Search Results (10)

The hydrolysis of proteins by proteases (proteolysis) plays a significant role in biology and food science. Despite the importance of proteolysis, a universal quantitative model of this phenomenon has not yet been created. This review considers approaches to modeling proteolysis in a batch reactor that take into account differences in the hydrolysis of the individual peptide bonds, as well as the limited accessibility (masking) for the enzymes of some hydrolysis sites in the protein substrate. Kinetic studies of the proteolysis of β-casein and β-lactoglobulin by various proteolytic enzymes throughout the whole degree of hydrolysis are reviewed. The two-step proteolysis model is regarded, which includes demasking of peptide bonds as a result of opening of the protein structure at the first stage, then hydrolysis of the demasked peptide bonds. To determine the kinetics of demasking, the shift in Trp fluorescence during opening of the protein substrate is analyzed. Two stages of demasking and secondary masking are also considered, explaining the appearance of unhydrolyzed peptide bonds at the end of proteolysis with decreasing enzyme concentrations. Proteolysis of a nanosized substrate is considered for the example of tryptic hydrolysis of β-CN micelles, leading to the formation and degradation of new nanoparticles and non-monotonic changes in the secondary protein structures during proteolysis. Full article

In this work, we present a novel four-channel coherent optical chaotic secure communication (COCSC) system, incorporating four simultaneous photonic reservoir computers in tandem with four coherent demodulation units. We employ a quartet of photonic reservoirs that capture the chaotic dynamics of four polarization components (PCs) emitted by a driving QD spin-VCSEL. These reservoirs are realized utilizing four PCs of a corresponding reservoir QD spin-VCSEL. Through these four concurrent photonic reservoir structures, we facilitate high-quality wideband-chaos synchronization across four pairs of PCs. Leveraging wideband chaos synchronization, our COCSC system boasts a substantial 4 × 100 GHz capacity. High-quality synchronization is pivotal for the precise demasking or decoding of four distinct signal types, QPSK, 4QAM, 8QAM and 16QAM, which are concealed within disparate chaotic PCs. After initial demodulation via correlation techniques and subsequent refinement through a variety of digital signal processing methods, we successfully reconstruct four unique baseband signals that conform to the QPSK, 4QAM, 8QAM and 16QAM specifications. Careful examination of the eye diagrams, bit error rates, and temporal trajectories of the coherently demodulated baseband signals indicates that each set of baseband signals is flawlessly retrieved. This is underscored by the pronounced eye openings in the eye diagrams and a negligible bit error rate for each channel of baseband signals. Our results suggest that delay-based optical reservoir computing employing a QD spin-VCSEL is a potent approach for achieving multi-channel coherent optical secure communication with optimal performance and enhanced security. Full article

The relationship between coronavirus disease 2019 (COVID-19) and myocardial injury was established at the onset of the COVID-19 pandemic. An increase in the incidence of out-of-hospital cardiac arrest was also observed. This case report aims to point to the prothrombotic and proinflammatory nature of coronavirus infection, leading to simultaneous coronary vessel thrombosis and subsequently to out-of-hospital cardiac arrest. During the COVID-19 pandemic, a 46-year-old male patient with no comorbidities suffered out-of-hospital cardiac arrest (OHCA) with ventricular fibrillation as the first recorded rhythm. The applied cardiopulmonary resuscitation (CPR) measures initiated by bystanders and continued by emergency medical service (EMS) resulted in the return of spontaneous circulation. The stabilized patient was transferred to the tertiary university center. Electrocardiogram (ECG) revealed “lambda-like” ST-segment elevation in DI and aVL leads, necessitating an immediate coronary angiography, which demonstrated simultaneous occlusion of the left anterior descending (LAD) and right coronary artery (RCA). Primary percutaneous coronary intervention (PCI) with the implantation of one drug-eluting stent (DES) in LAD and two DES in RCA was done. Due to the presence of cardiogenic shock (SCAI C), an intra-aortic balloon pump (IABP) was implanted during the procedure, and due to the comatose state and shockable cardiac arrest, targeted temperature management was initiated. The baseline chest X-ray revealed bilateral interstitial infiltrates, followed by increased proinflammatory markers and a positive polymerase chain reaction (PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demasking underlying COVID-19-related pneumonia. Within the following 48 h, the patient was hemodynamically stable, which enabled weaning from IABP and vasopressor discontinuation. However, due to the worsening of COVID-19 pneumonia, prolonged mechanical ventilation, together with antibiotics and other supportive measures, was needed. The applied therapy resulted in clinical improvement, and the patient was extubated and finally discharged on Day 26, with no neurological sequelae and with mildly reduced left ventricle ejection fraction. Full article

Prospects for predicting the fragmentation of polypeptide chains during their enzymatic hydrolysis using proteolysis models are considered. The opening of the protein substrate during proteolysis and the exposure of its internal peptide bonds for a successful enzymatic attack, the so-called demasking process, were taken into account. The two-step proteolysis model was used, including the parameters of demasking and the rate constants of hydrolysis of enzyme-specific peptide bonds. Herein, we have presented an algorithm for calculating the concentrations of intermediate and final peptide fragments depending on the time of hydrolysis or the degree of hydrolysis. The intermediate peptide fragments with two or one internal specific peptide bond were considered. The fragmentation of β-lactoglobulin (β-LG) by trypsin was predicted, and the calculated concentration curves for peptide fragments were compared with the experimental dependences of the concentrations on the degree of hydrolysis. Numerical parameters were proposed that characterize the concentration curves for intermediate and final peptide fragments, and they were used to compare the calculated and experimental dependences. The predicted distribution of the peptide fragments corresponded to the experimental data on the peptide release during the proteolysis of β-LG by trypsin. Full article

The opening of protein substrates during degradation by proteases and the corresponding exposure of their internal peptide bonds for a successful enzymatic attack, the so-called demasking effect, was studied for β-lactoglobulin (β-LG) and β-casein (β-CN) hydrolyzed by trypsin. Demasking was estimated by monitoring the redshift in intrinsic tryptophan fluorescence, characterizing the accessibility of polypeptide chains to aqueous medium. The secondary masking of intermediate polypeptides, giving an inverse effect to demasking, caused a restriction of the substrate opening. This led to the limitations in the red shift of fluorescence and the degree of hydrolysis with a long time of hydrolysis of β-LG and β-CN at a constant substrate concentration and reduced trypsin concentrations. The proposed proteolysis model included demasking of initially masked bonds in the protein globule or micelle, secondary masking of intermediate polypeptides, and their subsequent slow demasking. The hydrolysis of peptide bonds was modeled taking into account different hydrolysis rate constants for different peptide bonds. It was demonstrated that demasking competes with secondary masking, which is less noticeable at high trypsin concentrations. Modeling of proteolysis taking into account two demasking processes and secondary masking made it possible to simulate kinetic curves consistent with the experimental data. Full article

We analyzed the epitope evolution of the spike protein in 1,860,489 SARS-CoV-2 genomes. The structural dynamics of these epitopes was determined by molecular modeling approaches. The D614G mutation, selected in the first months of the pandemic, is still present in currently circulating SARS-CoV-2 strains. This mutation facilitates the conformational change leading to the demasking of the ACE2 binding domain. D614G also abrogated the binding of facilitating antibodies to a linear epitope common to SARS-CoV-1 and SARS-CoV-2. The main neutralizing epitope of the N-terminal domain (NTD) of the spike protein showed extensive structural variability in SARS-CoV-2 variants, especially Delta and Omicron. This epitope is located on the flat surface of the NTD, a large electropositive area which binds to electronegatively charged lipid rafts of host cells. A facilitating epitope located on the lower part of the NTD appeared to be highly conserved among most SARS-CoV-2 variants, which may represent a risk of antibody-dependent enhancement (ADE). Overall, this retrospective analysis revealed an early divergence between conserved (facilitating) and variable (neutralizing) epitopes of the spike protein. These data aid in the designing of new antiviral strategies that could help to control COVID-19 infection by mimicking neutralizing antibodies or by blocking facilitating antibodies. Full article

Systems pharmacology employs computational and mathematical methods to study the network of interactions a drug may have within complex biological pathways. These tools are well suited for research on multitarget drugs, such as natural compounds, in diseases with complex etiologies, such as osteoarthritis (OA). The present study focuses on cannabidiol (CBD), a non-psychoactive constituent of cannabis, targeting over 60 distinct molecular targets as a potential treatment for OA, a degenerative joint disease leading to chronic pain with a neuropathic component. We successfully identified molecular targets of CBD that were relevant in the context of OA treatment with both beneficial and detrimental effects. Our findings were confirmed by in vivo and molecular studies. A key role of PPARγ in mediating the therapeutic potential of CBD was revealed, whereas upregulation of multiple transient receptor potential channels demasked CBD-induced heat hyperalgesia. Our findings pave the way for novel CBD-based therapy with improved therapeutic potential but also encourage the use of bioinformatic tools to predict the mechanism of action of CBD in different conditions. We have also created an accessible web tool for analogous analysis of CBD pharmacology in the context of any disease of interest and made it publicly available. Full article

The opening of protein globules and corresponding exposure of their internal peptide bonds, the so-called demasking effect, is required for successful hydrolysis of peptide bonds by proteases. Under the proteolytic action of trypsin on β-lactoglobulin (β-LG), the evolution of tryptophan fluorescence spectra showed that the demasking process consists of two stages with different demasking rate constants for each stage. It was found that the ratio of these constants depends on the concentration of trypsin and changes are approximately threefold when the concentration of trypsin changes in the range of 0.3–15 mg/L. Simulation of hydrolysis taking into account the demasking effect demonstrated how the apparent first-order rate constants obtained experimentally are related to the true hydrolysis rate constants and demasking parameters. The lag phase in the kinetic curves corresponding to the hydrolysis of various peptide bonds in β-LG was also analyzed. The increased lag times indicated sites that are hydrolyzed by a two-stage demasking mechanism. Full article

To distinguish differences in enzymatic hydrolysis of various proteins, we propose an algorithm using a dataset of fluorescence spectra obtained at different moments of hydrolysis t. This algorithm was demonstrated in the example of β-lactoglobulin (β-LG) proteolysis by trypsin. The procedure involved processing the spectra to obtain the wavelength of the maximum fluorescence λ_max, which was found to be proportional to the fraction of tryptophanes in hydrated proteolysis products (demasked tryptophanes). Then, the dependence λ_max(t) was fitted by biexponential function with two exponential terms, one of which was responsible for the fast part of the fluorescence change during proteolysis. The contribution of this term was quite different for various protein substrates—it was positive for β-LG and negative for β-casein. The observed differences in proteolysis of different substrates were explained by different demasking processes. Combining the fluorescence data with the degrees of hydrolysis of peptide bonds allowed us to analyze the hydrolysis of β-LG in the framework of the two-step proteolysis model and estimate the ratio of rate constants of demasking and hydrolysis and the percentages of initially masked and resistant peptide bonds. This model predicted the existence of a bimodal demasking process with a fast part at the beginning of proteolysis and lag-type kinetics of release for some peptides. Compared with monitoring proteolysis in terms of the degree of hydrolysis only, the fluorescence data are helpful for the recognition of proteolysis patterns. Full article

Repair of parenchyma by stem/progenitor cells is seen as a possible alternative to cure acute and chronic renal failure in future. To learn about this therapeutic purpose, the formation of nephrons during organ growth is under focus of present research. This process is triggered by numerous morphogenetic interactions between epithelial and mesenchymal cells within the renal stem/progenitor cell niche. Recent data demonstrate that an astonishingly wide interstitial interface separates both types of stem/progenitor cells probably controlling coordinated cell-to-cell communication. Since conventional fixation by glutaraldehyde (GA) does not declare in transmission electron microscopy the spatial separation, improved contrasting procedures were applied. As a consequence, the embryonic cortex of neonatal rabbit kidneys was fixed in solutions containing glutaraldehyde in combination with cupromeronic blue, ruthenium red or tannic acid. To obtain a comparable view to the renal stem/progenitor cell niche, the specimens had to be orientated along the cortico-medullary axis of lining collecting ducts. Analysis of tissue samples fixed with GA, in combination with cupromeronic blue, demonstrates demasked extracellular matrix. Numerous braces of proteoglycans cover, as well, the basal lamina of epithelial stem/progenitor cells as projections of mesenchymal stem/progenitor cells crossing the interstitial interface. Fixation with GA containing ruthenium red or tannic acid illustrates strands of extracellular matrix that originate from the basal lamina of epithelial stem/progenitor cells and line through the interstitial interface. Thus, for the first time, improved contrasting techniques make it possible to analyze in detail a microheterogeneous composition of the interstitial interface within the renal stem/progenitor cell niche. Full article