Revisiting the enzymatic kinetics of pepsin using isothermal titration calorimetry

The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity

We discuss the diverse functions of proteases in the context of their biotechnological and medical significance, as well as analytical approaches used to determine the functional activity of these enzymes. An insight into modern approaches to studying the kinetics and specificity of proteases, based on spectral (absorption, fluorescence), mass spectrometric, immunological, calorimetric, and electrochemical methods of analysis is given. We also examine in detail electrochemical systems for determining the activity and specificity of proteases. Particular attention is given to exploring innovative electrochemical systems based on the detection of the electrochemical oxidation signal of amino acid residues, thereby eliminating the need for extra redox labels in the process of peptide synthesis. In the review, we highlight the main prospects for the further development of electrochemical systems for the study of biotechnologically and medically significant proteases, which will enable the miniaturization of the analytical process for determining the catalytic activity of these enzymes.

Purification and identification of novel antioxidant peptides derived from Bombyx mori pupae hydrolysates

The biological importance of antioxidant peptides was the focus of new natural sources of food preservatives. Bombyx mori pupae are considered a valuable by-product of the silk-reeling industry due to their high-quality protein content. This study aimed to purify and identify the antioxidant peptides obtained from enzymatically hydrolyzed B. mori pupae, which could be used as new sources of natural food preservatives. Among the prepared hydrolysates, pepsin hydrolysate with the highest antioxidant activities was purified sequentially using ultrafiltration and reversed-phase high-performance liquid chromatography (RP-HPLC). The DPPH radical scavenging and ferrous ion chelating activity were used to evaluate antioxidant activity. Fractions with high activity were further analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Three peptides were identified as Glu-Asn-Ile-Ile-Leu-Phe-Arg (ENIILFR), Leu-Asn-Lys-Asp-Leu-Met-Arg (LNKDLMR), and Met-Leu-Ile-Ile-Ile-Met-Arg (MLIIIMR), respectively. All three novel identified peptides exhibited significantly stronger antioxidant capacity than synthetic antioxidants used in the food industry, including butylated hydroxyanisole (BHA), and butylated hydroxytoluene (BHT). ENIILFR showed the best antioxidant activity. These findings indicate that the three peptides have potential applications as natural antioxidants in the food industry.

Efficacy and safety of iguratimod in the treatment of rheumatic and autoimmune diseases: a meta-analysis and systematic review of 84 randomized controlled trials

Objective: To evaluate efficacy and safety of iguratimod (IGU) in the treatment of rheumatic and autoimmune diseases. Methods: Databases such as Pubmed, Embase, Sinomed were searched (as of July 2022) to collect randomized controlled trials (RCTs) of IGU in the treatment of rheumatic and autoimmune diseases. Two researchers independently screened the literature, extracted data, assessed the risk of bias of the included literature, and performed meta-analysis using RevMan 5.4 software. Results: A total of 84 RCTs and 4 types of rheumatic and autoimmune diseases [rheumatoid arthritis (RA), ankylosing spondylitis (AS), primary Sjögren's syndrome (PSS) and Autoimmune disease with interstitial pneumonia]. Forty-three RCTs reported RA and showed that IGU + MTX therapy can improve ACR20 (RR 1.45 [1.14, 1.84], p = 0.003), ACR50 (RR 1.80 [1.43, 2.26], p < 0.0000), ACR70 (RR 1.84 [1.27, 2.67], p = 0.001), DAS28 (WMD -1.11 [-1.69, -0.52], p = 0.0002), reduce ESR (WMD -11.05 [-14.58, -7.51], p < 0.00001), CRP (SMD -1.52 [-2.02, -1.02], p < 0.00001), RF (SMD -1.65 [-2.48, -0.82], p < 0.0001), and have a lower incidence of adverse events (RR 0.84 [0.78, 0.91], p < 0.00001) than the control group. Nine RCTs reported AS and showed that IGU can decrease the BASDAI score (SMD -1.62 [-2.20, -1.05], p < 0.00001), BASFI score (WMD -1.07 [-1.39, -0.75], p < 0.00001), VAS (WMD -2.01 [-2.83, -1.19], p < 0.00001), inflammation levels (decreasing ESR, CRP and TNF-α). Thirty-two RCTs reported PSS and showed that IGU can reduce the ESSPRI score (IGU + other therapy group: WMD -1.71 [-2.44, -0.98], p < 0.00001; IGU only group: WMD -2.10 [-2.40, -1.81], p < 0.00001) and ESSDAI score (IGU + other therapy group: WMD -1.62 [-2.30, -0.94], p < 0.00001; IGU only group: WMD -1.51 [-1.65, -1.37], p < 0.00001), inhibit the inflammation factors (reduce ESR, CRP and RF) and increase Schirmer's test score (IGU + other therapy group: WMD 2.18 [1.76, 2.59], p < 0.00001; IGU only group: WMD 1.55 [0.35, 2.75], p = 0.01); The incidence of adverse events in IGU group was also lower than that in control group (IGU only group: RR 0.66 [0.48, 0.98], p = 0.01). Three RCTs reported Autoimmune disease with interstitial pneumonia and showed that IGU may improve lung function. Conclusion: Based on current evidence, IGU may be a safe and effective therapy for RA, AS, PSS and autoimmune diseases with interstitial pneumonia. Systematic Review Registration: (CRD42021289489).

Rise of tissue- and species-specific 3D bioprinting based on decellularized extracellular matrix-derived bioinks and bioresins

Thanks to its natural complexity and functionality, decellularized extracellular matrix (dECM) serves as an excellent foundation for creating highly cell-compatible bioinks and bioresins. This enables the bioprinted cells to thrive in an environment that closely mimics their native ECM composition and offers customizable biomechanical properties. To formulate dECM bioinks and bioresins, one must first pulverize and/or solubilize the dECM into non-crosslinked fragments, which can then be chemically modified as needed. In bioprinting, the solubilized dECM-derived material is typically deposited and/or crosslinked in a layer-by-layer fashion to build 3D hydrogel structures. Since the introduction of the first liver-derived dECM-based bioinks, a wide variety of decellularized tissue have been employed in bioprinting, including kidney, heart, cartilage, and adipose tissue among others. This review aims to summarize the critical steps involved in tissue-derived dECM bioprinting, starting from the decellularization of the ECM to the standardized formulation of bioinks and bioresins, ultimately leading to the reproducible bioprinting of tissue constructs. Notably, this discussion also covers photocrosslinkable dECM bioresins, which are particularly attractive due to their ability to provide precise spatiotemporal control over the gelation in bioprinting. Both in extrusion printing and vat photopolymerization, there is a need for more standardized protocols to fully harness the unique properties of dECM-derived materials. In addition to mammalian tissues, the most recent bioprinting approaches involve the use of microbial extracellular polymeric substances in bioprinting of bacteria. This presents similar challenges as those encountered in mammalian cell printing and represents a fascinating frontier in bioprinting technology.

Electrochemical biosensor for trypsin activity assay based on cleavage of immobilized tyrosine-containing peptide

In this work, we proposed a biosensor for trypsin proteolytic activity assay using immobilization of model peptides on screen-printed electrodes (SPE) modified with gold nanoparticles (AuNPs) prepared by electrosynthetic method. Sensing of proteolytic activity was based on electrochemical oxidation of tyrosine residues of peptides. We designed peptides containing N-terminal cysteine residue for immobilization on an SPE, modified with gold nanoparticles, trypsin-specific cleavage site and tyrosine residue as a redox label. The peptides were immobilized on SPE by formation of chemical bonds between mercapto groups of the N-terminal cysteine residues and AuNPs. After the incubation with trypsin, time-dependent cleavage of the immobilized peptides was observed by decline in tyrosine electrochemical oxidation signal. The kinetic parameters of trypsin, such as the catalytic constant (k_cat), the Michaelis constant (K_M) and the catalytic efficiency (k_cat/K_M), toward the CGGGRYR peptide were determined as 0.33 ± 0.01 min^-1, 198 ± 24 nM and 0.0016 min^-1 nM^-1, respectively. Using the developed biosensor, we demonstrated the possibility of analysis of trypsin specificity toward the peptides with amino acid residues disrupting proteolysis. Further, we designed the peptides with proline or glutamic acid residues after the cleavage site (CGGRPYR and CGGREYR), and trypsin had reduced activity toward both of them according to the existing knowledge of the enzyme specificity. The developed biosensor system allows one to perform a comparative analysis of the protease steady-state kinetic parameters and specificity toward model peptides with different amino acid sequences.

3-Hydroxyflavone - bovine serum albumin complex used as fluorescent probe for the detection of pepsin

In this study, a method for the determination of pepsin using a 3-hydroxyflavone (3-HF)-bovine serum albumin (BSA) complex as a fluorescent probe was established. Under acidic conditions, 3-HF can react with BSA to emit strong green fluorescence, which involves an excited state intramolecular proton transfer and fluorescence resonance energy transfer. After pepsin is added, the fluorescence of the 3-HF-BSA system is quenched due to the hydrolysis of BSA. The degree of 3-HF-BSA fluorescence quenching has a good linear relationship with the concentration of pepsin in the range of 10-80 μg/mL. The correlation coefficient was R² = 0.9932 and the detection limit was 2.41 μg/mL. This method has high selectivity and good stability and has been used to determine pepsin in real samples with satisfactory results.

Natural Small-Molecule-Based Carrier-Free Self-Assembly Library Originated from Traditional Chinese Herbal Medicine

The carrier-free self-assembly of small molecules opens a new window for the development of nanomaterials. This study is dedicated to developing binary small-molecular self-assemblies derived from phytochemicals in traditional Chinese herbal medicine. Among them, Rhei Radix et Rhizoma and Coptidis Rhizoma are a common pair used in clinics for thousands of years. Here, we found that there were numerous spherical supramolecular nanoparticles (NPs) originated from Rhei Radix et Rhizoma and Coptidis Rhizoma decoction. Ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) was used to analyze the composition of the supramolecules, and a total of 119 phytochemicals were identified (23 anthraquinones, 31 alkaloids, 24 organic acids, 8 tannins, and other components). Isothermal titration calorimetry (ITC) showed that the interaction between Rhei Radix et Rhizoma and Coptidis Rhizoma was a spontaneous exothermic reaction, indicating that their phytochemicals had the property of self-assembly and interacted to form supramolecules in the decocting process. Furthermore, scanning electron microscopy (SEM), UV, IR, NMR, and ITC were used to verify that rhein and coptisine could self-assemble into nanofibers (Rhe-Cop NFs), while emodin and coptisine could self-assemble into nanoparticles (Emo-Cop NPs). The formation mechanism analysis of the self-assemblies revealed that they were induced by electrostatic attraction, hydrogen bonding, and π-π stacking, forming nanospheres of about 50 nm and nanofibers. The current study not only provides an idea of discovering carrier-free self-assemblies from traditional herbal medicine decoction but also supplies a reference for the design of binary self-assembly of small molecules in the future.

Convergence in determining enzyme functional descriptors across Kemp eliminase variants

Molecular simulations have been extensively employed to accelerate biocatalytic discoveries. Enzyme functional descriptors derived from molecular simulations have been leveraged to guide the search for beneficial enzyme mutants. However, the ideal active-site region size for computing the descriptors over multiple enzyme variants remains untested. Here, we conducted convergence tests for dynamics-derived and electrostatic descriptors on 18 Kemp eliminase variants across six active-site regions with various boundary distances to the substrate. The tested descriptors include the root-mean-square deviation of the active-site region, the solvent accessible surface area ratio between the substrate and active site, and the projection of the electric field (EF) on the breaking C-H bond. All descriptors were evaluated using molecular mechanics methods. To understand the effects of electronic structure, the EF was also evaluated using quantum mechanics/molecular mechanics methods. The descriptor values were computed for 18 Kemp eliminase variants. Spearman correlation matrices were used to determine the region size condition under which further expansion of the region boundary does not substantially change the ranking of descriptor values. We observed that protein dynamics-derived descriptors, including RMSD_{active_site} and SASA_ratio, converge at a distance cutoff of 5 Å from the substrate. The electrostatic descriptor, EF_C-H, converges at 6 Å using molecular mechanics methods with truncated enzyme models and 4 Å using quantum mechanics/molecular mechanics methods with whole enzyme model. This study serves as a future reference to determine descriptors for predictive modeling of enzyme engineering.

Use of fungal and bacterial protease preparations to enhance extraction of lipid from fish roe: effect on lipidomic profile of extracted oil

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Lipid extraction of fish roe was evaluated after hydrolysis with HT, FP-II and Alcalase proteases.

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Alcalase hydrolysis of fish roe protein was more extensive than that of HT and FP-II.

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The highest total lipid yield was obtained following hydrolysis of fish roe with Alcalase.

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Alcalase hydrolysis achieved the greatest degree of hydrolysis and yielded less oxidised lipid.

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The yield of omega-3 fatty acids and phospholipids was highest after HT hydrolysis.

The present study investigated the hydrolysis of protein in hoki roe homogenate using a HT (bacterial), a FP-II (fungal) protease preparations and Alcalase (bacterial) to enhance lipid yield extraction. The degree of hydrolysis was determined at various pH, temperature and time using casein and hoki roe. Total lipid extraction and lipidomic analysis was carried out following proteolysis of hoki roe homogenate. The degree of hydrolysis and SDS-PAGE revealed that the hydrolytic capability of Alcalase was better than HT and FPII. The total extracted lipid yield was better following hydrolysis with Alcalase (19.29 %), compared to HT (18.29 %) and FPII (18.33 %). However, the total phospholipid (PL) and n-3 fatty acid yields were better from HT hydrolysed hoki roe homogenate (PL = 30.7 μmol/g; n-3 = 10.5 %), compared to Alcalase (PL = 22 μmol/g; n-3 = 5.95 %). Overall, this study indicates that HT protease preparation hydrolysis of fish roe homogenate can both enhance lipid extraction and retain lipid quality.

Spatial-temporal mapping of the intra-gastric pepsin concentration and proteolysis in pigs fed egg white gels

While there is a consensus that food structure affects food digestion, the underlying mechanisms remain poorly understood. A previous experiment in pigs fed egg white gels of same composition but different structures evidenced such effect on food gastric disintegration. In this study, we detailed the consequences on intra-gastric pH, pepsin concentration and proteolysis by sampling throughout the stomach over 6 h digestion. Subsequent amino acid absorption was investigated as well by blood sampling. While acidification was almost homogeneous after 6 h digestion regardless of the gel, pepsin distribution never became uniform. Pepsin started to accumulate in the pylorus/antrum region before concentrating in the body stomach beyond 4 h, time from which proteolysis really started. Interestingly, the more acidic and soft gel resulted in a soon (60 min) increase in proteolysis, an earlier and more intense peak of plasmatic amino acids, and a final pepsin concentration three times higher than with the other gels.

A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values

Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.

Exploration of interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide from Wakame (Undaria pinnatifida)

The interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide KNFL from Wakame was explored using isothermal titration calorimetry, multiple spectroscopic techniques and molecular dynamics simulations, and an inhibition model was established based on free energy binding theory. The experiments revealed that the binding of KNFL to ACE was a spontaneous exothermic process driven by enthalpy and entropy and occurred via multiple binding sites to form stable complexes. The complexes may be formed through multiple steps of inducing fit and conformational selection. The peptide KNFL had a fluorescence quenching effect on ACE and its addition not only affected the microenvironment around the ACE Trp and Tyr residues, but also increased the diameter and altered the conformation of ACE. This study should prove useful for improving our understanding of the mechanism of ACE inhibitory peptides.

A discussion on the affecting factors of the fitting procedures' reliability in isothermal titration calorimetry analysis

The standard isothermal titration calorimetry (ITC) curve, characterized as a typical sigmoid is strictly confined by the so-called c value, which is a ratio of titrand concentration to K_D. The proper c value with a range from 5 to 500 is commonly recommended as a standard protocol in routine detection process for acquiring the reliable fitting results in 1:1 binding mode. However, if the c value is less than "1" due to the weak binding or low concentration of analyte, fitting precision gets unstable and susceptible to the data noise. Herein, we first got a deep discussion into the reliability of the fitting procedure for 1:1 binding mode by data simulation, then quantized the effect of several affecting factors on the precision of parameters estimation through mathematical analysis. Finally, we proposed the value of 2~4 times K_D for final ligand concentration is optimal for the ITC titration in low c system (c < 1). All the theoretical derivations were further verified by a practical experiment of Magnesium-EDTA binding test.

Catechin Inhibits the Release of Advanced Glycation End Products during Glycated Bovine Serum Albumin Digestion and Corresponding Mechanisms In Vitro

Glycated proteins are the main source of dietary advanced glycation end products (AGEs). Glycated proteins are enzymatically hydrolyzed in the gastrointestinal tract, which releases more absorbable and smaller potentially harmful AGEs. This study investigated the inhibitory effect of catechin on AGE release from glycated bovine serum albumin (G-BSA) during gastrointestinal digestion. Catechin inhibited AGE release during gastrointestinal digestion, especially in the gastric digestion stage. Additionally, catechin altered these peptides in the small intestine by reducing G-BSA digestibility. The proposed mechanism involves interactions between catechin and G-BSA/digestive enzymes, inhibiting digestive enzyme activity and changing the conformation of G-BSA. Catechin reduced G-BSA β-sheet content and protected the helical conformation. Moreover, catechin enhanced the antioxidant capacity of G-BSA, which could attenuate postprandial oxidative stress in the gastrointestinal tract caused by the release of AGEs. This study improves our understanding of the nutritional and health effects of catechin on dietary AGEs during gastrointestinal digestion.

In vitro protein and starch digestion kinetics of individual chickpea cells: from static to more complex in vitro digestion approaches

Attention has been given to more (semi-)dynamic in vitro digestion approaches ascertaining the consequences of dynamic in vivo aspects on in vitro digestion kinetics. As these often come with time and economical constraints, evaluating the consequence of stepwise increasing the complexity of static in vitro approaches using easy-to-handle digestion set-ups has been the center of our interest. Starting from the INFOGEST static in vitro protocol, we studied the influence of static gastric pH versus gradual gastric pH change (pH 6.3 to pH 2.5 in 2 h) on macronutrient digestion in individual cotyledon cells derived from chickpeas. Little effect on small intestinal proteolysis was observed comparing the applied digestion conditions. Contrary, the implementation of a gradual gastric pH change, with and without the addition of salivary α-amylase, altered starch digestion kinetics rates, and extents by 25%. The evaluation of starch and protein digestion, being co-embedded in cotyledon cells, did not only confirm but account for the interdependent digestion behavior. The insights generated in this study demonstrate the possibility of using a hypothesis-based approach to introduce dynamic factors to in vitro models while sticking to simple and cost-efficient set-ups.

Protein acidification and hydrolysis by pepsin ensure efficient trypsin-catalyzed hydrolysis

Enzyme-catalysed hydrolysis is important in protein digestion. Protein hydrolysis is initiated by pepsin at low pH in the stomach. However, pepsin action and acidification happen simultaneously to gastric emptying, especially for liquid meals. Therefore, different extents of exposure to the gastric environment change the composition of the chyme that is emptied from the stomach into the small intestine over time. We assessed the susceptibility of a protein to trypsin-catalysed hydrolysis in the small intestine, depending on its pH and hydrolysis history, simulating chyme at different times after the onset of gastric emptying. Isothermal titration calorimetry was used to study the kinetics of pepsin and trypsin-catalysed hydrolysis. Bovine serum albumin (BSA) that was acidified and hydrolysed with pepsin, showed the highest extent and most efficient hydrolysis by trypsin. BSA in the chyme that would be first emptied from the stomach, virtually bypassing gastric acidity and peptic action, reduced trypsin-catalysed hydrolysis by up to 58% compared to the acidified, intact protein, and 77% less than the acidified, pepsin-hydrolysate. The least efficient substrate for trypsin-catalysed hydrolysis was the acidified, intact protein with a specificity constant (k_cat/K_m) nearly five times lower than that of the acidified, pepsin-hydrolysate. Our results illustrate the synergy between pepsin and trypsin hydrolysis, and indicate that gastric hydrolysis increases the efficiency of the subsequent trypsin-catalysed hydrolysis of a model protein in the small intestine.

Statistical modeling of in vitro pepsin specificity

The specificity of pepsin, the major protease of gastric digestion, has been previously investigated, but only regarding the primary sequence of the protein substrates. The present study aimed to consider in addition physicochemical and structural characteristics, at the molecular and sub-molecular scales. For six different proteins submitted to in vitro gastric digestion, the peptide bonds cleaved were determined from the peptides released and identified by LC-MS/MS. An original statistical approach, based on propensity scores calculated for each amino acid residue on both sides of the peptide bonds, concluded that preferential cleavage occurred after Leu and Phe, and before Ile. Moreover, reliable statistical models developed for predicting peptide bond cleavage, highlighted the predominant role of the amino acid residues at the N-terminal side of the peptide bonds, up to the seventh position (P7 and P7'). The significant influence of hydrophobicity, charge and structural constraints around the peptide bonds was also evidenced.

Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020

The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.

Food Matrix and Macronutrient Digestion

Food digestion may be regarded as a physiological interface between food and health. During digestion, the food matrix is broken down and the component nutrients and bioactive compounds are absorbed through a synergy of mechanical, chemical, and biochemical processes. The food matrix modulates the extent and kinetics to which nutrients and bioactive compounds make themselves available for absorption, hence regulating their concentration profile in the blood and their utilization in peripheral tissues. In this review, we discuss the structural and compositional aspects of food that modulate macronutrient digestibility in each step of digestion. We also discuss in silico modeling approaches to describe the effect of the food matrix on macronutrient digestion. The detailed knowledge of how the food matrix is digested can provide a mechanistic basis to elucidate the complex effect of food on human health and design food with improved functionality.

Modulating the in vitro gastric digestion of heat-induced beta-lactoglobulin aggregates: Incorporation with polysaccharide

Three heat-induced protein aggregates, beta-lactoglobulin fibrils (BLGF), nanoparticles (BLGN), and worm-like aggregates (BLGW) were chosen to probe the effect of disulfide bond and surface hydrophobicity on their gastric digestion behavior. Furthermore, the effect of polysaccharide (dextran sulfate sodium, DSS) on the digestion behavior of the protein aggregates was investigated. Results showed that disulfide bond had a mild restraint on the digestion extent (maximum up to 4.65%), especially when its content was below 1 mol/mol, while the surface hydrophobicity had a stronger influence (up to 8.96%), and there is definitive positive linear relationship between the surface hydrophobicity and the digestion extent. When incorporated with DSS, both the disulfide bond content and surface hydrophobicity of the aggregates decreased, consequently, and the digestion was impeded, confirming the stronger effect from the surface hydrophobicity. The digestion extent of the heat-induced protein aggregates could be modulated linearly by incorporation of polysaccharide.

Searching for conditions of protein self-assembly by protein crystallization screening method

The self-assembly of biomacromolecules is an extremely important process. It is potentially useful in the fields of life science and materials science. To carry out the study on the self-assembly of proteins, it is necessary to find out the suitable self-assembly conditions, which have always been a challenging task in practice. Inspired by the screening technique in the field of protein crystallization, we proposed using the same screening technique for seeking suitable protein self-assembly conditions. Based on this consideration, we selected 5 proteins (β-lactoglobulin, hemoglobin, pepsin, lysozyme, α-chymotrypsinogen (II) A) together with 5 screening kits (Index^TM, BML, Morpheus, JCSG, PEG/Ion Screen^TM) to investigate the performance of these crystallization screening techniques in order to discover new optimized conditions of protein self-assembly. The screens were all kept at 293 K for certain days, and were analyzed using optical microscope, scanning electron microscope, transmission electron microscope, atomic force microscope, fluorescence microscope, and atomic absorption spectroscope. The results demonstrated that the method of protein crystallization screening can be successfully applied in the screening of self-assembly conditions. This method is fast, high throughput, and easily implemented in an automated system, with a low protein consumption feature. These results suggested that such strategy can be applied to finding new conditions or forms in routine research of protein self-assembly. KEY POINTS: • Protein crystallization screening method is successfully applied in the screening of self-assembly conditions. • This screening method can be applied on various kinds of proteins and possess a feature of low protein consumption. • This screening method is fast, high throughput, and easily implemented in an automated system.

A target safety assessment of the potential toxicological risks of targeting plasmepsin IX/X for the treatment of malaria

The aspartic proteases plasmepsin IX/X are important antimalarial drug targets due to their specificity to the malaria parasite and their vital role as mediators of disease progression. Focusing on parasite-specific targets where no human homologue exists reduces the possibility of on-target drug toxicity. However, there is a risk of toxicity driven by inadequate selectivity for plasmepsins IX/X in Plasmodium over related mammalian aspartic proteases. Of these, CatD/E may be of most toxicological relevance as CatD is a ubiquitous lysosomal enzyme present in most cell types and CatE is found in the gut and in erythrocytes, the clinically significant site of malarial infection. Based on mammalian aspartic protease physiology and adverse drug reactions (ADRs) to FDA-approved human immunodeficiency virus (HIV) aspartic protease inhibitors, we predicted several potential toxicities including β-cell and congenital abnormalities, hypotension, hypopigmentation, hyperlipidaemia, increased infection risk and respiratory, renal, gastrointestinal, dermatological, and other epithelial tissue toxicities. These ADRs to the HIV treatments are likely to be a result of host aspartic protease inhibition due a lack of specificity for the HIV protease; plasmepsins are much more closely related to human CatD than to HIV proteinase. Plasmepsin IX/X inhibition presents an opportunity to specifically target Plasmodium as an effective antimalarial treatment, providing adequate selectivity can be obtained. Potential plasmepsin IX/X inhibitors should be assayed for inhibitory activity against the main human aspartic proteases and particularly CatD/E. An investigative rodent study conducted early in drug discovery would serve as an initial risk assessment of the potential hazards identified.

Novel Method for the Quantitative Analysis of Protease Activity: The Casein Plate Method and Its Applications

No simple methods are used for the quantitative analysis of the protease activity in colored food up till now. Thus, this study aims to establish a new and simple method for the quantitative detection of protease activity, especially in colored food. The detection accuracy, detection limit, and repeatability of the casein plate method were analyzed. Then, the application of the casein plate method in sample detection and recovery was further evaluated. The results showed that the casein plate method for the quantitative detection of protease activity has high accuracy, high precision, and low detection limit. The recoveries of eight kinds of colored samples were in the range of 92.26-97.84%, and the relative standard deviation (RSD) was in the range of 3.56-10.88%. The results of the casein plate method exhibited high accuracy. This indicated that the method was suitable for the detection of colored samples. The casein plate method for the quantitative detection of protease activity is simple. The newly constructed casein plate method has broad potential application value in food industry, especially for the detection of dark food.

Terahertz Spectroscopy Tracks Proteolysis by a Joint Analysis of Absorptance and Debye Model

Terahertz waves have attracted great attention in biomolecule research because of the fact that they cover the range of energy levels of weak interactions, skeleton vibrations, and dipole rotations during inter- and intramolecular interactions in biomacromolecules. In this study, we validated the feasibility of employing terahertz time-domain spectroscopy (THz-TDS) for the nondestructive and label-free monitoring of protein digestion. The acid protease, pepsin, was used at its optimal pH to hydrolyze bovine serum albumin. Correspondingly, the control group experiment was also conducted by adjusting the pH value to inactivate pepsin. The progress of these two experiments was tracked by a compact commercial THz-TDS for 1 h. On one hand, the reaction-time-dependent absorption coefficient was calculated, and a direct absorption coefficient analysis was completed. The results indicate that protein hydrolysis can be easily monitored over time by focusing on the variation tendency of the absorption coefficient from a macroscopic perspective. On the other hand, we explored the use of the Debye model to analyze the dielectric properties of the solution during protein hydrolysis. The results of the Debye analysis prove that it is possible to investigate in detail the microscopic dynamics of biomacromolecule solutions at the molecular level by THz-TDS. Our research examined the process of protein hydrolysis by a combination of absorption spectra and Debye analysis and demonstrated that terahertz spectroscopy is a powerful technology for the investigation of biomolecular reactions, with potential applications in variety of fields.

Advances in Analysis of Milk Proteases Activity at Surfaces and in a Volume by Acoustic Methods

This review is focused on the application of surface and volume-sensitive acoustic methods for the detection of milk proteases such as trypsin and plasmin. While trypsin is an important protein of human milk, plasmin is a protease that plays an important role in the quality of bovine, sheep and goat milks. The increased activity of plasmin can cause an extensive cleavage of β-casein and, thus, affect the milk gelation and taste. The basic principles of surface-sensitive acoustic methods, as well as high-resolution ultrasonic spectroscopy (HR-US), are presented. The current state-of-the-art examples of the application of acoustic sensors for protease detection in real time are discussed. The application of the HR-US method for studying the kinetics of the enzyme reaction is demonstrated. The sensitivity of the acoustics biosensors and HR-US methods for protease detection are compared.

Evidence of Pepsin-Related Ocular Surface Damage and Dry Eye (PROD Syndrome) in Patients with Laryngopharyngeal Reflux

Background: patients with laryngopharyngeal reflux (LPR) showed detectable levels of tear pepsin that explain the nasolacrimal obstruction. The purpose of this study was to determine whether patients with LPR show ocular surface changes and to investigate the relationship between lacrimal pepsin concentration and ocular alterations. Methods: Fifty patients with positive endoscopic signs for LPR and an equal or higher score of 13 and 7 for Reflux Symptom Index and Reflux Finding Score were enrolled. Twenty healthy patients with no reflux disease and dry eye were included as the control group. After evaluation of ocular discomfort symptoms, the tear break-up time test, corneal staining, and tear sampling were performed. Tear pepsin levels were measured using Pep-test^TM kit. Results: Patients with LPR showed ocular surface changes including epithelial damage (48%) and impairment of lacrimal function (72%). Tear pepsin levels were detectable in 32 out of 50 (64%) patients with LPR (mean ± SD: 55.4 ± 67.5 ng/mL) and in none of the control subjects. Most of the LPR patients complained of ocular discomfort symptoms, including itching (38%), redness (56%), or foreign body sensation (40%). Tear pepsin levels were significantly correlated with the severity of LPR disease and with ocular surface changes. Conclusions: A multidisciplinary approach, including ophthalmological evaluation, should be considered in order to improve the management of patients with LPR.

Presence of small resistant peptides from new in vitro digestion assays detected by liquid chromatography tandem mass spectrometry: An implication of allergenicity prediction of novel proteins?

The susceptibility of newly expressed proteins to digestion by gastrointestinal proteases (e.g., pepsin) has long been regarded as one of the important endpoints in the weight-of-evidence (WOE) approach to assess the allergenic risk of genetically modified (GM) crops. The European Food Safety Authority (EFSA) has suggested that current digestion study protocols used for this assessment should be modified to more accurately reflect the diverse physiological conditions encountered in human populations and that the post-digestion analysis should include analytical methods to detect small peptide digestion products.The susceptibility of two allergens (beta-lactoglobin (β-Lg) and alpha-lactalbumin (α-La)) and two non-allergens (hemoglobin (Hb) and phosphofructokinase (PFK)) to proteolytic degradation was investigated under two pepsin digestion conditions (optimal pepsin digestion condition: pH 1.2, 10 U pepsin/μg test protein; sub-optimal pepsin digestion condition: pH 5.0, 1 U pepsin/10 mg test protein), followed by 34.5 U trypsin/mg test protein and 0.4 U chymotrypsin/mg test protein digestion in the absence or presence of bile salts. All samples were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in conjunction with Coomassie Blue staining and, in parallel, liquid chromatography tandem mass spectrometry (LC-MS) detection. The results provide following insights: 1) LC-MS methodology does provide the detection of small peptides; 2) Peptides are detected in both allergens and non-allergens from all digestion conditions; 3) No clear differences among the peptides detected from allergen and non-allergens; 4) The differences observed in SDS-PAGE between the optimal and sub-optimal pepsin digestion conditions are expected and align with kinetics and properties of the specific enzymes; 5) The new methodology with new digestion conditions and LC-MS detection does not provide any differentiating information for prediction whether a protein is an allergen. The classic pepsin resistance assay remains the most useful assessment of the potential exposure of an intact newly expressed protein as part of product safety assessment within a WOE approach.

Physical chemistry of gastric digestion of proteins gels

In this paper, we present the rich physics and chemistry of the gastric digestion of protein gels. Knowledge of this matter is important for the development of sustainable protein foods that are based on novel proteins sources like plant proteins or insects. Their digestibility is an important question in the design of these new protein foods. As polyelectrolyte gels, they can undergo volume changes upon shifts in pH or ionic strengths, as protein gels experience when entering the gastric environment. We show that these volume changes can be modelled using the Flory-Rehner theory, combined with Gibbs-Donnan theory accounting for the distribution of electrolytes over gel and bath. In-vitro experiments of soy protein gels in simulated gastric fluid indeed show intricate swelling behaviour, at first the gels show swelling but at longer times they shrink again. Simulations performed with the Flory-Rehner/Gibbs-Donnan theory reproduce qualitatively similar behaviour. In the final part of the paper, we discuss how the model must be extended to model realistic conditions existing in the in-vivo gastric environment.

The antifungal peptide CGA-N12 inhibits cell wall synthesis of Candida tropicalis by interacting with KRE9

CGA-N12, an antifungal peptide derived from chromogranin A, has specific antagonistic activity against Candida spp., especially against Candida tropicalis, by inducing cell apoptosis. However, the effect of CGA-N12 on the Candida cell wall is unknown. The Candida protein KRE9, which possesses β-1,6-glucanase activity, was screened by affinity chromatography after binding to CGA-N12. In this study, the effect of CGA-N12 on KRE9 and the interaction between CGA-N12 and KRE9 was studied to clarify the effect of CGA-N12 on C. tropicalis cell wall synthesis. The effect of CGA-N12 on recombinant KRE9 β-1,6-glucanase activity was investigated by analyzing the consumption of glucose. The results showed that CGA-N12 inhibited the activity of KRE9. After C. tropicalis was treated with CGA-N12, the structure of the C. tropicalis cell wall was damaged. The interaction between CGA-N12 and KRE9 was analyzed by isothermal titration calorimetry (ITC). The results showed that their interaction process was involved an endothermic reaction, and the interaction force was mainly hydrophobic with a few electrostatic forces. The results of the fluorescence resonance energy transfer (FRET) assay showed that the distance between CGA-N12 and KRE9 was 7 ∼ 10 nm during their interaction. Therefore, we concluded that the target of CGA-N12 in the C. tropicalis cell membrane is KRE9, and that CGA-N12 weakly binds to KRE9 within a 7 ∼ 10 nm distance and inhibits KRE9 activity.

Isothermal Titration Calorimetry Enables Rapid Characterization of Enzyme Kinetics and Inhibition for the Human Soluble Epoxide Hydrolase

Isothermal titration calorimetry (ITC) is conventionally used to acquire thermodynamic data for biological interactions. In recent years, ITC has emerged as a powerful tool to characterize enzyme kinetics. In this study, we have adapted a single-injection method (SIM) to study the kinetics of human soluble epoxide hydrolase (hsEH), an enzyme involved in cardiovascular homeostasis, hypertension, nociception, and insulin sensitivity through the metabolism of epoxy-fatty acids (EpFAs). In the SIM method, the rate of reaction is determined by monitoring the thermal power, while the substrate is being depleted, overcoming the need for synthetic substrates and reducing postreaction processing. Our results show that ITC enables the detailed, rapid, and reproducible characterization of the hsEH-mediated hydrolysis of several natural EpFA substrates. Furthermore, we have applied a variant of the single-injection ITC method for the detailed description of enzyme inhibition, proving the power of this approach in the rapid screening and discovery of new hsEH inhibitors using the enzyme’s physiological substrates. The methods described herein will enable further studies on EpFAs’ metabolism and biology, as well as drug discovery investigations to identify and characterize hsEH inhibitors. This also promises to provide a general approach for the characterization of lipid catalysis, given the challenges that lipid metabolism studies pose to traditional spectroscopic techniques.

Bovine Serum Albumin Amplified Reactive Oxygen Species Generation from Anthrarufin-Derived Carbon Dot and Concomitant Nanoassembly for Combination Antibiotic-Photodynamic Therapy Application

Amplification of reactive oxygen species (ROS) generation through covalent conjugation of bovine serum albumin (BSA) with newly synthesized, ROS-producing carbon dots (CDs) upon visible light irradiation is reported for the first time. Derivatization of surface carboxyl functional groups of Anthrarufin-derived, green-emitting CD with the amine functionality of BSA ushers distinct changes in the photophysics of CD including an unprecedented ∼50 nm shift in its excitation maxima, decrease in fluorescence lifetime, and concomitant increase in ROS generation. Substantial conformational changes of BSA were witnessed upon conjugation with CD, rendering the BSA-CD conjugate resistant to pepsinolysis. A protease-proof nanoassembly was derived from the BSA-CD conjugate through desolvation that simultaneously hosts a prototype antibiotic and generates ROS with excellent efficiency, making it an attractive platform for antibacterial photodynamic therapy (A-PDT) applications. Systemic annihilation of both Gram-positive and -negative bacteria was achieved with the BSA-CD nanoassembly and envisioned as alternatives to traditional photosensitizers.