD-NMR) spectroscopy, fluorescence quenching, and nephelometry were used to evaluate the interaction process. Using STD-NMR, it was possible to identify the binding of procyanidin B3 to trypsin. The tested carbohydrates prevented the association of procyanidin B3 and trypsin by a competition mechanism in which the ionic character of carbohydrates and their ability to encapsulate procyanidins seem crucial leading to a reduction in STD signal and light scattering and to a recovery of the proteins intrinsic fluorescence. On the basis of these results, it was possible to grade the carbohydrates in their aggregation inhibition ability: XG > PA > AG ≫ PC. These effects may be relevant since the coingestion of procyanidins and ionic carbohydrates are frequent and furthermore since these might negatively affect the antinutritional properties ascribed to procyanidins in the past.

Mechanisms of tannin-induced trypsin inhibition: a molecular approach

Association of procyanidins with enzymes has drawn attention over the past few years. This work aimed to bring insights on interaction of the protease trypsin with the procyanidin dimer (B3). This interaction was characterized by fluorescence quenching, saturation transfer difference (STD) NMR, molecular modeling, and through an enzymatic inhibition assay. Further studies were conducted regarding the influence of pectin on the binding process. A general overview of the binding process may be outlined as follows: a) at low procyanidin concentrations (below the critical micellar concentration-(CMC)) a specific interaction probably driven by hydrogen bonds between the protein backbone and the procyanidin occurs and is associated with the reduction of both enzyme activity and fluorescence; b) at high procyanidin concentration (above the CMC) the interaction becomes nonspecific. This variation in both nature and extent of the interaction with the variation of procyanidin concentration shows how tannin self-association may affect the interaction between tannins and proteins. It was also shown that the mechanism through which pectin affects the interaction between procyanidin B3 and trypsin is of a competitive type.

Effects of water on the structure and low/high temperature stability of confined proteins

In this study well-characterized model proteins were confined in silica nanoporous matrices. Confinement of the proteins in silica matrices allowed us to explore the role of water hydrogen bonding on the structures of the proteins in a broad range of temperatures (-120 degrees C to 95 degrees C). At low temperatures confinement suppressed freezing of water, which remained in the liquid state. We obtained direct evidence that the changes in the hydrogen bonding of water induced changes in the structure of confined proteins. At high temperatures, a reduction of hydrogen bonding of water facilitated protein-silica interactions and the confined proteins underwent denaturation. However, the incorporation of the osmolyte, trehalose, reduced protein-silica interactions, and altered the hydrogen bonding of water. As a result, the high temperature thermal stability of the confined proteins was greatly improved.