Distinct β-sheet structure in protein aggregates determined by ATR-FTIR spectroscopy

Thermal effects and drugs competition on the palmitate binding capacity of human serum albumin

Human serum albumin (HSA) is the most abundant plasma protein of the circulatory system. It is a multidomain, multifunctional protein that, combining diverse affinities and wide specificity, binds, stores, and transports a variety of biological compounds, pharmacores, and fatty acids. HSA is finding increasing uses in drug-delivery due to its ability to carry functionalized ligands and prodrugs. All this raises the question of competition for binding sites occupancy in case of multiple ligands, which in turn influences the protein structure/dynamic/function relationship and also has an impact on the biomedical applications. In this work, the effects of interactive binding of palmitic acid (PA), warfarin (War) and ibuprofen (Ibu) on the thermal stability of HSA were studied using DSC, ATR-FTIR, and EPR. PA is a high-affinity physiological ligand, while the two drugs are widely used for their anticoagulant (War) and anti-inflammatory (Ibu) efficacy, and are exogenous compounds that accommodate in the deputed drug site DS1 and DS2, respectively overlapping with some of the fatty acid binding sites. The results indicate that HSA acquires the highest thermal stability when it is fully saturated with PA. The binding of this physiological ligand does not hamper the binding of War or Ibu to the native state of the protein. In addition, the three ligands bind simultaneously, suggesting a synergic cooperative influence due to allosteric effects. The increased thermal stability subsequent to binary and multiple ligands binding moderates protein aggregation propensity and restricts protein dynamics. The biophysics findings provide interesting features about protein stability, aggregation, and dynamics in interaction with multiple ligands and are relevant in drug-delivery.

Attenuated total reflection Fourier-transform infrared spectroscopy for the prediction of hormone concentrations in plants

Plant hormones are important in the control of physiological and developmental processes including seed germination, senescence, flowering, stomatal aperture, and ultimately the overall growth and yield of plants. Many currently available methods to quantify such growth regulators quickly and accurately require extensive sample purification using complex analytic techniques. Herein we used ultra-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) to create and validate the prediction of hormone concentrations made using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectral profiles of both freeze-dried ground leaf tissue and extracted xylem sap of Japanese knotweed (Reynoutria japonica) plants grown under different environmental conditions. In addition to these predictions made with partial least squares regression, further analysis of spectral data was performed using chemometric techniques, including principal component analysis, linear discriminant analysis, and support vector machines (SVM). Plants grown in different environments had sufficiently different biochemical profiles, including plant hormonal compounds, to allow successful differentiation by ATR-FTIR spectroscopy coupled with SVM. ATR-FTIR spectral biomarkers highlighted a range of biomolecules responsible for the differing spectral signatures between growth environments, such as triacylglycerol, proteins and amino acids, tannins, pectin, polysaccharides such as starch and cellulose, DNA and RNA. Using partial least squares regression, we show the potential for accurate prediction of plant hormone concentrations from ATR-FTIR spectral profiles, calibrated with hormonal data quantified by UHPLC-HRMS. The application of ATR-FTIR spectroscopy and chemometrics offers accurate prediction of hormone concentrations in plant samples, with advantages over existing approaches.

Effect of Organic Solvents on the Activity, Stability and Secondary Structure of asclepain cI, Using FTIR and Molecular Dynamics Simulations

The present study aims at understanding the effect of organic solvents on the specific proteolytic activity and operational stability of asclepain cI in aqueous-organic media, using correlations between geometrical and structural parameters of asclepain cI. These correlations were determined by molecular dynamics (MD) simulations and the secondary structure of the enzyme validated by Fourier-transform Infrared (FTIR) spectroscopy. Asclepain cI exhibited significantly higher catalytic potential in 29 of the 42 aqueous-organic media tested, composed by 0.1 mM TRIS hydrochloride buffer pH 8 (TCB) and an organic solvent, than in buffer alone. Asclepain cI in water-organic miscible systems showed high FTIR spectral similarity with that obtained in TCB, while in immiscible systems the enzyme acquired different secondary structures than in buffer. Among the conditions studied, asclepain cI showed the highest catalytic potential in 50% v/v ethyl acetate in TCB. According to MD simulations, that medium elicited solvation and flexibility changes around the active center of asclepain cI and conducted to a new secondary structure with the active center preserved. These results provide valuable insights into the elucidation of the molecular mechanism of asclepain cI tolerance to organic solvents and pave the way for its future application for the synthesis of peptides in aqueous-organic media.

Harnessing prion-inspired amyloid self-assembly for sustainable and biocompatible proton conductivity

Protein-based materials have emerged as promising candidates for proton-conducting biomaterials. Therefore, drawing inspiration from the amino acid composition of prion-like domains, we designed short self-assembling peptides incorporating the (X-Tyr) motif, with X representing Asn, Gly and Ser, which form fibrillar structures capable of conducting protons. In this study, we conducted an analysis of the conductivity capacity of these fibers, with a focus on temperature and frequency dependence of conductivity. The loss tangent curves data and the electrode polarization model with the Debye approximation were employed to calculate transport properties, including conductivity, diffusivity, and density of charge carriers. Results revealed the prion-like fibers can transport protons more efficiently than biomaterials and other synthetic proton conducting materials, and that a significant increase in conductivity is observed with fibrillar orientations. The temperature dependence of conductivity of the peptides, measured in wet conditions, showed conductivities following the trend σ(NY7) < σ(GY7) < σ(SY7), in all the range of temperatures studied. The Arrhenius behavior, and the activation energy associated with conductivity followed the trend: Eact (SY7) = 8.2 ± 0.6 kJ mol-1 < Eact (GY7) < 13 ± 5 kJ mol-1 < Eact (NY7) = 31 ± 7 kJ mol-1, in different range of temperatures depending of the peptide. Furthermore, the diffusion coefficient correlated with increasing temperature in GY7 and SY7 fibers for temperatures compress between 20 °C and 80 °C, while NY7 only below 60 °C. However, it is noteworthy that the diffusivity observed in the SY7 peptide is lower, compared to GY7 and NY7 presumably due to its enlarged length. This observation can be attributed to two factors: firstly, the higher conductivity values observed in SY7 compared to GY7 and NY7, and secondly, to the value of relation observed of cations present in the peptide SY7 compared with GY7 and NY7, which in turn is dependent on temperature. In light of these findings, we envision our prion-inspired nanofibers as highly efficient proton-conducting natural biopolymers that are both biocompatible and biodegradable. These properties provide the opportunity for the development of next-generation bioelectrical interfaces and protonic devices.

Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.

Formation of Calprotectin Inhibits Amyloid Aggregation of S100A8 and S100A9 Proteins

Calcium-binding S100A8 and S100A9 proteins play a significant role in various disorders due to their pro-inflammatory functions. Substantially, they are also relevant in neurodegenerative disorders via the delivery of signals for the immune response. However, at the same time, they can aggregate and accelerate the progression of diseases. Natively, S100A8 and S100A9 exist as homo- and heterodimers, but upon aggregation, they form amyloid-like oligomers, fibrils, or amorphous aggregates. In this study, we aimed to elucidate the aggregation propensities of S100A8, S100A9, and their heterodimer calprotectin by investigating aggregation kinetics, secondary structures, and morphologies of the aggregates. For the first time, we followed the in vitro aggregation of S100A8, which formed spherical aggregates, unlike the fibrillar structures of S100A9 under the same conditions. The aggregates were sensitive to amyloid-specific ThT and ThS dyes and had a secondary structure composed of β-sheets. Similarly to S100A9, S100A8 protein was stabilized by calcium ions, resulting in aggregation inhibition. Finally, the formation of S100A8 and S100A9 heterodimers stabilized the proteins in the absence of calcium ions and prevented their aggregation.

Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes

Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.

Confinement of Oligopeptides by Terminally Functionalized Polyisoprene to Improve Their Mechanical Strength, Creep Resistance, and Antifatigue Properties

A small amount of terminal polar phase endows natural rubber (NR) with excellent comprehensive properties superior to those of synthetic isoprene rubber. In this work, the comprehensive properties of synthetic rubber were remarkably improved by introducing a stable terminal nanoconfinement structure by combining terminal hydroxyl groups and pentapeptide molecules noncovalently into the same phases. The results show that the stable terminal phases hardly affect the free chain motion but enhance the entanglement. Under cyclic loading, the terminal polar phases undergo hierarchically structural changes such as reversible dissociation of the weak bonds, phase deformation, and crystalline reorganization, all of which dissipate the stress and are beneficial for high strength and extensibility. At the same time, synthetic rubbers demonstrate much superior fatigue resistance and lower hysteresis relative to NR and maintain comparable dimensional stability. This strategy suggests that the comprehensive properties of elastomers can be regulated and upgraded by facile terminal noncovalent interactions.

FTIR Spectroscopy and Blood-Derived Extracellular Vesicles Duo in Alzheimer's Disease

Background

Alzheimer's disease (AD) diagnosis is difficult, and new accurate tools based on peripheral biofluids are urgently needed. Extracellular vesicles (EVs) emerged as a valuable source of biomarker profiles for AD, since their cargo is disease-specific and these can be easily isolated from easily accessible biofluids, as blood. Fourier Transform Infrared (FTIR) spectroscopy can be employed to analyze EVs and obtain the spectroscopic profiles from different regions of the spectra, simultaneously characterizing carbohydrates, nucleic acids, proteins, and lipids.

Objective

The aim of this study was to identify blood-derived EVs (bdEVs) spectroscopic signatures with AD discriminatory potential.

Methods

Herein, FTIR spectra of bdEVs from two biofluids (serum and plasma) and distinct sets of Controls and AD cases were acquired, and EVs' spectra analyzed.

Results

Analysis of bdEVs second derivative peaks area revealed differences between Controls and AD cases in distinct spectra regions, assigned to carbohydrates and nucleic acids, amides, and lipids.

Conclusions

EVs' spectroscopic profiles presented AD discriminatory value, supporting the use of bdEVs combined with FTIR as a screening or complementary tool for AD diagnosis.

UVB pretreatment of β-lactoglobulin affects the temperature-induced formation of functional amyloid-like aggregates and promotes oxidative degradation

Unfolding in combination with or without acid hydrolysis is crucial for the formation of functional amyloid (fibrillar) or amyloid-like (worm-like) β-lactoglobulin (BLG) aggregates, which can be induced through temperature treatment for several hours at pH 2-4. A preceding conformational destabilization of BLG might affect its aggregation. We investigated ultraviolet (UV) B radiation as conformational perturbing treatment to facilitate temperature-induced protein aggregation. 2-h UVB pretreated BLG (UV-BLG) exhibited an accelerated worm-like aggregation at pH 3.5, while at pH 2 the formation of fibrils was decelerated. The UV-induced conformational destabilization lowered the thermal stability and thus facilitates unfolding during thermal treatment. Thereby, the formation of covalent and non-covalent intermolecular interactions was favored, which promoted assembly of intact proteins resulting in worm-like aggregates. The oxidative degradation of UV-BLG was suggested to alter fibrillation-prone protein regions and thereby impede peptide assembly.

Quantifying the effects of pre-roasting on structural and functional properties of yellow pea proteins

Roasting could modify the protein structure/conformation, contributing to changes in functional properties. Here we investigated the effects of pre-roasting on the extraction efficiency, structural and functional properties of pea protein concentrates and isolates (PPC and PPI) produced from yellow split peas. The shorter roasting times (150 °C, 10 and 20 min) had little effect on protein yields and could increase the solubility of PPC or PPI by ∼ 12% at pH 7 and enhance the solubility of PPI by ∼ 12% (10-min roasting) and ∼ 24% (20-min roasting) at pH 3. However, a longer duration of pre-roasting (150 °C, 30 min) significantly reduced the extraction efficiency of PPC and PPI by ∼ 30% and ∼ 61%, respectively. Meanwhile, pre-roasting had minor effects on SDS-PAGE profiles and the secondary structures of pea proteins but significantly altered tertiary structures by reducing free sulfhydryl groups, increasing disulfide bonds and surface hydrophobicity. As for the emulsifying properties, pre-roasting improved the emulsion ability index (EAI) of PPC and PPI but decreased the emulsion stability index (ESI) of PPC and had no significant effect on PPI. Moreover, PPC and PPI with shorter pre-roasting duration (10 and 20 min) had endothermic peaks and showed a slight decrease in the denaturation temperature (Td) and the onset temperature (To), respectively. Overall, the study demonstrated that controlled pre-roasting at 150 °C for 10 min and 20 min altered protein structures (mainly tertiary structures), improving the solubility and EAI of pea proteins at pH 7, while retaining their thermal properties in comparison to unroasted samples.

Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation

A large group of hormones are stored as amyloid fibrils in acidic secretion vesicles before they are released into the bloodstream and readopt their functional state. Here, we identify an evolutionarily conserved hexapeptide sequence as the major aggregation-prone region (APR) of gastrointestinal peptides of the glucagon family: xFxxWL. We determine nine polymorphic crystal structures of the APR segments of glucagon-like peptides 1 and 2, and exendin and its derivatives. We follow amyloid formation by CD, FTIR, ThT assays, and AFM. We propose that the pH-dependent changes of the protonation states of glutamate/aspartate residues of APRs initiate switching between the amyloid and the folded, monomeric forms of the hormones. We find that pH sensitivity diminishes in the absence of acidic gatekeepers and amyloid formation progresses over a broad pH range. Our results highlight the dual role of short aggregation core motifs in reversible amyloid formation and receptor binding.

Lipid oxidation induced protein scission in an oleogel as a model food

Lipid oxidation induced protein scission was investigated in oleogel using beta-lactoglobulin (whey protein isolate) as gelator. Extracted cleaved peptides were measured using high resolution mass spectrometry (FT-ICR-MS), which was provided by an automatically generated annotation list approach to identify relevant masses and sum formula using the isotopic pattern. The identified oxidized peptides were then further evaluated using partial least squares regression to relevant lipid hydroperoxide formation data, which provide the significance and importance of the peptides toward lipid induced scission. Thereby, the most important peptides are located at the surface of the protein in random coil segments and especially at the ends of the protein sequence. The most important amino acids were cysteine and aliphatic amino acids, which undergo scission mostly by the α-amidation pathway. The findings compare well with studies investigating depletion of amino acids initiated by lipid oxidation in systems containing bovine albumin or gamma-globulin.

Biomimetic and Multifunctional Hemostatic Hydrogel with Rapid Thermoresponsive Gelation and Robust Wet Adhesion for Emergency Hemostasis: A Rational Design Based on Photo-Cross-Linking Coordinated Hydrophilic-Hydrophobic Balance Strategies

Uncontrolled bleeding in emergency situations is a great threat to both military and civilian lives, and an ideal hemostat for effectively controlling prehospital hemorrhage is urgently needed but still lacking. Although hemostatic hydrogels are promising for emergency hemostasis, they are currently challenged by either the mutual exclusion between a short gelation time and strong adhesive network or the insufficient functionality of ingredients and complicated operations for in situ curing. Herein, an extracellular matrix biopolymer-based and multifunctional hemostatic hydrogel that simultaneously integrates rapid thermoresponsive gelation, robust wet adhesion, and ease of use in emergencies is rationally engineered. This hydrogel can be conveniently used via simple injection and achieves instant sol-gel phase transition at body temperature. Its comprehensive performance could be facilely regulated by tuning the proportions of components, and the optimal performance (gelation time 6-8 s, adhesion strength 125 ± 3.6 kPa, burst pressure 282 ± 4.1 mmHg) is established due to the coordinated enhancement of the photo-cross-linking pretreatment and the hydrophilic-hydrophobic balance among various interactions in the hydrogel system. Additionally, it exhibits significant coagulation effect in vitro and enables effective hemostasis and wound healing in vivo. This work provides a promising platform for versatile applications of hydrogel-based materials, including emergency hemostasis.

Distinct effects of heat shock temperatures on mitotic progression by influencing the spindle assembly checkpoint

Heat shock is a physiological and environmental stress that leads to the denaturation and inactivation of cellular proteins and is used in hyperthermia cancer therapy. Previously, we revealed that mild heat shock (42 °C) delays the mitotic progression by activating the spindle assembly checkpoint (SAC). However, it is unclear whether SAC activation is maintained at higher temperatures than 42 °C. Here, we demonstrated that a high temperature of 44 °C just before mitotic entry led to a prolonged mitotic delay in the early phase, which was shortened by the SAC inhibitor, AZ3146, indicating SAC activation. Interestingly, mitotic slippage was observed at 44 °C after a prolonged delay but not at 42 °C heat shock. Furthermore, the multinuclear cells were generated by mitotic slippage in 44 °C-treated cells. Immunofluorescence analysis revealed that heat shock at 44 °C reduces the kinetochore localization of MAD2, which is essential for mitotic checkpoint activation, in nocodazole-arrested mitotic cells. These results indicate that 44 °C heat shock causes SAC inactivation even after full activation of SAC and suggest that decreased localization of MAD2 at the kinetochore is involved in heat shock-induced mitotic slippage, resulting in multinucleation. Since mitotic slippage causes drug resistance and chromosomal instability, we propose that there may be a risk of cancer malignancy when the cells are exposed to high temperatures.

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike's conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended β-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments.

Amyloid-like aggregation of recombinant β-lactoglobulin at pH 3.5 and 7.0: Is disulfide bond removal the key to fibrillation?

Functional nanofibrils from globular proteins are usually formed by heating for several hours at pH 2.0, which induces acidic hydrolysis and consecutive self-association. The functional properties of these micro-metre-long anisotropic structures are promising for biodegradable biomaterials and food applications, but their stability at pH > 2.0 is low. The results presented here show that modified β-lactoglobulin can also form nanofibrils by heating at neutral pH without prior acidic hydrolysis; the key is removing covalent disulfide bonds. The aggregation behaviour of various recombinant β-lactoglobulin variants was systemically studied at pH 3.5 and 7.0. The suppression of intra- and intermolecular disulfide bonds by eliminating one to three out of the five cysteines makes the non-covalent interactions more prevalent and allow for structural rearrangement. This stimulated the linear growth of worm-like aggregates. Full elimination of all five cysteines led to the transformation of worm-like aggregates into actual fibril structures (several hundreds of nanometres long) at pH 7.0. This understanding of the role of cysteine in protein-protein interactions will help to identify proteins and protein modifications to form functional aggregates at neutral pH.

Temperature-Induced Effects on the Structure of Gramicidin S

We report on the structure of Gramicidin S (GS) in a model membrane mimetic environment represented by the amphipathic solvent 1-octanol using one-dimensional (1D) and two-dimensional (2D) IR spectroscopy. To explore potential structural changes of GS, we also performed a series of spectroscopic measurements at differing temperatures. By analyzing the amide I band and using 2D-IR spectral changes, results could be associated to the disruption of aggregates/oligomers, as well as structural and conformational changes happening in the concentrated solution of GS. The ability of 2D-IR to enable differentiation in melting transitions of oligomerized GS structures is attributed to the sensitivity of the technique to vibrational coupling. Two melting transition temperatures were identified; at T_m1 in the range 41-47 °C where the GS aggregates/oligomers disassemble and at T_m2 = 57 ± 2 °C where there is significant change involving GS β-sheet-type hydrogen bonds, whereby it is proposed that there is loss of interpeptide hydrogen bonds and we are left with mainly intrapeptide β-sheet and β-turn hydrogen bonds of the smaller oligomers. Further analysis with quantum mechanical/molecular mechanics (QM/MM) simulations and second derivative results highlighted the participation of active GS side chains. Ultimately, this work contributes toward understanding the GS structure and the formulation of GS analogues with improved bioactivity.

Molecular Insights for Alzheimer's Disease: An Unexplored Storyline on the Nanoscale Impact of Nascent Aβ1-42 toward the Lipid Membrane

Deciphering the mechanism of Alzheimer's disease is a key element for designing an efficient therapeutic strategy. Molecular dynamics (MD) calculations, atomic force microscopy, and infrared spectroscopy were combined to investigate β-amyloid (Aβ_1-42) peptide interactions with supported lipid bilayers (SLBs). The MD simulations showed that nascent Aβ_1-42 monomers remain anchored within a model phospholipid bilayer's hydrophobic core, which suggests their stability in their native environment. We tested this prediction experimentally by studying the behavior of Aβ_1-42 monomers and oligomers when interacting with SLBs. When Aβ_1-42 monomers and oligomers were self-assembled with a lipid bilayer and deposited as an SLB, they remain within the bilayers. Their presence in the bilayers induces destabilization of the model membranes. No specific interactions between Aβ_1-42 and the SLBs were detected when SLBs free of Aβ_1-42 were exposed to Aβ_1-42. This study suggests that Aβ can remain in the membrane after cleavage by γ-secretase and cause severe damage to the membrane.

Protease-catalyzed synthesis of α-poly-L-Lysine and amphiphilic poly(L-lysine-co-L-phenylalanine) in a neat non-toxic organic solvent

Subtilisin Carlsberg (alkaline protease from Bacillus licheniformis) catalyzes the syntheses of high molecular weights (ca. 20 KDa) cationic α-poly-L-lysine and amphiphilic poly(α-L-lysine-co-L-phenylalanine) in neat organic solvent. The synthesis is conducted in liquid 1,1,1,2-tetrafluoroethane solvent, which is a hydrophobic non-toxic gas that does not deplete the ozone layer and approved for pharmaceutical applications. Solubility of substrates and adequate protease activity in this system with low water environment limits the reaction of hydrolysis of the growing peptide chains. The pressurization of this organic compressed fluid to liquid has low-pressure requirements (25 bar, 40 ºC), and its complete evaporation at atmospheric pressure after completing the reaction ensures solvent-free residues in products. The resulting polypeptides present null cytotoxicity according to MTT and NR analyses, as well as Calcein/EthD-1 assay in human cells.

Bacterial Lectin FimH and Its Aggregation Hot-Spots: An Alternative Strategy against Uropathogenic Escherichia coli

Type I fimbriae are the main adhesive organelles of uropathogenic Escherichia coli (UPEC), consisting of four different subunits. Their component with the most important role in establishing bacterial infections is the FimH adhesin located at the fimbrial tip. This two-domain protein mediates adhesion to host epithelial cells through interaction with terminal mannoses on epithelial glycoproteins. Here, we propose that the amyloidogenic potential of FimH can be exploited for the development of therapeutic agents against Urinary Tract Infections (UTIs). Aggregation-prone regions (APRs) were identified via computational methods, and peptide-analogues corresponding to FimH lectin domain APRs were chemically synthesized and studied with the aid of both biophysical experimental techniques and molecular dynamic simulations. Our findings indicate that these peptide-analogues offer a promising set of antimicrobial candidate molecules since they can either interfere with the folding process of FimH or compete for the mannose-binding pocket.

ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals

The development of fast, cheap and reliable methods to determine seroconversion against infectious agents is of great practical importance. In the context of the COVID-19 pandemic, an important issue is to study the rate of formation of the immune layer in the population of different regions, as well as the study of the formation of post-vaccination immunity in individuals after vaccination. Currently, the main method for this kind of research is enzyme immunoassay (ELISA, enzyme-linked immunosorbent assay). This technique is sufficiently sensitive and specific, but it requires significant time and material costs. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in blood plasma to detect seroconversion against SARS-CoV-2. The study included samples of 60 patients. Clear spectral differences in plasma samples from recovered COVID-19 patients and conditionally healthy donors were identified using multivariate and statistical analysis. The results showed that ATR-FTIR spectroscopy, combined with principal components analysis (PCA) and linear discriminant analysis (LDA) or artificial neural network (ANN), made it possible to efficiently identify specimens from recovered COVID-19 patients. We built classification models based on PCA associated with LDA and ANN. Our analysis led to 87% accuracy for PCA-LDA model and 91% accuracy for ANN, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective tool for detecting seroconversion against SARS-CoV-2. This approach could be used as an alternative to ELISA.

Proteolysis of Micellar β-Casein by Trypsin: Secondary Structure Characterization and Kinetic Modeling at Different Enzyme Concentrations

Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles dried on a mica surface were characterized by atomic force microscopy (AFM) when the proteolytic reaction had been stopped by tryptic inhibitor or by heating. The changes in the content of β-sheets, α-helices, and hydrolysis products during proteolysis were estimated by using Fourier-transform infrared (FTIR) spectroscopy. In the current study, a simple kinetic model with three successive stages is proposed to predict the rearrangement of nanoparticles and the formation of proteolysis products, as well as changes in the secondary structure during proteolysis at various enzyme concentrations. The model determines for which steps the rate constants are proportional to the enzyme concentration, and in which intermediate nano-components the protein secondary structure is retained and in which it is reduced. The model predictions were in agreement with the FTIR results for tryptic hydrolysis of β-CN at different concentrations of the enzyme.

The pH-responsive precipitation-redissolution of the CspB fusion protein, CspB50TEV-Teriparatide, triggered by changes in secondary structure

Cell surface protein B (CspB) fusion proteins can undergo reversible pH-responsive precipitation-redissolution. A pH-responsive precipitation-redissolution of CspB tag purification (pPRCP) method was established for protein purification using this property. However, the mechanism of the pH-responsive precipitation of CspB fusion proteins is unknown, which has made it difficult to set process parameters for pPRCP. In this study, we investigated the mechanism of the pH-responsive precipitation of CspB fusion proteins using CspB50TEV-Teriparatide (CspB-teri) as a model. As expected, CspB-Teri was reversibly precipitated at acidic pH. By contrast, CspB-Teri was not precipitated under unfolding conditions induced by trifluoroethanol, urea, or guanidine hydrochloride, even at acidic pH. The conformation of CspB-Teri changed to a β-sheet-rich structure as the pH decreased, followed by the formation of intermolecular interactions, which caused precipitation. The particle size of the CspB-Teri precipitate increased in a protein concentration-dependent manner. These results indicated that the pH-responsive precipitation of CspB-Teri is triggered by the formation of a β-sheet structure in response to decreasing pH, and the growth of the precipitate particles occurred through intermolecular interactions.

Infrared Spectroscopy for Structure Analysis of Protein Inclusion Bodies

Infrared (IR) spectroscopy is a widely used technique for evaluation of protein secondary structure. In this chapter, we focus on the application of this analytical technique for analysis of inclusion bodies. After a general introduction to protein analysis by IR spectroscopy, different approaches for spectra acquisition, data processing, and secondary structure evaluation are presented.

Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins

NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of cellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we explore the diverse world of effector and signaling domains of fungal NLRs using state-of-the-art bioinformatic methods including MMseqs2 for fast clustering, probabilistic context-free grammars for sequence analysis, and AlphaFold2 deep neural networks for structure prediction. In addition to substantially improving the overall annotation, especially in basidiomycetes, the study identifies novel domains and reveals the structural similarity of MLKL-related HeLo- and Goodbye-like domains forming the most abundant superfamily of fungal NLR effectors. Moreover, compared to previous studies, we found several times more amyloid motif instances, including novel families, and validated aggregating and prion-forming properties of the most abundant of them in vitro and in vivo. Also, through an extensive in silico search, the NLR-associated amyloid signaling was identified in basidiomycetes. The emerging picture highlights similarities and differences in the NLR architectures and amyloid signaling in ascomycetes, basidiomycetes and other branches of life.

Distinguishing Asphyxia from Sudden Cardiac Death as the Cause of Death from the Lung Tissues of Rats and Humans Using Fourier Transform Infrared Spectroscopy

The ability to determine asphyxia as a cause of death is important in forensic practice and helps us to judge whether a case is criminal. However, in some cases where the deceased has underlying heart disease, death by asphyxia cannot be determined by traditional autopsy and morphological observation under a microscope because there are no specific morphological features for either asphyxia or sudden cardiac death (SCD). Here, Fourier transform infrared (FTIR) spectroscopy was employed to distinguish asphyxia from SCD. A total of 40 lung tissues (collected at 0 h and 24 h postmortem) from 20 rats (10 died from asphyxia and 10 died from SCD) and 16 human lung tissues from 16 real cases were used for spectral data acquisition. After data preprocessing, 2675 spectra from rat lung tissues and 1526 spectra from human lung tissues were obtained for subsequent analysis. First, we found that there were biochemical differences in the rat lung tissues between the two causes of death by principal component analysis and partial least-squares discriminant analysis (PLS-DA), which were related to alterations in lipids, proteins, and nucleic acids. In addition, a PLS-DA classification model can be built to distinguish asphyxia from SCD. Second, based on the spectral data obtained from lung tissues allowed to decompose for 24 h, we could still distinguish asphyxia from SCD even when decomposition occurred in animal models. Nine important spectral features that contributed to the discrimination in the animal experiment were selected and further analyzed. Third, 7 of the 9 differential spectral features were also found to be significantly different in human lung tissues from 16 real cases. A support vector machine model was finally built by using the seven variables to distinguish asphyxia from SCD in the human samples. Compared with the linear PLS-DA model, its accuracy was significantly improved to 0.798, and the correct rate of determining the cause of death was 100%. This study shows the application potential of FTIR spectroscopy for exploring the subtle biochemical differences resulting from different death processes and determining the cause of death even after decomposition.

Mannosylated Systems for Targeted Delivery of Antibacterial Drugs to Activated Macrophages

Macrophages are a promising target for drug delivery to influence macrophage-associated processes in the body, namely due to the presence of resistant microorganisms in macrophages. In this work, a series of mannosylated carriers based on mannan, polyethylenimine (PEI) and cyclodextrin (CD) was synthesized. The molecular architecture was studied using FTIR and 1H NMR spectroscopy. The particle size, from small 10-50 nm to large 500 nm, depending on the type of carrier, is potentially applicable for the creation of various medicinal forms: intravenous, oral and inhalation. Non-specific capture by cells with a simultaneous increase in selectivity to CD206+ macrophages was achieved. ConA was used as a model mannose receptor, binding galactosylated (CD206 non-specific) carriers with constants of the order of 104 M-1 and mannosylated conjugates of 106-107 M-1. The results of such primary "ConA-screening" of ligands are in a good agreement in terms of the comparative effectiveness of the interaction of ligands with the CD206+ macrophages: non-specific (up to 10%) absorption of highly charged and small particles; weakly specific uptake of galactosylated polymers (up to 50%); and high affine capture (more than 70-80%) of the ligands with grafted trimannoside was demonstrated using the cytometry method. Double and multi-complexes of antibacterials (moxifloxacin with its adjuvants from the class of terpenoids) were proposed as enhanced forms against resistant pathogens. In vivo pharmacokinetic experiments have shown that polymeric carriers significantly improve the efficiency of the antibiotic: the half-life of moxifloxacin is increased by 2-3 times in conjugate-loaded forms, bio-distribution to the lungs in the first hours after administration of the drug is noticeably greater, and, after 4 h of observation, free moxifloxacin was practically removed from the lungs of rats. Although, in polymer systems, its content is significant-1.2 µg/g. Moreover, the importance of the covalent crosslinking carrier with mannose label was demonstrated. Thus, this paper describes experimental, scientifically based methods of targeted drug delivery to macrophages to create enhanced medicinal forms.

ATR-FTIR Biosensors for Antibody Detection and Analysis

Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, impacting the drug product quality. Conditions for obtaining highly reproducible grafting of 11-mercaptoundecanoic acid were determined. On that basis, we developed an easy-to-use, cost effective, and timesaving biosensor based on ATR-FTIR spectroscopy able to detect immunoglobulins during their production. A germanium crystal, used as an internal reflection element (IRE) for FTIR spectroscopy, was covalently coated with immunoglobulin-binding proteins. This thereby functionalized surface could bind only immunoglobulins present in complex media such as culture media or biopharmaceutical products. The potential subsequent analysis of their structure by ATR-FTIR spectroscopy makes this biosensor a powerful tool to monitor the production of biotherapeutics and assess important critical quality attributes (CQAs) such as high-order structure and aggregation level.

Mass spectrometry and synchrotron-FTIR microspectroscopy reveal the anti-inflammatory activity of Bua Bok extracts

INTRODUCTION

Bua Bok or Centella asiatica (CA) is an Asian vegetable with anti-inflammatory benefits. Asiaticoside, asiatic acid, madecassoside and madecassic have been characterised as major active ingredients with a wide range of pharmacological advantages. In manufacturing processes, high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LCMS) are used to routinely determine the active compounds in raw materials.

OBJECTIVES

This research aims to explore anti-inflammatory properties, characterise metabolites and observe the biochemical changes of the inflammatory induced macrophages after pretreatment with the potential extracted fractions.

METHODS

Bua Bok leaf extracts were prepared. Macrophages were pretreated with non-toxic fractions to determine the anti-inflammatory action. Tentative metabolites of effective fractions were identified by LC-MS. Synchrotron fourier-transform infrared (S-FTIR) microspectroscopy was utilised to observe the biochemical change of the lipopolysaccharide (LPS)-induced cells after pretreatment with potential fractions.

RESULTS

Fractions of ethyl acetate, 30% and 100% ethanol highly increased the nitrile scavenging and suppressed the function of phospholipase A₂ . Fractions of 70% and 100% ethanol strongly decreased nitric oxide production. The comparison of 39 chemical compounds was presented. The change of proteins was improved after pretreatment of macrophages with fraction 70% ethanol. Fraction of 100% ethanol revealed the lipid accumulation was lower than 70% ethanol and diclofenac.

CONCLUSION

While the anti-inflammatory actions of 70% and 100% ethanol were similar. S-FTIR expressed they inhibited inflammatory response with the distinct features of biomolecules. The S-FTIR, LC-MS and biological assay confidently provided the efficient strategies to inform the advantage of herbal extract on cellular organisation instead of a single compound.

Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers

Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.

Expression of membrane beta-barrel protein in E. coli at low temperatures: Structure of Yersinia pseudotuberculosis OmpF porin inclusion bodies

The recombinant OmpF porin of Yersinia pseudotuberculosis as a model of transmembrane protein of the β-barrel structural family was used to study low growth temperature effect on the structure of the produced inclusion bodies (IBs). This porin showed a very low expression level in E. coli at a growth temperature below optimal 37 °C. The introduction of a N-terminal hexahistidine tag into the mature porin molecule significantly increased the biosynthesis of the protein at low cultivation temperatures. The recombinant His-tagged porin (rOmpF-His) was expressed in E. coli at 30 and 18 °C as inclusion bodies (IB-30 and IB-18). The properties and structural organization of IBs, as well as the structure of rOmpF-His solubilized from the IBs with urea and SDS, were studied using turbidimetry, electron microscopy, dynamic light scattering, optical spectroscopy, and amyloid-specific dyes. IB-18, in comparison with IB-30, has a higher solubility in denaturants, suggesting a difference between IBs in the conformation of the associated polypeptide chains. The spectroscopic analysis revealed that rOmpF-His IBs have a high content of secondary structure with a tertiary-structure elements, including a native-like conformation, the proportion of which in IB-18 is higher than in IB-30. Solubilization of the porin from IBs is accompanied by a modification of its secondary structure. The studied IBs also contain amyloid-like structures. The results obtained in this study expand our knowledge of the structural organization of IBs formed by proteins of different structural classes and also have a contribution into the new approaches development of producing functionally active recombinant membrane proteins.

Methodological advances and strategies for high resolution structure determination of cellular protein aggregates

Aggregation of proteins is at the nexus of molecular processes crucial to aging, disease, and employing proteins for biotechnology and medical applications. There has been much recent progress in determining the structural features of protein aggregates that form in cells; yet, owing to prevalent heterogeneity in aggregation, many aspects remain obscure and often experimentally intractable to define. Here, we review recent results of structural studies for cell-derived aggregates of normally globular proteins, with a focus on high-resolution methods for their analysis and prediction. Complementary results obtained by solid-state NMR spectroscopy, FTIR spectroscopy and microspectroscopy, cryo-EM, and amide hydrogen/deuterium exchange measured by NMR and mass spectrometry, applied to bacterial inclusion bodies and disease inclusions, are uncovering novel information on in-cell aggregation patterns as well as great diversity in the structural features of useful and aberrant protein aggregates. Using these advances as a guide, this review aims to advise the reader on which combination of approaches may be the most appropriate to apply to their unique system.

New Insights into the Multivariate Analysis of SER Spectra Collected on Blood Samples for Prostate Cancer Detection: Towards a Better Understanding of the Role Played by Different Biomolecules on Cancer Screening: A Preliminary Study

Simple Summary

In recent years, research on biofluids using Raman and SERS has expanded dramatically, indicating the enormous promise of this technology as a high-throughput tool for identifying cancer and other disorders. In the investigations thus far, researchers have concentrated on a specific illness or condition, but the techniques employed to acquire experimental spectra prevent direct comparison of the data. This necessitates comparative research of a variety of diseases and an increase in scientific cooperation to standardize experimental conditions. In our study, positive results were reached by applying a combined SERS multivariate analysis (MVA) to the urgent problem of prostate cancer diagnosis that was directly linked to real-world settings in healthcare. Moreover, in comparison to the prostate-specific antigen (PSA) test, which has a high sensitivity but limited specificity, our combined SERS-MVA method has greater specificity, which may assist in preventing the overtreatment of patients.

Abstract

It is possible to obtain diagnostically relevant data on the changes in biochemical elements brought on by cancer via the use of multivariate analysis of vibrational spectra recorded on biological fluids. Prostate cancer and control groups included in this research generated almost similar SERS spectra, which means that the values of peak intensities present in SERS spectra can only give unspecific and limited information for distinguishing between the two groups. Our diagnostic algorithm for prostate cancer (PCa) differentiation was built using principal component analysis and linear discriminant analysis (PCA-LDA) analysis of spectral data, which has been widely used in spectral data management in many studies and has shown promising results so far. In order to fully utilize the entire SERS spectrum and automatically determine the most meaningful spectral features that can be used to differentiate PCa from healthy patients, we perform a multivariate analysis on both the entire and specific spectral intervals. Using the PCA-LDA model, the prostate cancer and control groups are clearly distinguished in our investigation. The separability of the following two data sets is also evaluated using two alternative discrimination techniques: principal least squares discriminant analysis (PLS-DA) and principal component analysis—support vector machine (PCA-SVM).

Experimental and theoretical studies on the anti-amyloidogenic and destabilizing effects of pyrogallol against human insulin protein

One of the major problems caused by repeated subcutaneous insulin injections in patients with diabetes is insulin amyloidosis. Understanding the molecular mechanism of amyloid fibril formation of insulin and finding effective compounds to inhibit or eliminate them is very important, and extensive research has been done on it. In this study, the anti-amyloidogenic and destabilizing effects of the pyrogallol, as a phenolic compound, on human insulin protein were investigated by CR absorbance, ThT and ANS fluorescence, FTIR spectroscopy, and atomic force microscopy. According to the obtained results, the formation of amyloid fibrils at pH 2.0 and 50°C was confirmed by CR, ThT, ANS, and FTIR assays. Microscopic images also showed the twisted and long structures of amyloid fibrils. Simultaneous incubation of the protein with pyrogallol at different concentrations reduced the intensities of CR, ThT, and ANS in a dose-dependent manner, and no trace of fibrillar structures was observed in the microscopic images. FTIR spectroscopy also showed that the position of the amide I band in the spectrum of samples containing pyrogallol was shifted. Based on the findings of this study, it can be concluded that pyrogallol can be effective in preventing and suppressing human insulin amyloid fibrils. PRACTICAL APPLICATIONS: In recent years, finding a strategy for the treatment of amyloid diseases has been considered by many researchers. Targeting protein aggregates by small organic molecules such as polyphenols is one of the most desirable and effective strategies to prevent and improve amyloid disease, which has received much attention in recent years. 1,2,3-Trihydroxybenzene, commonly known as pyrogallol (Py), is a phenolic compound like other natural polyphenols that are present in human food sources, including fruits and vegetables, and a variety of edible and medicinal plants. So far, many beneficial activities for pyrogallol such as anti-cancer, antioxidant, antibacterial, antiviral, and antifungal have been reported in various studies. Since various studies have shown that natural polyphenols have special properties to prevent amyloid disease, the present study could be useful in advancing the design purposes of new anti-amyloid drugs in the future.

dl-Polyalanine as a PEG-Free Thermogel

Thermogelling behavior of aqueous polymer solutions comes from the delicate balance between hydrophilic and hydrophobic moieties of the polymer. Typically, poly(ethylene glycol) (PEG) has been used as a hydrophilic block in most thermogels reported to date. However, recent papers have suggested the potential immunogenicity of PEG-conjugated compounds. Here, we report that aqueous solutions of dl-polyalanine (DL-PA) with a specific molecular weight can exhibit thermogelling behavior. In particular, DL-PA with a molecular weight (M_n) of 6690 Da, DL-PA67, exhibited sol-to-gel transition at the physiologically important temperature range of 30-40 °C. ¹H NMR and FTIR data indicated that the mechanism of thermogelation is related to dehydration and conformational changes of DL-PA67 from random coil to β-sheet structures. Subcutaneous injection of an aqueous DL-PA67 solution into rats confirmed the gel formation and its histocompatibility with mild tissue irritation.

NAMPT Inhibitor and P73 Activator Represses P53 R175H Mutated HNSCC Cell Proliferation in a Synergistic Manner

The p53 family has the following three members: p53, p63 and p73. p53 is a tumor suppressor gene that frequently exhibits mutation in head and neck cancer. Most p53 mutants are loss-of-function (LoF) mutants, but some acquire some oncogenic function, such as gain of function (GoF). It is known that the aggregation of mutant p53 can induce p53 GoF. The p73 activators RETRA and NSC59984 have an anti-cancer effect in p53 mutation cells, but we found that p73 activators were not effective in all head and neck squamous cell carcinoma (HNSCC) cell lines, with different p53 mutants. A comparison of the gene expression profiles of several regulator(s) in mutant HNSCC cells with or without aggregation of p53 revealed that nicotinamide phosphoribosyltransferase (NAMPT) is a key regulator of mutant p53 aggregation. An NAMPT inhibitor, to reduce abnormal aggregation of mutant p53, used in combination with a p73 activator, was able to effectively repress growth in HNSCC cells with p53 GoF mutants. This study, therefore, suggests a potential combination therapy approach for HNSCC with a p53 GoF mutation.

Glyoxal induced glycative insult suffered by immunoglobulin G and fibrinogen proteins: A comparative physicochemical characterization to reveal structural perturbations

Glycation of proteins results in structural alteration, functional deprivation, and generation of advanced glycation end products (AGEs). Reactive oxygen species (ROS) that are generated during in vivo autoxidation of glucose induces glycoxidation of intermediate glycation-adducts, which in turn give rise to aldehyde and/or ketone groups containing dicarbonyls or reactive carbonyl species (RCS). RCS further reacts non-enzymatically and starts the glycation-oxidation vicious cycle, thus exacerbating oxidative, carbonyl, and glycative stress in the physiological system. Glyoxal (GO), a reactive dicarbonyl that generates during glycoxidation and lipid peroxidation, contributes to glycation. This in vitro physicochemical characterization study focuses on GO-induced glycoxidative damage suffered by immunoglobulin G (IgG) and fibrinogen proteins. The structural alterations were analyzed by UV-vis, fluorescence, circular dichroism, and Fourier transform infrared (FT-IR) spectroscopy. Ketoamines, protein carbonyls, hydroxymethylfurfural (HMF), free lysine, free arginine, carboxymethyllysine (CML), and protein aggregation were also quantified. Structural perturbations, increased concentration of ketoamines, protein carbonyls, HMF, and malondialdehyde (MDA) were reported in glycated proteins. The experiment results also validate increased oxidative stress and AGEs formation i.e. IgG-AGEs and Fib-AGEs. Thus, we can conclude that AGEs formation during GO-mediated glycation of IgG and fibrinogen could hamper normal physiology and might play a significant role in the pathogenesis of diabetes-associated secondary complications.

The impact of concurrent training and antioxidant supplementation on the factors associated with the ocular lens opacity in diabetic rats

The current study was aimed to investigate the protective effect of vitamins C and E (VCE) supplementation, exercise, and their concurrent application against cataract incidence in the diabetic rats. The obtained results indicated that different supplementation and training treatments were capable to preserve the lens transparency in the diabetic rats. Also, upon applying different supplementation and training treatments, the level of glutathione (GSH) and activity of antioxidant enzymes in the diabetic rats was preserved approximately close to their control levels. In addition, different treatments were capable to maintain the structural integrity of the lens proteins in diabetic rats. Moreover, VCE supplementation, exercise and their simultaneous application prevented lens crystallins of diabetic rats against fibrillation and formation of the increased oligomeric sizes. The results of this study signify the importance of antioxidant supplementation and exercise in reducing the detrimental effects of hyperglycemia on the eye lenses.

Challenges in Experimental Methods

Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.

Direct observation of peptide hydrogel self-assembly

The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon–deuterium (C–D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in drug delivery and medical applications. C–D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C–D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate self-assembly, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 self-assembly occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics.

To facilitate the characterization of phase-transitioning molecules, site-specific non-perturbative infrared probes are leveraged for continuous observation of the self-assembly of fibrils in a peptide hydrogel following stopped-flow initiation.