Evaluation of the information content in infrared spectra for protein secondary structure determination

Modulation of physico-chemical and technofunctional properties of quinoa protein isolate: Effect of precipitation acid

The typically low solubility and gelation capacity of plant proteins can impose challenges in the design of high-quality plant-based foods. The acid used during the precipitation step of plant protein isolate extraction can influence protein functionality. Here, acetic acid and citric acid were used to extract quinoa protein isolate (QPI) from quinoa flour, as these acids are more kosmotropic than the commonly used HCl, promoting the stabilisation of the native protein structure. While proximate analysis showed that total protein was similar for the three isolates, precipitation with kosmotropic acids increased soluble protein, which correlated positively with gel strength. Microstructure analysis revealed that these gels contained a less porous protein network with lipid droplet inclusions. This study shows that the choice of precipitation acid offers an opportunity to tailor the properties of quinoa protein isolate for application, a strategy that is likely applicable to other plant protein isolates.

Identification and classification of proteins by FTIR microspectroscopy. A proof of concept

FTIR spectroscopy is well known for its molecule fingerprinting capability but is also able to differentiate classes in complex biological systems. This includes strain typing and species level identification of bacterial, yeast or fungal cells, as well as distinguishing between cell layers in eukaryotic tissues. However, its use for the identification of macromolecules such as proteins remains underexplored and rarely used in practice. Here we demonstrate the efficacy of FTIR microspectroscopy coupled with machine learning methods for rapid and accurate identification of proteins in their dry state within minutes, from very small quantities of material, if they are obtained in a pure aqueous solution. FTIR microspectroscopy can provide additional information beside identification: it can detect small differences among different purification batches potentially originating from post-translational modifications or distinct folding states. Moreover, it distinguishes glycoproteins and evaluate glycosylation while detecting contaminants. This methodology presents itself as a valuable quality control tool in protein purification processes or any process requiring the utilization of precisely identified, pure proteins.

Influence of EGCG (Epigallocatechin Gallate) on Physicochemical-Rheological Properties of Surimi Gel and Mechanism Based on Molecular Docking

The influence of epigallocatechin gallate (EGCG) on the physicochemical-rheological properties of silver carp surimi gel was investigated. The gel strength, texture, water-holding capacity (WHC), dynamic distribution of water, and rheological properties of surimi gels added with different levels (0, 0.02, 0.04, 0.06, 0.08, and 0.1%) of EGCG were measured. The results showed that with the increase of EGCG content, the gel strength, hardness, WHC, and immobilized water contents of surimi gels showed a trend of first increasing and then decreasing, and EGCG 0.02% and EGCG 0.04% showed better gel performance as compared with the control. EGCG 0.02% had the highest gel strength (406.62 g·cm), hardness (356.67 g), WHC (64.37%), and immobilized water contents (98.958%). The gel performance decreased significantly when the amounts of EGCG were higher than 0.06%. The viscosity, G', and G″ of the rheological properties also showed the same trends. The chemical interaction of surimi gels, secondary structure of myofibrillar protein (MP), and molecular docking results of EGCG and silver carp myosin showed that EGCG mainly affected the structure and aggregation behavior of silver carp myosin through non-covalent interactions such as those of hydrogen bonds, hydrophobic interactions, and electrostatic interactions. The microstructures of EGCG 0.02% and EGCG 0.04% were compact and homogeneous, and had better gel formation ability. The lower concentrations of EGCG formed a large number of chemical interactions such as those of disulfide bonds and hydrophobic interactions inside the surimi gels by proper cross-linking with MP, and also increased the ordered β-sheet structure of MP, which facilitated the formation of the compact three-dimensional network gel.

Horseradish Peroxidase Immobilized onto Mesoporous Magnetic Hybrid Nanoflowers for Enzymatic Decolorization of Textile Dyes: A Highly Robust Bioreactor and Boosted Enzyme Stability

Recently, hybrid nanoflowers (hNFs), which are accepted as popular carrier supports in the development of enzyme immobilization strategies, have attracted much attention. In this study, the horseradish peroxidase (HRP) was immobilized to mesoporous magnetic Fe3O4-NH2 by forming Schiff base compounds and the HRP@Fe3O4-NH2/hNFs were then synthesized. Under optimal conditions, 95.0% of the available HRP was immobilized on the Fe3O4-NH2/hNFs. Structural morphology and characterization of synthesized HRP@Fe3O4-NH2/hNFs were investigated. The results demonstrated that the average size of HRP@Fe3O4-NH2/hNFs was determined to be around 220 nm. The ζ-potential and magnetic saturation values of HRP@Fe3O4-NH2/hNFs were -33.58 mV and ∼30 emu/g, respectively. Additionally, the optimum pH, optimum temperature, thermal stability, kinetic parameters, reusability, and storage stability were examined. It was observed that the optimum pH value shifted from 5.0 to pH 8.0 after immobilization, while the optimum temperature shifted from 30 to 80 °C. K m values were calculated to be 15.5502 and 7.6707 mM for free HRP and the HRP@Fe3O4-NH2/hNFs, respectively, and V max values were calculated to be 0.0701 and 0.0038 mM min-1. The low K m value observed after immobilization indicated that the affinity of HRP for its substrate increased. The HRP@Fe3O4-NH2/hNFs showed higher thermal stability than free HRP, and its residual activity after six usage cycles was approximately 45%. While free HRP lost all of its activity within 120 min at 65 °C, the HRP@Fe3O4-NH2/hNFs retained almost all of its activity during the 6 h incubation period at 80 °C. Most importantly, the HRP@Fe3O4-NH2/hNFs demonstrated good potential efficiency for the biodegradation of methyl orange, phenol red, and methylene blue dyes. The HRP@Fe3O4-NH2/hNFs were used for a total of 8 cycles to degrade methyl orange, phenol red, and methylene blue, and degradation of around 81, 96, and 56% was obtained in 8 h, respectively. Overall, we believe that the HRP@Fe3O4-NH2/hNFs reported in this work can be potentially used in various industrial and environmental applications, particularly for the biodegradation of recalcitrant compounds, such as textile dyes.

Supramolecular Hydrogels and Water Channels of Differing Diameters from Dipeptide Isomers

Dipeptides stereoisomers and regioisomers composed of norleucine (Nle) and phenylalanine (Phe) self-assemble into hydrogels under physiological conditions that are suitable for cell culture. The supramolecular behavior, however, differs as the packing modes comprise amphipathic layers or water channels, whose diameter is defined by either four or six dipeptide molecules. A variety of spectroscopy, microscopy, and synchrotron-radiation-based techniques unveil fine details of intermolecular interactions that pinpoint the relationship between the chemical structure and ability to form supramolecular architectures that define soft biomaterials.

Preparation of a novel metallothionein-AuNP composite material by genetic modification and AuS covalent combination

Metallothionein (MTs) can be used in the prevention and treatment of tumors and diabetes due to its antioxidant properties. However, it is necessary to solve its non-transmembrane properties and further improve its antioxidant activity, increase its fluorescence visualization and enhance its stability to meet practical applications in the biomedical field. Here, we report the preparation of a novel metallothionein-AuNP composite material with high transmembrane ability, fluorescence visualization, antioxidant activity, and stability by genetic modification (introducing transduction peptide TAT, fluorescence tag GFP and increasing sulfydryl groups) and immobilization technology (covalently bonding with AuNPs). The transmembrane activity of modified proteins was verified by immunofluorescence. Increasing the sulfhydryl content within a certain range can enhance the antioxidant activity of the protein. In addition, GFP were used to further simplify the imaging of the metallothionein-AuNP composite in cells. XPS results indicated that AuNPs can immobilize metallothionein through AuS covalent bonds. TGA characterization and degradation experiments showed that thermal and degradation stability of the immobilized material was significantly improved. This work provides new ideas to construct metallothionein composites with high transmembrane ability, antioxidant activity, fluorescence visualization and stability to meet novel applications in the biomedical field.

In the presence of the other: How glyphosate and peptide molecules alter the dynamics of sorption on goethite

The interactions with soil mineral surfaces are among the factors that determine the mobility and bioavailability of organic contaminants and of nutrients present in dissolved organic matter (DOM) in soil and aquatic environments. While most studies focus on high molar mass organic matter fractions (e.g., humic and fulvic acids), very few studies investigate the impact of DOM constituents in competitive sorption. Here we assess the sorption behavior of a heavily used herbicide (i.e., glyphosate) and a component of DOM (i.e., a peptide) at the water/goethite interface, inclusive of potential glyphosate-peptide interactions. We used in-situ ATR-FTIR (attenuated total reflectance Fourier-transform infrared) spectroscopy to study sorption kinetics and mechanisms of interaction as well as conformational changes to the secondary structure of the peptide. NMR (nuclear magnetic resonance) spectroscopy was used to assess the level of interaction between glyphosate and the peptide and changes to the peptide' secondary structure in solution. For the first time, we illustrate competition for sorption sites results in co-sorption of glyphosate and peptide molecules that affects the extent, kinetics, and mechanism of interaction of each with the surface. In the presence of the peptide, the formation of outer-sphere glyphosate-goethite complexes is favored albeit inner-sphere glyphosate-goethite bonds (i.e., POFe) are still formed. The presence of glyphosate induces secondary structural shifts of the sorbed peptide that maximizes the formation of H-bonds with the goethite surface. However, glyphosate and the peptide do not seem to interact with one another in solution nor at the goethite surface upon sorption. The results of this work highlight potential consequences of competition for sorption sites, for example the transport of organic contaminants and nutrient-rich (i.e., nitrogen) DOM components in relevant environmental systems. Predicting the rate and extent with which organic pollutants are removed from solution by a given solid is also one of the most critical factors for the design of effective sorption systems in engineering applications.

Amyloid Modifier SERF1a Accelerates Alzheimer's Amyloid-β Fibrillization and Exacerbates the Cytotoxicity

Alzheimer's disease (AD) is a devastating, progressive neurodegenerative disease affecting the elderly in the world. The pathological hallmark senile plaques are mainly composed of amyloid-β (Aβ), in which the main isoforms are Aβ40 and Aβ42. Aβ is prone to aggregate and ultimately forms amyloid fibrils in the brains of AD patients. Factors that alter the Aβ aggregation process have been considered to be potential targets for treatments of AD. Modifier of aggregation 4 (MOAG-4)/small EDRK-rich factor (SERF) was previously selected from a chemical mutagenesis screen and identified as an amyloid modifier that promotes amyloid aggregation for α-synuclein, huntingtin, and Aβ40. The interaction and effect of yeast ScSERF on Aβ40 were previously described. Here, we examined the human SERF1a effect on Aβ40 and Aβ42 fibrillization by the Thioflavin T assay and found that SERF1a accelerated Aβ fibrillization in a dose-dependent manner without changing the fibril amount and without incorporation. By Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM), we found that SERF1a altered the secondary structures and the morphology of Aβ fibrils. The electrospray ionization mass spectrometry (ESI-MS) and analytical ultracentrifugation (AUC) results showed that SERF1a binds to Aβ in a 1:1 stoichiometry. Moreover, the NMR study showed that SERF1a interacts with Aβ via its N-terminal region. Cytotoxicity assay demonstrated that SERF1a enhanced toxicity of Aβ intermediates, and the effect can be rescued by SERF1a antibody. Overall, our study provides the underlying molecular mechanism for the SERF1a effect on Aβ fibrillization and facilitates the therapeutic development of AD.

Advances in far-infrared research: therapeutic mechanisms of disease and application in cancer detection

Far infrared (FIR) irradiation is commonly used as a convenient, non-contact, non-invasive treatment for diseases such as myocardial ischemia, diabetes, and chronic kidney disease. In this review, we focus on reviewing the potential therapeutic mechanisms of FIR and its cutting-edge applications in cancer detection. Firstly, we searched the relevant literature in the last decade for systematic screening and briefly summarized the biophysical properties of FIR. We then focused on the possible mechanisms of FIR in wound healing, cardiovascular diseases, and other chronic diseases. In addition, we review recent applications of FIR in cancer detection, where Fourier transform infrared spectroscopy and infrared thermography provide additional diagnostic methods for the medical diagnosis of cancer. Finally, we conclude and look into the future development of FIR for disease treatment and cancer detection. As a high-frequency non-ionizing wave, FIR has the advantages of safety, convenience, and low cost. We hope that this review can provide biological information reference and relevant data support for those who are interested in FIR and related high-frequency non-ionizing waves, to promote the further application of FIR in the biomedical field.

A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones

Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.

Tuning Phase Transition of Molecular Self-Assembly by Artificial Chaperones through Aromatic-Aromatic Interactions

The molecular chaperones are essential and play significant roles in controlling the protein phase transition and maintaining physiological homeostasis. However, manipulating phase transformation in biomimetic peptide self-assembly is still challenging. This work shows that an artificial chaperone modulates the energy landscape of supramolecular polymerization, thus controlling the phase transition of amyloid-like assemblies from crystals to hydrogels to solution. The absence of a chaperone allows the NapP to form crystals, while the presence of the chaperone biases the pathway to form nanofibrous hydrogels to soluble oligomers by adjusting the chaperone ratios. Mechanistic studies reveal that the aromatic-aromatic interaction is the key to trapping the molecules in a higher energy fold. Adding the chaperone relieves this restriction, lowers the energy barrier, and transforms the crystal into a hydrogel. This phase transformation can also be achieved in the macromolecular crowding environment, thus providing new insights into understanding molecular self-assembly in multiple component systems.

Exploration of macromolecular phenotype of human skeletal muscle in diabetes using infrared spectroscopy

Introduction

The global burden of diabetes mellitus is escalating, and more efficient investigative strategies are needed for a deeper understanding of underlying pathophysiological mechanisms. The crucial role of skeletal muscle in carbohydrate and lipid metabolism makes it one of the most susceptible tissues to diabetes-related metabolic disorders. In tissue studies, conventional histochemical methods have several technical limitations and have been shown to inadequately characterise the biomolecular phenotype of skeletal muscle to provide a holistic view of the pathologically altered proportions of macromolecular constituents.

Materials and methods

In this pilot study, we examined the composition of five different human skeletal muscles from male donors diagnosed with type 2 diabetes and non-diabetic controls. We analysed the lipid, glycogen, and collagen content in the muscles in a traditional manner with histochemical assays using different staining techniques. This served as a reference for comparison with the unconventional analysis of tissue composition using Fourier-transform infrared spectroscopy as an alternative methodological approach.

Results

A thorough chemometric post-processing of the infrared spectra using a multi-stage spectral decomposition allowed the simultaneous identification of various compositional details from a vibrational spectrum measured in a single experiment. We obtained multifaceted information about the proportions of the different macromolecular constituents of skeletal muscle, which even allowed us to distinguish protein constituents with different structural properties. The most important methodological steps for a comprehensive insight into muscle composition have thus been set and parameters identified that can be used for the comparison between healthy and diabetic muscles.

Conclusion

We have established a methodological framework based on vibrational spectroscopy for the detailed macromolecular analysis of human skeletal muscle that can effectively complement or may even serve as an alternative to histochemical assays. As this is a pilot study with relatively small sample sets, we remain cautious at this stage in drawing definitive conclusions about diabetes-related changes in skeletal muscle composition. However, the main focus and contribution of our work has been to provide an alternative, simple and efficient approach for this purpose. We are confident that we have achieved this goal and have brought our methodology to a level from which it can be successfully transferred to a large-scale study that allows the effects of diabetes on skeletal muscle composition and the interrelationships between the macromolecular tissue alterations due to diabetes to be investigated.

Albumin from sera of rheumatoid arthritis patients share multiple biochemical, biophysical and immunological properties with in vitro generated glyco-nitro-oxidized-albumin

The purpose of the present study is to explore the effects of endogenous stressors on structure and function of rheumatoid arthritis (RA) patients' albumin. In contrast to glycated-albumin or nitro-oxidized-albumin, high titre antibodies against glyco-nitro-oxidized-albumin were found in the sera of RA patients. Also, compared to the other two modified forms of albumin, glyco-nitro-oxidized-albumin showed highest percent inhibition. Albumin isolated from RA patients' sera displayed hyperchromicity and quenching of tyrosine and tryptophan fluorescence. Fluorescence spectroscopy studies also revealed the presence of dityrosine and advanced glycation end products in RA patient's albumin. RA patients' albumin showed weaker binding with 1-anilinonaphthalene-8-sulfonic acid dye. Secondary structure alterations were demonstrated by circular dichroism and Fourier transform infrared spectroscopy. Biochemical investigations revealed substantial decline in the availability of free side chains of amino acid residues; increased carbonyls and decreased sulfhydryls in RA patients' albumin. The functional impairment in RA patients' albumin was revealed by their low binding with bilirubin and cobalt. Liquid chromatography mass spectrometry analysis revealed the presence of Nε-(carboxymethyl) lysine and 3-nitrotyrosine in RA patients' albumin. The amyloidogenic aggregation of RA patients' albumin was confirmed by Congo red absorption and thioflavin-T fluorescence assays. The morphology of the aggregates was visualized under scanning and transmission electron microscope. From the above findings, we inferred that endogenous stress in RA patients have modified albumin and produce structural/functional abnormalities. Also, the presence of anti-glyco-nitro-oxidized-albumin antibodies along with other clinical features may be used as biomarker for the diagnosis and assessment of treatment responses in RA patients.Communicated by Ramaswamy H. Sarma.

Spectroscopy and dynamics of beta-lactoglobulin complexed with rifampicin

In this paper, we report the binding interaction of milk protein, beta-lactoglobulin (BLG), with an antibiotic against tuberculosis, rifampicin (RIF). BLG intrinsic fluorescence from tryptophan (Trp) amino acids was monitored to understand protein-drug interactions. Binding parameters and stoichiometry were estimated with the help of fluorescence spectral changes. Synchronous fluorescence spectroscopy was employed to exclusively monitor the Trp and Tyrosine (Tyr) environment in the presence of RIF. With the help of steady state fluorescence at different temperatures supported by time-resolved fluorescence, we confirmed that the protein forms a static complex with RIF. Thermodynamic parameters, ΔH and ΔS values, showed the involvement of hydrophobic forces between the RIF and BLG. Competitive displacement assay with ANS confirmed the BLG calyx as the binding site for RIF. Energy transfer mechanism from Trp to RIF was attributed to the fluorescence changes in protein upon complexation. The Förster resonance energy transfer (FRET) was used to find distance, energy transfer efficiency and rate of energy transfer between donor (BLG) and acceptor (RIF). Fourier-transform infrared (FTIR) spectroscopy was utilized for estimating changes in the secondary structure of BLG induced by RIF. Molecular docking was used to visualise the binding location of RIF on BLG. Molecular dynamics (MD) simulation studies showed a consistent binding interactions between BLG and RIF during the 100 ns simulation period and this well supported the increased beta sheet content in FTIR. Overall our results establish the potential of intrinsic fluorescence of BLG in combination with biophysical tools to rationalize drug-protein interactions.Communicated by Ramaswamy H. Sarma.

A Novel Approach for Therapeutic Drug Monitoring of Valproic Acid Using FT-IR Spectroscopy and Nonlinear Support Vector Regression

BACKGROUND

Recent technological progress has bolstered efforts to bring personalized medicine from theory into clinical practice. However, progress in areas such as therapeutic drug monitoring (TDM) has remained somewhat stagnant. In drugs with well-known dose-response relationships, TDM can enhance patient outcomes and reduce health care costs. Traditional monitoring methods such as chromatography-based or immunoassay techniques are limited by their higher costs and slow turnaround times, making them unsuitable for real-time or onsite analysis.

OBJECTIVE

In this work, we propose the use of a fast, direct, and simple approach using Fourier transform infrared spectroscopy (FT-IR) combined with chemometric techniques for the therapeutic monitoring of valproic acid (VPA).

METHOD

In this context, a database of FT-IR spectra was constructed from human plasma samples containing various concentrations of VPA; these samples were characterized by the reference method (immunoassay technique) to determine the VPA contents. The FT-IR spectra were processed by two chemometric regression methods: partial least-squares regression (PLS) and support vector regression (SVR).

RESULTS

The results provide good evidence for the effectiveness of the combination of FT-IR spectroscopy and SVR modeling for estimating VPA in human plasma. SVR models showed better predictive abilities than PLS models in terms of root-mean-square error of calibration and prediction RMSEC, RMSEP, R2Cal, R2Pred, and residual predictive deviation (RPD).

CONCLUSIONS

This analytical tool offers potential for real-time TDM in the clinical setting.

HIGHLIGHTS

FTIR spectroscopy was evaluated for the first time to predict VPA in human plasma for TDM. Two regressions were evaluated to predict VPA in human plasma, and the best-performing model was obtained using nonlinear SVR.

Rheological, Physical, and Spectroscopical Characterization of Gamma-Irradiated Albumin Nanoparticles Loaded with Anthocyanin

Anthocyanins are the main active compounds in blueberry. However, they have poor oxidation stability. If anthocyanins are encapsulated in protein nanoparticles, their oxidation resistance could be increased as a result of the slowing down of the oxidation process. This work describes the advantages of using a γ-irradiated bovine serum albumin nanoparticle bound to anthocyanins. The interaction was characterized biophysically, mainly by rheology. By computational calculation and simulation based on model nanoparticles, we estimated the number of molecules forming the albumin nanoparticles, which allowed us to infer the ratio of anthocyanin/nanoparticles. Measurements by UV-vis spectroscopy, FTIR spectroscopy, fluorescence spectroscopy, dynamic light scattering (DLS), ζ potential, electron transmission microscopy, and rheology at room (25 °C) and physiological (37 °C) temperatures were performed. The spectroscopy measurements allowed identifying additional hydrophobic sites created during the irradiation process of the nanoparticle. On the basis of the rheological studies, it was observed that the BSA-NP trend is a Newtonian flow behavior type for all the temperatures selected, and there is a direct correlation between dynamic viscosity and temperature values. Furthermore, when anthocyanins are added, the system increases its resistance to the flow as reflected in the morphological changes observed by TEM, thus confirming the relationship between viscosity values and aggregate formation.

Spectral Features Differentiate Aging-Induced Changes in Parchment-A Combined Approach of UV/VIS, µ-ATR/FTIR and µ-Raman Spectroscopy with Multivariate Data Analysis

From the moment of production, artworks are constantly exposed to changing environmental factors potentially inducing degradation. Therefore, detailed knowledge of natural degradation phenomena is essential for proper damage assessment and preservation. With special focus on written cultural heritage, we present a study on the degradation of sheep parchment employing accelerated aging with light (295-3000 nm) for one month, 30/50/80% relative humidity (RH) and 50 ppm sulfur dioxide with 30/50/80%RH for one week. UV/VIS spectroscopy detected changes in the sample surface appearance, showing browning after light-aging and increased brightness after SO₂-aging. Band deconvolution of ATR/FTIR and Raman spectra and factor analysis of mixed data (FAMD) revealed characteristic changes of the main parchment components. Spectral features for degradation-induced structural changes of collagen and lipids turned out to be different for the employed aging parameters. All aging conditions induced denaturation (of different degrees) indicated by changes in the secondary structure of collagen. Light treatment resulted in the most pronounced changes for collagen fibrils in addition to backbone cleavage and side chain oxidations. Additional increased disorder for lipids was observed. Despite shorter exposure times, SO₂-aging led to a weakening of protein structures induced by transitions of stabilizing disulfide bonds and side chain oxidations.

Oncogenic CALR mutant C-terminus mediates dual binding to the thrombopoietin receptor triggering complex dimerization and activation

Calreticulin (CALR) frameshift mutations represent the second cause of myeloproliferative neoplasms (MPN). In healthy cells, CALR transiently and non-specifically interacts with immature N-glycosylated proteins through its N-terminal domain. Conversely, CALR frameshift mutants turn into rogue cytokines by stably and specifically interacting with the Thrombopoietin Receptor (TpoR), inducing its constitutive activation. Here, we identify the basis of the acquired specificity of CALR mutants for TpoR and define the mechanisms by which complex formation triggers TpoR dimerization and activation. Our work reveals that CALR mutant C-terminus unmasks CALR N-terminal domain, rendering it more accessible to bind immature N-glycans on TpoR. We further find that the basic mutant C-terminus is partially α-helical and define how its α-helical segment concomitantly binds acidic patches of TpoR extracellular domain and induces dimerization of both CALR mutant and TpoR. Finally, we propose a model of the tetrameric TpoR-CALR mutant complex and identify potentially targetable sites.

New insights in the molecular regulation of the NADPH oxidase 2 activity: Negative modulation by Poldip2

Poldip2 was shown to be involved in oxidative signaling to ensure certain biological functions. It was proposed that, in VSMC, by interaction with the Nox4-associated membrane protein p22^phox, Poldip2 stimulates the level of reactive oxygen species (ROS) production. In vitro, with fractionated membranes from HEK393 cells over-expressing Nox4, we confirmed the up-regulation of NADPH oxidase 4 activity by the recombinant and purified Poldip2. Besides Nox4, the Nox1, Nox2, or Nox3 isoforms are also established partners of the p22^phox protein raising the question of their regulation by Poldip2 and of the effect in cells expressing simultaneously different Nox isoforms. In this study, we have addressed this issue by investigating the potential regulatory role of Poldip2 on NADPH oxidase 2, present in phagocyte cells. Unexpectedly, the effect of Poldip2 on phagocyte NADPH oxidase 2 was opposite to that observed on NADPH oxidase 4. Using membranes from circulating resting neutrophils, the ROS production rate of NADPH oxidase 2 was down-regulated by Poldip2 (2.5-fold). The down-regulation effect could not be correlated to the interaction of Poldip2 with p22^phox but rather, to the interaction of Poldip2 with the p47^phox protein, one of the regulatory proteins of the phagocyte NADPH oxidase. Our results show that the interaction of Poldip2 with p47^phox constitutes a novel regulatory mechanism that can negatively modulate the activity of NADPH oxidase 2 by trapping the so-called "adaptor" subunit of the complex. Poldip2 could act as a tunable switch capable of specifically regulating the activities of NADPH oxidases. This selective regulatory role of Poldip2, positive for Nox4 or negative for Nox2 could orchestrate the level and the type of ROS generated by Nox enzymes in the cells.

Interaction of Lysozyme with Poly(L-lysine)/Hyaluronic Acid Multilayers: An ATR-FTIR Study

Polyelectrolyte multilayers (PEM) loaded with bioactive molecules such as proteins serve as excellent mimics of an extracellular matrix and may find applications in fields such as biomedicine and cell biology. A question which is crucial to the successful employment of PEMs is whether conformation and bioactivity of the loaded proteins is preserved. In this work, the polarized attenuated total reflection Fourier transform infrared (ATR-FTIR) technique is applied to investigate the conformation of the protein lysozyme (Lys) loaded into the poly(L-lysine)/hyaluronic acid (PLL/HA) multilayers. Spectra are taken from the protein in the PEMs coated onto an ATR crystal during protein adsorption and desorption. For comparison, a similar investigation is performed for the case of Lys in contact with the uncoated crystal. The study highlights the presence of both "tightly" and "poorly bound" Lys fractions in the PEM. These fractions differ in their conformation and release behavior from the PEM upon washing. Comparison of spectra recorded with different polarizations suggests preferential orientation of alpha helical structures, beta sheets and turns in the "tightly bound" Lys. In contrast, the "poorly bound" fraction shows isotropic orientation and its conformation is well preserved.

Detoxification of Meghalayan cherry (Prunus nepalensis) kernel and its effect on structural and thermal properties of proteins

Valorizing food wastes and by-products can improve economic and environmental sustainability of the food production chain. In this regard, Meghalayan cherry kernels are a good source of proteins, but the presence of toxic compounds like amygdalin, makes them underutilized. Therefore, the present study was focused on detoxifying Meghalayan cherry kernel using thermal, soaking and ultrasound treatments and studying their impact on the structural and thermal characteristics of protein isolate. The results showed that all three treatments significantly reduced amygdalin content, with complete detoxification achieved after 30 and 60 min at 70 °C and 60 °C, respectively, in ultrasound, and after 90 and 120 min at 70 °C and 60 °C, respectively, in soaking + thermal treatment. The detoxification treatments significantly affected the protein content and weight-loss of Meghalayan cherry kernel. Fluorescence spectroscopy and FTIR showed alterations in Meghalayan cherry kernel protein isolate (MCKPI) secondary and tertiary structure. The fluorescence intensity was observed at 340 nm for native and detoxified protein isolate, and the lowest peak for MCKPI-US depicts conformational changes. The fading of bands in SDS-PAGE confirms structural changes due to thermal and sonication effects. SEM images demonstrated that more cracks and porous structures were seen in treated MCKPI than native MCKPI. Detoxification treatment increased thermal stability, resulting in lesser weight loss and higher denaturation temperature than native MCKPI. In this study, ultrasound treatment demonstrated the most pronounced effects on the detoxification of MCKPI and its thermal and structural properties, suggesting that Meghalayan cherry kernel is one of the most promising substrates for zero-waste bioprocess development.

Determination of Secondary Structure of Proteins by Nanoinfrared Spectroscopy

Nanoscale infrared spectroscopy (AFMIR) is becoming an important tool for the analysis of biological sample, in particular protein assemblies, at the nanoscale level. While the amide I band is usually used to determine the secondary structure of proteins in Fourier transform infrared spectroscopy, no tool has been developed so far for AFMIR. The paper introduces a method for the study of secondary structure of protein based on a protein library of 38 well-characterized proteins. Ascending stepwise linear regression (ASLR) and partial least square (PLS) regression were used to correlate spectrum characteristic bands with the major secondary structures (α-helixes and β-sheets). ASLR appears to provide better results than PLS. The secondary structure predictions are characterized by a root mean square standard error in a cross validation of 6.39% for α-helixes and 6.23% for β-sheets.

Toward Reagent-Free Discrimination of Alzheimer's Disease Using Blood Plasma Spectral Digital Biomarkers and Machine Learning

BACKGROUND

Alzheimer's disease (AD) is the most prevalent neurodegenerative disease. The detection of early-stage AD is particularly desirable because it would allow early intervention. However, a minimally invasive, low-cost, and accurate discrimination or diagnostic method for AD is especially difficult in the earliest stage of AD.

OBJECTIVE

The aim of this research is to discover blood plasma spectral digital biomarkers of AD, develop a novel intelligent method for the discrimination of AD and accelerate the translation of Fourier transform infrared (FTIR) spectral-based disease discrimination methods from the laboratory to clinical practice.

METHODS

Since vibration spectroscopy can provide the structure and chemical composition information of biological samples at the molecular level, we investigated the potential of FTIR spectral biomarkers of blood plasma to differentiate between AD patients and healthy controls. Combined with machine learning technology, we designed a hierarchical discrimination system that provides reagent-free and accurate AD discrimination based on blood plasma spectral digital biomarkers of AD.

RESULTS

Accurate segregation between AD patients and healthy controls was achieved with 89.3% sensitivity and 85.7% specificity for early-stage AD patients, 92.8% sensitivity and 87.5% specificity for middle-stage AD patients, and 100% sensitivity and 100% specificity for late-stage AD patients.

CONCLUSIONS

Our results show that blood plasma spectral digital biomarkers hold great promise as discrimination markers of AD, indicating the potential for the development of an inexpensive, reagent-free, and less laborious clinical test. As a result, our research outcome will accelerate the clinical application of spectral digital biomarkers and machine learning.

Structural equation modelling of mercury intra-skeletal variability on archaeological human remains

Archaeological burial environments are useful archives to investigate the long-term trends and the behaviour of mercury. In order to understand the relationship between mercury, skeletons and soil, we applied Partial Least Squares - Structural Equation Modelling (PLS-SEM) to a detailed, multisampling (n = 73 bone samples +37 soil samples) design of two archaeological graves dating to the 6th to 7th centuries CE (A Lanzada site, NW Spain). Mercury content was assessed using a DMA-80, and data about bone structure and the grave soil/sediments were obtained using FTIR-ATR spectroscopy. The theoretical model is supported by proxies of bone structure, grave soil/sediments, and location of the bone within the skeleton. The general model explained 61 % of mercury variance. Additionally, Partial Least Square - Prediction Oriented Segmentation (PLS-POS) was also used to check for segmentation in the dataset. POS revealed two group of samples depending on the bone phase (hydroxyapatite or collagen) controlling the Hg content, and the corresponding models explained 86 % and 76 % of Hg variance, respectively. The results suggest that mercury behaviour in the graves is complex, and that mercury concentrations were influenced by i) the ante-mortem status of the bone matrix, related to the weight of each bone phase; ii) post-mortem evolution of bone crystallinity, where bone loses mercury with increasing alteration; and iii) the proximity of the skeletal pieces to mercury target organs, as decomposition and collapse of the thoracic and abdominal soft tissues causes a secondary mercury enrichment in bones from the body trunk during early post-mortem. Skeletons provide a source of mercury to the soil whereas soil/sediments contribute little to skeletal mercury content.

Chitosan-Based Gastric Dressing Materials Loaded with Pomegranate Peel as Bioactive Agents: Pharmacokinetics and Effects on Experimentally Induced Gastric Ulcers in Rabbits

This study reported the fabrication and characterization of gastric dressing, composed of gelatine (GEL), chitosan (CH), and pomegranate peel (PP) extract. The structural changes occurring after γ-irradiation of GEL−CH−PP dressing were reported. The results showed that the electron paramagnetic resonance (EPR) spectroscopy of un-irradiated GEL−CH−PP showed two paramagnetic centers, which corresponded to g = 2.19 and g = 2.002. After irradiation, a new active centre appeared at g = 2.0035 at 10 kGy. The Fourier transform infrared spectroscopy (FTIR) analyses revealed an increase in peak intensity at C−H chains, as well as the C=O carboxyl groups at 10 kGy, due to the cross-linking phenomenon. The X-ray diffraction analysis showed a low change of crystallinity between the range of 2θ (15−30°). Moreover, γ-rays enhanced scavenging DPPH radical activity (51±%) and chelating power activities 79.12%. A significant inhibition of antibacterial and anti-biofilm activities (p < 0.01) was noticed. The hemolysis rates showed 0.42%, suggesting a high hemocompatibility, and exhibited significant anti-inflammatory activity in vitro (48%). In vivo, the healing effects of GEL−CH−PP dressing showed that the incidence and severity of gastric histopathological lesions decreased, compared with the ulcerated group, which could explain the bioavailability and the pharmacokinetic findings. The results highlight the loading of bioactive agents into polymer-based gastric dressings, with promising pharmacokinetics properties and effects on the induced ulcera in rabbits.

Amyloidogenesis: What Do We Know So Far?

The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.

Bone surface mimicked PDMS membranes stimulate osteoblasts and calcification of bone matrix

Cellular microenvironments play a crucial role in cell behavior. In addition to the biochemical cues present in the microenvironments, biophysical and biomechanical properties on surfaces have an impact on cellular functionality and eventually cellular fate. Effects of surface topography on cell behavior are being studied extensively in the literature. However, these studies often try to replicate topographical features of tissue surfaces by using techniques such as chemical etching, photolithography, and electrospinning, which may result in the loss of crucial micro- and nano- features on the tissue surfaces such as bone. This study investigates the topographical effects of bone surface by transferring its surface features onto polydimethylsiloxane (PDMS) membranes using soft lithography from a bovine femur. Our results have shown that major features on bone surfaces were successfully transferred onto PDMS using soft lithography. Osteoblast proliferation and calcification of bone matrix have significantly increased along with osteoblast-specific differentiation and maturation markers such as osteocalcin (OSC), osterix (OSX), collagen type I alpha 1 chain (COL1A1), and alkaline phosphatase (ALP) on bone surface mimicked (BSM) PDMS membranes in addition to a unidirectional alignment of osteoblast cells compared to plain PDMS surfaces. This presented bone surface mimicking method can provide a versatile native-like platform for further investigation of intracellular pathways regarding osteoblast growth and differentiation.

Application of FTIR Spectroscopy to Detect Changes in Skeletal Muscle Composition Due to Obesity with Insulin Resistance and STZ-Induced Diabetes

Age, obesity, and diabetes mellitus are pathophysiologically interconnected factors that significantly contribute to the global burden of non-communicable diseases. These metabolic conditions are associated with impaired insulin function, which disrupts the metabolism of carbohydrates, lipids, and proteins and can lead to structural and functional changes in skeletal muscle. Therefore, the alterations in the macromolecular composition of skeletal muscle may provide an indication of the underlying mechanisms of insulin-related disorders. The aim of this study was to investigate the potential of Fourier transform infrared (FTIR) spectroscopy to reveal the changes in macromolecular composition in weight-bearing and non-weight-bearing muscles of old, obese, insulin-resistant, and young streptozotocin (STZ)-induced diabetic mice. The efficiency of FTIR spectroscopy was evaluated by comparison with the results of gold-standard histochemical techniques. The differences in biomolecular phenotypes and the alterations in muscle composition in relation to their functional properties observed from FTIR spectra suggest that FTIR spectroscopy can detect most of the changes observed in muscle tissue by histochemical analyses and more. Therefore, it could be used as an effective alternative because it allows for the complete characterization of macromolecular composition in a single, relatively simple experiment, avoiding some obvious drawbacks of histochemical methods.

A Nanofocused Light on Stradivari Violins: Infrared s-SNOM Reveals New Clues Behind Craftsmanship Mastery

It is well-known that all the phases of the manufacturing influence the extraordinary aesthetic and acoustic features of Stradivari's instruments. However, these masterpieces still keep some of their secrets hidden by the lack of documentary evidence. In particular, there is not a general consensus on the use of a protein-based ground coating directly spread on the wood surface by the Cremonese Master. The present work demonstrates that infrared scattering-type scanning near-fields optical microscopy (s-SNOM) may provide unprecedented information on very complex cross-sectioned microsamples collected from two of Stradivari's violins, nanoresolved chemical sensitivity being the turning point for detecting minute traces of a specific compound, namely proteins, hidden by the matrix when macro or micro sampling approaches are exploited. This nanoresolved chemical-sensitive technique contributed new and robust evidence to the long-debated question about the use of proteinaceous materials by Stradivari.

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.

Sensitive Detection of Rosmarinic Acid Using Peptide-Modified Graphene Oxide Screen-Printed Carbon Electrode

Peptides have been used as components in biological analysis and fabrication of novel sensors due to several reasons, including well-known synthesis protocols, diverse structures, and acting as highly selective substrates for enzymes. Bio-conjugation strategies can provide a simple and efficient way to convert peptide-analyte interaction information into a measurable signal, which can be further used for the manufacture of new peptide-based biosensors. This paper describes the sensitive properties of a peptide-modified graphene oxide screen-printed carbon electrode for accurate and sensitive detection of a natural polyphenol antioxidant compound, namely rosmarinic acid. Glutaraldehyde was chosen as the cross-linking agent because it is able to bind nonspecifically to the peptide. We demonstrated that the strong interaction between the immobilized peptide on the surface of the sensor and rosmarinic acid favors the addition of rosmarinic acid on the surface of the electrode, leading to an efficient preconcentration that determines a high sensitivity of the sensor for the detection of rosmarinic acid. The experimental conditions were optimized using different pH values and different amounts of peptide to modify the sensor surface, so that its analytical performances were optimal for rosmarinic acid detection. By using cyclic voltammetry (CV) as a detection method, a very low detection limit (0.0966 μM) and a vast linearity domain, ranging from 0.1 µM to 3.20 µM, were obtained. The novelty of this work is the development of a novel peptide-based sensor with improved performance characteristics for the quantification of rosmarinic acid in cosmetic products of complex composition. The FTIR method was used to validate the voltammetric method results.

Synergistic effects of epigallocatechin gallate and l-theanine in nerve repair and regeneration by anti-amyloid damage, promoting metabolism, and nourishing nerve cells

Green tea has significant protective activity on nerve cells, but the mechanism of action is unclear. Epigallocatechin gallate (EGCG) and N-ethyl-L-glutamine (L-theanine) are the representative functional components of green tea (Camellia sinensis). In this study, an AD model of Aβ_25–35-induced differentiated neural cell line PC12 cells was established to study the synergistic effect of EGCG and L-theanine in protecting neural cells. The results showed that under Aβ_25–35 stress conditions, mitochondria and axons degenerated, and the expression of cyclins was up-regulated, showing the gene and protein characteristics of cellular hyperfunction. EGCG + L-theanine inhibited inflammation and aggregate formation pathways, significantly increased the percentage of G0/G1 in the cell cycle, downregulated the expression of proteins such as p-mTOR, Cyclin D1, and Cyclin B1, upregulated the expression of GAP43, Klotho, p-AMPK, and other proteins, promoted mitochondrial activity and energy metabolism, and had repair and regeneration effects on differentiated nerve cells. The synergistic mechanism study showed that under the premise that EGCG inhibits amyloid stress and inflammation and promotes metabolism, L-theanine could play a nourish nerve effect. EGCG + L-theanine keeps differentiated nerve cells in a quiescent state, which is beneficial to the repair and regeneration of nerve cells. In addition, EGCG + L-theanine maintains the high-fidelity structure of cellular proteins. This study revealed for the first time that the synergistic effect of EGCG with L-theanine may be an effective way to promote nerve cell repair and regeneration and slow down the progression of AD. Our findings provide a new scientific basis for the relationship between tea drinking and brain protection.

Natural Antimicrobial Peptides Self-assemble as α/β Chameleon Amyloids

Amyloid protein fibrils and some antimicrobial peptides (AMPs) share biophysical and structural properties. This observation suggests that ordered self-assembly can act as an AMP-regulating mechanism, and, vice versa, that human amyloids play a role in host defense against pathogens, as opposed to their common association with neurodegenerative and systemic diseases. Based on previous structural information on toxic amyloid peptides, we developed a sequence-based bioinformatics platform and, led by its predictions, experimentally identified 14 fibril-forming AMPs (ffAMPs) from living organisms, which demonstrated cross-β and cross-α amyloid properties. The results support the amyloid-antimicrobial link. The high prevalence of ffAMPs produced by amphibians and marine creatures among other species suggests that they confer unique advantageous properties in distinctive environments, potentially providing stability and adherence properties. Most of the newly identified 14 ffAMPs showed lipid-induced and/or time-dependent secondary structure transitions in the fibril form, indicating structural and functional cross-α/β chameleons. Specifically, ffAMP cytotoxicity against human cells correlated with the inherent or lipid-induced α-helical fibril structure. The findings raise hypotheses about the role of fibril secondary structure switching in regulation of processes, such as the transition between a stable storage conformation and an active state with toxicity against specific cell types.

Investigations of pH-dependent dynamic properties of OmpG-16SL, an outer membrane protein G mutant by ATR-FTIR spectroscopy

In this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 β-strands in its structure, the mutant is designed to have 16 β-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the ¹H/²H exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.

Insight on the microscopic binding mechanism of bisphenol compounds (BPs) with transthyretin (TTR) based on multi-spectroscopic methods and computational simulations

Thyroid hormones are involved in numerous physiological processes as regulators of metabolism, regulating organ growth, and mental state. Bisphenol compounds (BPs) are recognized as chemicals that interfere with endocrine balance. Because BPs have a similar structure to thyroxine, they can compete for binding to thyroid protein and disrupt the normal physiological activity of the thyroid system. In this study, three typical bisphenol compounds were selected to explore the interaction between BPs and TTR by computer simulations and multi-spectroscopic methods. The results revealed that BPs quenched the endogenous fluorescence of TTR via the combination of static quenching and non-radiative energy transfer, and the van der Waals forces and hydrogen bonding played a synergistic role in the binding process of BPs and TTR. Furthermore, the three-dimensional fluorescence spectroscopy, UV-vis spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy, which were employed to determine the conformation of protein, revealed that binding of BPs with TTR could induce conformational changes in TTR. In addition, the binding sites and the residues surrounding the BPs within the TTR were determined through molecular docking and molecular dynamics simulation. Therefore, this work provides new insights into the interaction between BPs and TTR to evaluate the potential toxicity of BPs.

A new alternative tool to analyse glycosylation in pharmaceutical proteins based on infrared spectroscopy combined with nonlinear support vector regression

Almost 60% of commercialized pharmaceutical proteins are glycosylated. Glycosylation is considered a critical quality attribute, as it affects the stability, bioactivity and safety of proteins. Hence, the development of analytical methods to characterise the composition and structure of glycoproteins is crucial. Currently, existing methods are time-consuming, expensive, and require significant sample preparation steps, which can alter the robustness of the analyses. In this work, we suggest the use of a fast, direct, and simple Fourier transform infrared spectroscopy (FT-IR) combined with a chemometric strategy to address this challenge. In this context, a database of FT-IR spectra of glycoproteins was built, and the glycoproteins were characterised by reference methods (MALDI-TOF, LC-ESI-QTOF and LC-FLR-MS) to estimate the mass ratio between carbohydrates and proteins and determine the composition in monosaccharides. The FT-IR spectra were processed first by Partial Least Squares Regression (PLSR), one of the most used regression algorithms in spectroscopy and secondly by Support Vector Regression (SVR). SVR has emerged in recent years and is now considered a powerful alternative to PLSR, thanks to its ability to flexibly model nonlinear relationships. The results provide clear evidence of the efficiency of the combination of FT-IR spectroscopy, and SVR modelling to characterise glycosylation in therapeutic proteins. The SVR models showed better predictive performances than the PLSR models in terms of RMSECV, RMSEP, R2CV, R2Pred and RPD. This tool offers several potential applications, such as comparing the glycosylation of a biosimilar and the original molecule, monitoring batch-to-batch homogeneity, and in-process control.

Feature selection of infrared spectra analysis with convolutional neural network

Data-driven deep learning analysis, especially for convolution neural network (CNN), has been developed and successfully applied in many domains. CNN is regarded as a black box, and the main drawback is the lack of interpretation. In this study, an interpretable CNN model was presented for infrared data analysis. An ascending stepwise linear regression (ASLR)-based approach was leveraged to extract the informative neurons in the flatten layer from the trained model. The characteristic of CNN network was employed to visualize the active variables according to the extracted neurons. Partial least squares (PLS) model was presented for comparison on the performance of extracted features and model interpretation. The CNN models yielded accuracies with extracted features of 93.27%, 97.50% and 96.65% for Tablet, meat, and juice datasets on the test set, while the PLS-DA models obtained accuracies with latent variables (LVs) of 95.19%, 95.50% and 98.17%. Both the CNN and PLS models demonstrated the stable patterns on active variables. The repeatability of CNN model and proposed strategies were verified by conducting the Monte-Carlo cross-validation.

SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data

A protein's structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600-1700 cm-1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.

Direct, Rapid, and Simple Evaluation of the Expression and Conformation of Beta-Amyloid in Bacterial Cells by FTIR Spectroscopy

The expression and conformation of bacterial proteins and peptides can be monitored in situ by Fourier transform infrared spectroscopy (FTIR), provided that the concentration of the protein of interest is sufficient. Here, we describe a simple protocol to analyze the conformation adopted by a specific amyloid protein in Escherichia coli cells, the pleiotropic regulator Hfq.E. coli cells expressing Hfq under an inducible promoter are analyzed. The change in protein conformation is analyzed by comparing the different populations versus controls (i.e., Δhfq cells, totally devoid of the Hfq protein) by difference spectroscopy, second derivation, curve-fitting, and principal component analysis. All the analyses were performed in the free, open-source software Quasar. We describe the detailed protocol for analyzing the data in Quasar. We show that the specific absorption of the β-amyloid conformation can be easily detected in the WT-Hfq, with bands at 1624 cm^-1 and 1693 cm^-1 indicating the presence of both parallel and antiparallel β-sheets. Furthermore, we show that FTIR spectroscopy is sensitive enough to probe the conformation of an amyloid protein backbone in vivo and to analyze its conformation in situ, directly in bacterial cells, without the need for protein purification.

Graphene Oxide as a Collagen Modifier of Amniotic Membrane and Burnt Skin

Introduction

The aim of this interdisciplinary study was to answer the question of whether active antioxidants as graphene oxide (GO), sodium ascorbate, and L-ascorbic acid modify at a molecular and supramolecular level the tissue of pathological amnion and the necrotic eschar degraded in thermal burn. We propose new solutions of modifiers based on GO that will become innovative ingredients to be used in transplants (amnion) and enhance regeneration of epidermis degraded in thermal burn.

Methods

A Nicolet 6700 spectrophotometer with Omnic software and the EasiDiff diffusion accessory were used in FTIR spectroscopic analysis. A Nicolet Magna-IR 860 spectrometer with an FT Raman accessory was used to record the Raman spectra of the samples. The surface of the samples was examined using a Phenom ProX scanning electron microscope with an energy-dispersive X-ray spectroscopy detector to diagnose and illustrate morphological effects on skin and amnion samples. SAXS measurements were carried out with a compact Kratky camera equipped with the SWAXS optical system.

Results

Characterisation of amide I-III regions, important for molecular structure, on both FTIR and FTR spectra revealed distinct shifts, testifying to organization of protein structure after GO modification. A wide lipid band associated with ester-group vibrations in phospholipids of cell membranes and vibrations of the carbonyl group of GO in the 1,790-1,720 cm^-1 band were observed in the spectra of thermally degraded and GO-modified epidermis and pathological amnion. SAXS studies revealed that GO caused a significant change in the structure of the burnt skin, but its influence on the structure of the amnion was weak.

Conclusion

Modification of burn-damaged epidermis and pathological amnion by means of GO results in stabilization and regeneration of tissue at the level of molecular (FTIR, FTR) and supramolecular (SAXS) interactions.

Self-Assembly of Unprotected Dipeptides into Hydrogels: Water-Channels Make the Difference

Unprotected dipeptides are attractive building blocks for environmentally friendly hydrogel biomaterials by virtue of their low‐cost and ease of preparation. This work investigates the self‐assembling behaviour of the distinct stereoisomers of Ile‐Phe and Phe‐Ile in phosphate buffered saline (PBS) to form hydrogels, using transmission electron microscopy (TEM), attenuated total reflectance infrared spectroscopy (ATR‐IR), circular dichroism (CD), and oscillatory rheometry. Each peptide purity and identity was also confirmed by ¹H‐ and ¹³C‐NMR spectroscopy and HPLC‐MS. Finally, single‐crystal XRD data allowed the key interactions responsible for the supramolecular packing into amphipathic layers or water‐channels to be revealed. The presence of the latter in the crystal structure is a distinctive feature of the only gelator of this work that self‐organizes into stable hydrogels, with fast kinetics and the highest elastic modulus amongst its structural isomers and stereoisomers.

Dissection of the amyloid formation pathway in AL amyloidosis

In antibody light chain (AL) amyloidosis, overproduced light chain (LC) fragments accumulate as fibrils in organs and tissues of patients. In vitro, AL fibril formation is a slow process, characterized by a pronounced lag phase. The events occurring during this lag phase are largely unknown. We have dissected the lag phase of a patient-derived LC truncation and identified structural transitions that precede fibril formation. The process starts with partial unfolding of the V_L domain and the formation of small amounts of dimers. This is a prerequisite for the formation of an ensemble of oligomers, which are the precursors of fibrils. During oligomerization, the hydrophobic core of the LC domain rearranges which leads to changes in solvent accessibility and rigidity. Structural transitions from an anti-parallel to a parallel β-sheet secondary structure occur in the oligomers prior to amyloid formation. Together, our results reveal a rate-limiting multi-step mechanism of structural transitions prior to fibril formation in AL amyloidosis, which offers, in the long run, opportunities for therapeutic intervention.

AL amyloidosis is caused by the accumulation of overproduced light chain (LC) fragments as fibrils in patient organs and it is the most prevalent systemic amyloidosis. Here, the authors combine biochemical and biophysical experiments to characterise the lag phase of a patient-derived truncated LC and they identify structural transitions that precede fibril formation.

Protein Structural Denaturation Evaluated by MCR-ALS of Protein Microarray FTIR Spectra

The loss of native structure is common in proteins. Among others, aggregation is one structural modification of particular importance as it is a major concern for the efficiency and safety of biotherapeutic proteins. Yet, recognizing the structural features associated with intermolecular bridging in a high-throughput manner remains a challenge. We combined here the use of protein microarrays spotted at a density of ca 2500 samples per cm² and Fourier transform infrared (FTIR) imaging to analyze structural modifications in a set of 85 proteins characterized by widely different secondary structure contents, submitted or not to mild denaturing conditions. Multivariate curve resolution alternating least squares (MCR-ALS) was used to model a new spectral component appearing in the protein set subject to denaturing conditions. In the native protein set, 6 components were found to be sufficient to obtain good modeling of the spectra. Furthermore, their shape allowed them to be assigned to α-helix, β-sheet, and other structures. Their content in each protein was correlated with the known secondary structure, confirming these assignments. In the denatured proteins, a new component was necessary and modeled by MCR-ALS. This new component could be assigned to the intermolecular β-sheet, bridging protein molecules. MCR-ALS, therefore, unveiled a potential spectroscopic marker of protein aggregation and allowed a semiquantitative evaluation of its content. Insight into other structural rearrangements was also obtained.

Quality Assurance of Commercial Insulin Formulations: Novel Assay Using Infrared Spectroscopy

BACKGROUND

For insulins in commercial formulations, degradation can be observed within the certified shelf life when not stored at recommended conditions. Elevated temperatures and exposure to shear forces can cause changes in the secondary structure of the hormone, leading to a decrease in pharmaceutical potency. International pharmacopoeia recommendations for insulin quality monitoring assays mainly rely on liquid chromatography methods. These methods are unable to distinguish between active and inactive forms, both of which may exist in pharmaceutical insulins exposed to stress conditions.

METHOD

Infrared attenuated total reflection spectroscopy has been used for the analysis of insulin dry film preparations using affordable instrumentation. This method can be applied to either formulated insulin specimens or pure insulins obtained by ultrafiltration. Such samples have been stored under different temperatures (0°C, 20°C, and 37°C), and degradation processes have been monitored up to a period of a few months.

RESULTS

By analyzing specific shifts of absorption bands in the infrared spectra, which are sensitive to the protein secondary structure, even small structural changes in the hormone become evident. Another option is amide I band deconvolution into individual bands, which can be attributed to secondary structure subunits that are part of the insulin tertiary structure.

CONCLUSION

A novel and innovative method based on infrared attenuated total reflection spectroscopy of insulin dry films is a promising analytical tool for quantifying the degree of insulin degradation, as it provides information on indicating a decrease in biological potency. The established methods for insulin potency assays require animal testing or clamp experiments on people with diabetes.