The optimization of protein secondary structure determination with infrared and circular dichroism spectra

Human anti-apoptotic Bcl-2 and Bcl-xL proteins protect yeast cells from aging induced oxidative stress

Aging is a degenerative, biological, and time-dependent process that affects all organisms. Yeast aging is a physiological phenomenon characterized by the progressive transformation of yeast cells, resulting in modifications to their viability and vitality. Aging in yeast cells is comparable to that in higher organisms in some respects; however, due to their straightforward and well-characterized genetic makeup, these cells present unique advantages when it comes to researching the aging process. Here, we assessed the impact of human anti-apoptotic Bcl-2 and Bcl-xL proteins on aging using a yeast model. The findings clearly showed that these proteins exhibited remarkable anti-aging properties in yeast cells. Our data indicate that the presence of both proteins enhanced the reproductive survival of aging cells, likely by effecting the components functioning as both pro- and anti-oxidants, depending on the stage of yeast cell lifespan. Both proteins partially protected yeast cells from aging-related morphological deformations and cellular damage during the aging period. In particular, Bcl-xL expressing yeast cells reached the maximum activity levels for almost all of the major antioxidant enzymes and the total antioxidant status on the 8th day of lifespan and could provide effective protection at the latest stage of the investigated aging period. The chemometric data analysis of IR spectra confirmed the findings of the morphological and biochemical analyses. In this regard, specifically, understanding the mechanism of action on the cellular redox state of Bcl-xL in yeast may facilitate comprehension of its indirect antioxidant function in higher eukaryotes.

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.

Direct hydrolysis of einkorn whole grain flour proteins for the generation of bioactive peptides using various proteases

In this study, it was aimed to investigate the direct release of BAPs from einkorn flour in one-step process. Thus, the protein extraction step was eliminated, thereby reducing processing cost. Commercial proteases (Alcalase, Flavourzyme, Neutrase, and Trypsin), and crude enzyme from Bacillus mojavensis sp. EBTA7 were used for hydrolyzing einkorn flour (30 %, w/v) solutions at 50-60 °C. The supernatants after centrifugation were used for bioactivity and techno-functionality tests. All hydrolysates demonstrated significant antioxidant capacities, with values ranging from 17.7 to 33.0 μmol TE/g for DPPH, 107 to 190 μmol TE/g for ABTS, and 0.09 to 3.08 mg EDTA/g for ion-chelating activities. Alcalase and Flavourzyme hydrolysis had the highest DPPH activities, while Bacillus mojavensis sp. EBTA7 enzyme yielded relatively high ABTS and ion-chelating activities. Notably, Bacillus mojavensis sp. EBTA7 crude enzyme hydrolysates demonstrated higher oil absorption capacity (2.94 g oil/g hydrolysate), robust emulsion (227 min), and foam stability (94 %) compared to commercial enzymes. FTIR spectroscopy confirmed variations in the secondary structure of peptides. All hydrolysates exhibited negative zeta potentials. The SDS-PAGE showcased MW ranged from 14 to 70 kDa, which was influenced by both the enzyme type and the degree of hydrolysis. Overall, Bacillus mojavensis sp. EBTA7 hydrolysates revealed considerable bio and techno-functional characteristics.

Identification of a multi-modal mechanism for Se(VI) reduction and Se(0) allotropic transition by Stenotrophomonas bentonitica

Microorganisms can play a key role in selenium (Se) bioremediation and the fabrication of Se-based nanomaterials by reducing toxic forms (Se(VI) and Se(IV)) into Se(0). In recent years, omics have become a useful tool in understanding the metabolic pathways involved in the reduction process. This paper aims to elucidate the specific molecular mechanisms involved in Se(VI) reduction by the bacterium Stenotrophomonas bentonitica. Both cytoplasmic and membrane fractions were able to reduce Se(VI) to Se(0) nanoparticles (NPs) with different morphologies (nanospheres and nanorods) and allotropes (amorphous, monoclinic, and trigonal). Proteomic analyses indicated an adaptive response against Se(VI) through the alteration of several metabolic pathways including those related to energy acquisition, synthesis of proteins and nucleic acids, and transport systems. Whilst the thioredoxin system and the Painter reactions were identified to play a crucial role in Se reduction, flagellin may also be involved in the allotropic transformation of Se. These findings suggest a multi-modal reduction mechanism is involved, providing new insights for developing novel strategies in bioremediation and nanoparticle synthesis for the recovery of critical materials within the concept of circular economy.

HydrogelFinder: A Foundation Model for Efficient Self-Assembling Peptide Discovery Guided by Non-Peptidal Small Molecules

Self-assembling peptides have numerous applications in medicine, food chemistry, and nanotechnology. However, their discovery has traditionally been serendipitous rather than driven by rational design. Here, HydrogelFinder, a foundation model is developed for the rational design of self-assembling peptides from scratch. This model explores the self-assembly properties by molecular structure, leveraging 1,377 self-assembling non-peptidal small molecules to navigate chemical space and improve structural diversity. Utilizing HydrogelFinder, 111 peptide candidates are generated and synthesized 17 peptides, subsequently experimentally validating the self-assembly and biophysical characteristics of nine peptides ranging from 1-10 amino acids-all achieved within a 19-day workflow. Notably, the two de novo-designed self-assembling peptides demonstrated low cytotoxicity and biocompatibility, as confirmed by live/dead assays. This work highlights the capacity of HydrogelFinder to diversify the design of self-assembling peptides through non-peptidal small molecules, offering a powerful toolkit and paradigm for future peptide discovery endeavors.

Inhibitor Design Strategy for Myostatin: Dynamics and Interaction Networks Define the Affinity and Release Mechanisms of the Inhibited Complexes

Myostatin, an important negative regulator of muscle mass, is a therapeutic target for muscle atrophic disorders such as muscular dystrophy. Thus, the inhibition of myostatin presents a strategy to treat these disorders. It has long been established that the myostatin prodomain is a strong inhibitor of the mature myostatin, and the minimum peptide of the prodomain-corresponding to the α1-helix of its lasso-region-responsible for the inhibitory efficiency was defined and characterized as well. Here we show that the minimum peptide segment based on the growth differentiation factor 11 (GDF11), which we found to be more helical in its stand-alone solvated stfate than the similar segment of myostatin, is a promising new base scaffold for inhibitor design. The proposed inhibitory peptides in their solvated state and in complex with the mature myostatin were analyzed by in silico molecule modeling supplemented with the electronic circular dichroism spectroscopy measurements. We defined the Gaussian-Mahalanobis mean score to measure the fraction of dihedral angle-pairs close to the desired helical region of the Ramachandran-plot, carried out RING analysis of the peptide-protein interaction networks and characterized the internal motions of the complexes using our rigid-body segmentation protocol. We identified a variant-11m2-that is sufficiently ordered both in solvent and within the inhibitory complex, forms a high number of contacts with the binding-pocket and induces such changes in its internal dynamics that lead to a rigidified, permanently locked conformation that traps this peptide in the binding site. We also showed that the naturally evolved α1-helix has been optimized to simultaneously fulfill two very different roles: to function as a strong binder as well as a good leaving group. It forms an outstanding number of non-covalent interactions with the mature core of myostatin and maintains the most ordered conformation within the complex, while it induces independent movement of the gate-keeper β-hairpin segment assisting the dissociation and also results in the least-ordered solvated form which provides extra stability for the dissociated state and discourages rebinding.

A class of peptides designed to replicate and enhance the Receptor for Hyaluronic Acid Mediated Motility binding domain

The extra-cellular matrix (ECM) is a complex and rich microenvironment that is exposed and over-expressed across several injury or disease pathologies. Biomaterial therapeutics are often enriched with peptide binders to target the ECM with greater specificity. Hyaluronic acid (HA) is a major component of the ECM, yet to date, few HA adherent peptides have been discovered. A class of HA binding peptides was designed using B(X₇)B hyaluronic acid binding domains inspired from the helical face of the Receptor for Hyaluronic Acid Mediated Motility (RHAMM). These peptides were bioengineered using a custom alpha helical net method, allowing for the enrichment of multiple B(X₇)B domains and the optimisation of contiguous and non-contiguous domain orientations. Unexpectedly, the molecules also exhibited the behaviour of nanofiber forming self-assembling peptides and were investigated for this characteristic. Ten 23-27 amino acid residue peptides were assessed. Simple molecular modelling was used to depict helical secondary structures. Binding assays were performed with varying concentrations (1-10 mg/mL) and extra-cellular matrices (HA, collagens I-IV, elastin, and Geltrex). Concentration mediated secondary structures were assessed using circular dichroism (CD), and higher order nanostructures were visualized using transmission electron microscopy (TEM). All peptides formed the initial apparent 3₁₀/alpha-helices, yet peptides 17x-3, 4, BHP3 and BHP4 were HA specific and potent (i.e., a significant effect) binders at increasing concentrations. These peptides shifted from apparent 3₁₀/alpha-helical structures at low concentration to beta-sheets at increasing concentration and also formed nanofibers which are noted as self-assembling structures. Several of the HA binding peptides outperformed our positive control (mPEP35) at 3-4 times higher concentrations, and were enhanced by self-assembly as each of these groups had observable nanofibers. STATEMENT OF SIGNIFICANCE: Specific biomolecules or peptides have played a crucial role in developing materials or systems to deliver key drugs and therapeutics to a broad spectrum of diseases and disorders. In these diseased tissues, cells build protein/sugar networks, which are uniquely exposed and great targets to deliver drugs to. Hyaluronic acid (HA) is involved in every stage of injury and is abundant in cancer. To date, only two HA specific peptides have been discovered. In our work, we have designed a way to model and trace binding regions as they appear on the face of a helical peptide. Using this method we have created a family of peptides enriched with HA binding domains that stick with 3-4 higher affinity than those previously discovered.

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.

In vitro investigation of protein assembly by combined microscopy and infrared spectroscopy at the nanometer scale

The nanoscale structure and dynamics of proteins on surfaces has been extensively studied using various imaging techniques, such as transmission electron microscopy and atomic force microscopy (AFM) in liquid environments. These powerful imaging techniques, however, can potentially damage or perturb delicate biological material and do not provide chemical information, which prevents a fundamental understanding of the dynamic processes underlying their evolution under physiological conditions. Here, we use a platform developed in our laboratory that enables acquisition of infrared (IR) spectroscopy and AFM images of biological material in physiological liquids with nanometer resolution in a cell closed by atomically thin graphene membranes transparent to IR photons. In this work, we studied the self-assembly process of S-layer proteins at the graphene-aqueous solution interface. The graphene acts also as the membrane separating the solution containing the proteins and Ca²⁺ ions from the AFM tip, thus eliminating sample damage and contamination effects. The formation of S-layer protein lattices and their structural evolution was monitored by AFM and by recording the amide I and II IR absorption bands, which reveal the noncovalent interaction between proteins and their response to the environment, including ionic strength and solvation. Our measurement platform opens unique opportunities to study biological material and soft materials in general.

Different interactions driving the binding of soy proteins (7S/11S) and flavonoids (quercetin/rutin): Alterations in the conformational and functional properties of soy proteins

The purpose of this research was to comparatively investigate the interactions between bioactive flavonoids (quercetin and rutin) and two predominant soy proteins (β-conglycinin and glycinin), and the structural and functional properties of their complexes. The binding affinities of quercetin/rutin toward 7S/11S were structure-dependent, in that rutin had a higher binding affinity than that of quercetin, and 11S exhibited higher affinity toward quercetin/rutin than that of 7S. The interactions in the 7S/11S-quercetin complexes were driven by van der Waals forces and hydrogen-bonding interactions, whereas the 7S/11S-rutin complexes exhibited hydrophobic interactions. Binding to quercetin or rutin altered the secondary structures (decrease in the α-helix and random coil contents and increase in the β-sheet content), decreased the surface hydrophobicity and thermal stability, and enhanced the antioxidant capacity of 7S and 11S. These findings provide valuable information that can facilitate the design of custom-tailored protein-flavonoid macromolecules.

The 2-hydroxy-3-(4-aryl-1-piperazinyl)propyl Phthalimide Derivatives as Prodrugs—Spectroscopic and Theoretical Binding Studies with Plasma Proteins

Many publications in databases deal with the interactions of new drugs with albumin. However, it is not only albumin that is responsible for binding pharmaceutical molecules to proteins in the human body. There are many more proteins in plasma that are important for the study of the ADME pathway. Therefore, in this study, we have shown the results of the interactions between the plasma proteins albumin, orosomucoid, and gamma globulins and non-toxic anti-inflammatory phthalimide analogs, which due to the promising obtained results, may be potential candidates in the group of analgesic and anti-inflammatory drugs. Using spectroscopic methods and molecular modeling, we showed that all four tested compounds form complexes with the analyzed proteins. The formation of a complex with proteins raises the pharmacological efficacy of the drug. Therefore, the obtained results could be a step in the study of the pharmacokinetics and pharmacodynamics of new potential pharmaceuticals.

Electrochemical biosensors based on peptide-kinase interactions at the kinase docking site

Kinases are important cancer biomarkers and are conventionally detected based on their catalytic activity. Kinases regulate cellular activities by phosphorylation of motif-specific multiple substrate proteins, resulting in a lack of selectivity of activity-based kinase biosensors. We present an alternative approach of sensing kinases based on the interactions of their allosteric docking sites with a specific partner protein. The new approach was demonstrated for the ERK2 kinase and its substrate ELK-1. A peptide derived from ELK-1 was bound to a gold electrode and ERK2 sensing was performed by electrochemical impedance spectroscopy. We performed a detailed analysis of the interaction between the ELK-1 peptide and the kinase on gold surfaces. Atomic force microscopy, variable angle spectroscopic ellipsometry, X-ray Photoelectron Spectroscopy, and polarization modulation IR reflection-absorption spectroscopy analysis of the gold surface revealed the adsorbed layer of the ERK2 on the peptide monolayer. The sensors showed a high level of target selectivity for ERK2 compared to the p38γ kinase and BSA. ERK2 was detected in its cellular concentration range, 0.5-2.0 μM, and the limit of detection was calculated to be 0.35 μM. Using the flexibility of peptide design, our method is generic for developing sensitive and substrate-specific biosensors and other disease-related enzymes based on their interactions.

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.

Multimodal Spectroscopic Imaging of Pea Root Nodules to Assess the Nitrogen Fixation in the Presence of Biofertilizer Based on Nod-Factors

Multimodal spectroscopic imaging methods such as Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI), Fourier Transform Infrared spectroscopy (FT-IR) and Raman spectroscopy were used to monitor the changes in distribution and to determine semi quantitatively selected metabolites involved in nitrogen fixation in pea root nodules. These approaches were used to evaluate the effectiveness of nitrogen fixation by pea plants treated with biofertilizer preparations containing Nod factors. To assess the effectiveness of biofertilizer, the fresh and dry masses of plants were determined. The biofertilizer was shown to be effective in enhancing the growth of the pea plants. In case of metabolic changes, the biofertilizer caused a change in the apparent distribution of the leghaemoglobin from the edges of the nodule to its centre (the active zone of nodule). Moreover, the enhanced nitrogen fixation and presumably the accelerated maturation form of the nodules were observed with the use of a biofertilizer.

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.

Structure and adsorption behavior of high hydrostatic pressure-treated β-lactoglobulin

HYPOTHESIS

High hydrostatic pressure treatment causes structural changes in interfacial-active β-lactoglobulin (β-lg). We hypothesized that the pressure-induced structural changes affect the intra- and intermolecular interactions which determine the interfacial activity of β-lg. The conducted experimental and numerical investigations could contribute to the mechanistic understanding of the adsorption behavior of proteins in food-related emulsions.

EXPERIMENTS

We treated β-lg in water at pH 7 with high hydrostatic pressures up to 600 MPa for 10 min at 20 °C. The secondary structure was characterized with Fourier-transform infrared spectroscopy (FTIR) and circular dichroism (CD), the surface hydrophobicity and charge with fluorescence-spectroscopy and ζ-potential, and the quaternary structure with membrane-osmometry, analytical ultracentrifugation (AUC) and mass spectrometry (MS). Experimental analyses were supported through molecular dynamic (MD) simulations. The adsorption behavior was investigated with pendant drop analysis.

FINDINGS

MD simulation revealed a pressure-induced molten globule state of β-lg, confirmed by an unfolding of β-sheets with FTIR, a stabilization of α-helices with CD and loss in tertiary structure induced by an increase in surface hydrophobicity. Membrane-osmometry, AUC and MS indicated the formation of non-covalently linked dimers that migrated slower through the water phase, adsorbed more quickly due to hydrophobic interactions with the oil, and lowered the interfacial tension more strongly than reference β-lg.

Silk fibroin nanocomposites as tissue engineering scaffolds - A systematic review

Silk fibroin is a protein with intrinsic characteristics that make it a good candidate as a scaffold for tissue engineering. Recent works have enhanced its benefits by adding inorganic phases that interact with silk fibroin in different ways. A systematic review was performed in four databases to study the physicochemical and biological performance of silk fibroin nanocomposites. In the last decade, only 51 articles contained either in vitro cell culture models or in vivo tests. The analysis of such works resulted in their classification into the following scaffold types: particles, mats and textiles, films, hydrogels, sponge-like structures, and mixed conformations. From the physicochemical perspective, the inorganic phase imbued in silk fibroin nanocomposites resulted in better stability and mechanical performance. This review revealed that the inorganic phase may be associated with specific biological responses, such as neovascularisation, cell differentiation, cell proliferation, and antimicrobial and immunomodulatory activity. The study of nanocomposites as tissue engineering scaffolds is a highly active area mostly focused on bone and cartilage regeneration with promising results. Nonetheless, there are still many challenges related to their application in other tissues, a better understanding of the interaction between the inorganic and organic phases, and the associated biological response.

Effects of compaction and storage conditions on stability of intravenous immunoglobulin - Implication on developing oral tablets of biologics

Biological products, such as therapeutic proteins, vaccines and cell - based therapeutics have a rapidly growing global market. Monoclonal antibody represents a major portion of the biologics market. For biologics that target gastrointestinal tract, the oral delivery route offers many advantages, such as better patient compliance, easy administration and increased stability, over the parental route of administration. To lay the ground work for the oral delivery of biologics, we studied the solid state properties and effects of compaction pressure, particle size, and storage relative humidity on the stability of immunoglobulin G (IVIG). We employed complementary analytical and biophysical techniques, such as size exclusion chromatography and Dynamic light scattering to characterize the aggregates, circular dichroism and solid state Fourier-transform infrared spectroscopy to evaluate protein secondary structure and nano-DSC to probe thermal stability of protein conformations. Our results showed storage relative humidity could induce conformational changes and aggregation of IVIG. However, the IVIG binding activity did not significantly change with relative humidity. The commonly used compaction pressures did not promote protein aggregation, but noticeably reduced binding activity.

Detection and Quantification of Myocardial Fibrosis Using Stain-Free Infrared Spectroscopic Imaging

CONTEXT.—

Myocardial fibrosis underpins a number of cardiovascular conditions and is difficult to identify with standard histologic techniques. Challenges include imaging, defining an objective threshold for classifying fibrosis as mild or severe, as well as understanding the molecular basis for these changes.

OBJECTIVE.—

To develop a novel, rapid, label-free approach to accurately measure and quantify the extent of fibrosis in cardiac tissue using infrared spectroscopic imaging.

DESIGN.—

We performed infrared spectroscopic imaging and combined that with advanced machine learning-based algorithms to assess fibrosis in 15 samples from patients belonging to the following 3 classes: (1) nonpathologic (control) donor hearts; (2) patients receiving transplant; and (3) tissue from patients undergoing implantation of ventricular assist device.

RESULTS.—

Our results show excellent sensitivity and accuracy for detecting myocardial fibrosis as demonstrated by high area under the curve of 0.998 in the receiver-operating characteristic curve measured from infrared imaging. Fibrosis of various morphologic subtypes are then demonstrated with virtually generated picrosirius red images, which show good visual and quantitative agreement (correlation coefficient = 0.92, ρ = 7.76 × 10-15) with stained images of the same sections. Underlying molecular composition of the different subtypes were investigated with infrared spectra showing reproducible differences presumably arising from differences in collagen subtypes and/or crosslinking.

CONCLUSIONS.—

Infrared imaging can be a powerful tool in studying myocardial fibrosis and gleaning insights into the underlying chemical changes that accompany it. Emerging methods suggest that the proposed approach is compatible with conventional optical microscopy and its consistency makes it translatable to the clinical setting for real-time diagnoses as well as for objective and quantitative research.

FTIR Imaging of Protein Microarrays for High Throughput Secondary Structure Determination

The paper introduces a new method designed for high-throughput protein structure determination. It is based on spotting proteins as microarrays at a density of ca. 2000-4000 samples per cm² and recording Fourier transform infrared (FTIR) spectra by FTIR imaging. It also introduces a new protein library, called cSP92, which contains 92 well-characterized proteins. It has been designed to cover as well as possible the structural space, both in terms of secondary structures and higher level structures. Ascending stepwise linear regression (ASLR), partial least square (PLS) regression, and support vector machine (SVM) have been used to correlate spectral characteristics to secondary structure features. ASLR generally provides better results than PLS and SVM. The observation that secondary structure prediction is as good for protein microarray spectra as for the reference attenuated total reflection spectra recorded on the same samples validates the high throughput microarray approach. Repeated double cross-validation shows that the approach is suitable for the high accuracy determination of the protein secondary structure with root mean square standard error in the cross-validation of 4.9 ± 1.1% for α-helix, 4.6 ± 0.8% for β-sheet, and 6.3 ± 2.2% for the "other" structures when using ASLR.

Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation

Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm⁻¹ is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF₂ slides and FTIR spectra were acquired with an imaging system.

Evaluation of protein secondary structure from FTIR spectra improved after partial deuteration

FTIR spectroscopy has become a major tool to determine protein secondary structure. One of the identified obstacle for reaching better predictions is the strong overlap of bands assigned to different secondary structures. Yet, while for instance disordered structures and α-helical structures absorb almost at the same wavenumber, the absorbance bands are differentially shifted upon deuteration, in part because exchange is much faster for disordered structures. We recorded the FTIR spectra of 85 proteins at different stages of hydrogen/deuterium exchange process using protein microarrays and infrared imaging for high throughput measurements. Several methods were used to relate spectral shape to secondary structure content. While in absolute terms, β-sheet is always better predicted than α-helix content, results consistently indicate an improvement of secondary structure predictions essentially for the α-helix and the category called “Others” (grouping random, turns, bends, etc.) after 15 min of exchange. On the contrary, the β-sheet fraction is better predicted in non-deuterated conditions. Using partial least square regression, the error of prediction for the α-helix content is reduced after 15-min deuteration. Further deuteration degrades the prediction. Error on the prediction for the “Others” structures also decreases after 15-min deuteration. Cross-validation or a single 25-protein test set result in the same overall conclusions.

Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra?

Circular dichroism spectroscopy is an important tool for determining the structural characteristics of biomolecules, particularly the secondary structure of proteins. In this paper we propose a Bayesian model that estimates the covariance structure within a measured spectrum and quantifies the uncertainty associated with the inferred secondary structures and characteristic spectra associated with each secondary structure type. Furthermore, we used tools from Bayesian model selection to determine the best secondary structure classification scheme and illustrate a technique for comparing whether or not two or more measured protein spectra share the same secondary structure. Our findings suggest that it is not possible to identify more than 3 distinct secondary structure classes from CD spectra above 175 nm. The inclusion of data from wavelengths between 175 and 200 nm did not substantially affect the ability to determine secondary structure fractions.

Searching for a Better Match between Protein Secondary Structure Definitions and Protein FTIR Spectra

Obtaining protein secondary structure content from high-resolution structures requires definitions and thresholds for the various parameters involved, typically hydrogen bond energy or length/angle and backbone φ/ψ angles. Several definitions are currently used and can have a profound impact on secondary structure content. Fourier transform infrared (FTIR) spectroscopy has its own sensitivity to molecular geometry. It is, therefore, important to select a set of definitions that matches this sensitivity. Here, we used a new protein set consisting of 92 proteins designed for the calibration of spectroscopic methods. Spectra have been obtained from protein microarrays in a high throughput process. The potential for improving secondary structure predictions from FTIR spectra has been tested using 71 structures determined according to different definitions. The paper demonstrates that different secondary structure definitions result in large variations in secondary structure content that are not equivalent in view of the protein FTIR spectra. The prediction quality factor ζ can be improved by ca. 20-50% by selecting an adequate definition set. The results also indicate that the dictionary of secondary structure of proteins (DSSP) algorithm, which is currently widely used to evaluate protein secondary structure content, is a good choice when dealing with FTIR spectra.

Nonlinear and vibrational microscopy for label-free characterization of amyloid-β plaques in Alzheimer's disease model

Multimodal optical imaging was used for characterization of amyloid-β plaques in mouse brain tissues. We obtained high-resolution images for different biomarkers and investigated vibrational fingerprints that could be used for diagnostic purposes.

Preparation and Characterization of Electrospun Collagen Based Composites for Biomedical Applications

Electrospinning is a widely used technology for obtaining nanofibers from synthetic and natural polymers. In this study, electrospun mats from collagen (C), polyethylene terephthalate (PET) and a blend of the two (C-PET) were prepared and stabilized through a cross-linking process. The aim of this research was to prepare and characterize the nanofiber structure by Fourier-transform infrared with attenuated total reflectance spectroscopy (FTIR-ATR) in close correlation with dynamic vapor sorption (DVS). The studies indicated that C-PET nanofibrous mats shows improved mechanical properties compared to collagen samples. A correlation between morphological, structural and cytotoxic proprieties of the studied samples were emphasized and the results suggest that the prepared nanofiber mats could be a promising candidate for tissue-engineering applications, especially dermal applications.

Highlighting Protective Effect of Encapsulation on Yeast Cell Response to Dehydration Using Synchrotron Infrared Microspectroscopy at the Single-Cell Level

In the present paper, the Layer by Layer (LbL) method using β-lactoglobulin and sodium alginate was performed to individually encapsulate Saccharomyces cerevisiae cells in microorganized shells in order to protect them against stresses during dehydration. Higher survival (∼1 log) for encapsulated yeast cells was effectively observed after air dehydration at 45°C. For the first time, the potentiality of Synchrotron-Fourier Transform InfraRed microspectroscopy (S-FTIR) was used at the single-cell level in order to analyze the contribution of the biochemical composition of non-encapsulated vs. encapsulated cells in response to dehydration. The microspectroscopy measurements clearly differentiated between non-encapsulated and encapsulated yeast cells in the amide band region. In the spectral region specific to lipids, the S-FTIR results indicated probably the decrease in membrane fluidity of yeast after dehydration without significant distinction between the two samples. These data suggested minor apparent chemical changes in cell attributable to the LbL system upon dehydration. More insights are expected regarding the lower mortality among encapsulated cells. Indeed the hypothesis that the biopolymeric layers could induce less damage in cell by affecting the transfer kinetics during dehydration-rehydration cycle, should be verified in further work.

FTIR microspectroscopy revealed biochemical changes in liver and kidneys as a result of exposure to low dose of iron oxide nanoparticles

Iron oxide nanoparticles (IONPs) have biomedical and biotechnological applications in magnetic imaging, drug-delivery, magnetic separation and purification. The biocompatibility of such particles may be improved by covering them with coating. In presented paper the biochemical anomalies of liver and kidney occurring in animals exposed to d-mannitol-coated iron(III) oxide nanoparticles (M-IONPs) were examined with Fourier transform infrared (FTIR) microspectroscopy. The dose of IONPs used in the study was significantly lower than those used so far in other research. Liver and kidney tissue sections were analysed by chemical mapping of infrared absorption bands originating from proteins, lipids, compounds containing phosphate groups, cholesterol and cholesterol esters. Changes in content and/or structure of the selected biomolecules were evaluated by comparison of the results obtained for animals treated with M-IONPs with those from control group. Biochemical analysis of liver samples demonstrated a few M-IONPs induced anomalies in the organ, mostly concerning the relative content of the selected compounds. The biomolecular changes, following exposition to nanoparticles, were much more intense within the kidney tissue. Biochemical aberrations found in the organ samples indicated at increase of tissue density, anomalies in fatty acids structure as well as changes in relative content of lipids and proteins. The simultaneous accumulation of lipids, phosphate groups as well as cholesterol and cholesterol esters in kidneys of rats exposed to IONPs may indicate that the particles stimulated formation of lipid droplets within the organ.

A convenient protein library for spectroscopic calibrations

While several Raman, CD or FTIR spectral libraries are available for well-characterized proteins of known structure, proteins themselves are usually very difficult to acquire, preventing a convenient calibration of new instruments and new recording methods. The problem is particularly critical in the field of FTIR spectroscopy where numerous new methods are becoming available on the market.

The present papers reports the construction of a protein library (cSP92) including commercially available products, that are well characterized experimentally for their purity and solubility in conditions compatible with the recording of FTIR spectra and whose high-resolution structure is available.

Overall, 92 proteins were selected. These proteins cover well the CATH space at the level of classes and architectures. In terms of secondary structure content, an analysis of their high-resolution structure by DSSP shows that the mean content in the different secondary structures present in cSP92 is very similar to the mean content found in the PDB.

The 92-protein set is analyzed in details for the distribution of helix length, number of strands in β- sheets, length of β-strands and amino acid content, all features that may be important for the interpretation of FTIR spectra.

Vibrational Spectroscopic Based Approach for Diagnosing Babesia bovis Infection

Babesia bovis parasites present a serious and significant health concern for the beef and dairy industries in many parts of the world. Difficulties associated with the current diagnostic techniques include the following: they are prone to human error (microscopy) or expensive and time-consuming (polymerase chain reaction) to perform. Little is known about the biochemical changes in blood that are associated with Babesia infections. The discovery of new biomarkers will lead to improved diagnostic outcomes for the cattle industry. Vibrational spectroscopic technologies can record a chemical snapshot of the entire organism and the surrounding cell thereby providing a phenotype of the organism and the host infected cell. Here, we demonstrate the applicability of vibrational spectroscopic imaging techniques including Atomic Force Microscopy Infrared (AFM-IR) and confocal Raman microscopy to discover new biomarkers for B. bovis infections. Furthermore, we applied Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) to detect B. bovis in red blood cells (RBCs). Based on changes in the IR spectral bands, with ATR-FTIR in combination with Partial Least Squares-Discriminant Analysis we were able to discriminate infected samples from controls with a sensitivity and specificity of 92.0% and 91.7%, respectively, in less than 2 min, excluding sample extraction and preparation. The proposed method utilized a lysis approach to remove hemoglobin from the suspension of infected and uninfected cells, which significantly increased the sensitivity and specificity compared to measurements performed on intact infected red blood cells (intact infected RBC, 77.3% and 79.2%). This work represents a holistic spectroscopic study from the level of the single infected RBC using AFM-IR and confocal Raman to the detection of the parasite in a cell population using ATR-FTIR for a babesiosis diagnostic.

Spectroscopic studies on the temperature-dependent molecular arrangements in hybrid chitosan/1,3-β-D-glucan polymeric matrices

Chitosan/1,3-β-D-glucan matrices have been recently used in various biomedical applications. Within this study, the structural changes in hybrid polysaccharide chitosan/1,3-β-D-glucan matrices cross-linked at 70 °C and 80 °C were detected with Attenuated Total Reflection Fourier Transform Infrared spectroscopy (ATR FT-IR) and Raman spectroscopy enabled thorough insights into molecular structure of studied biomaterials, whereas X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) provided their surface characteristics with confirmation of their effective and non-destructive properties. There are temperature-dependent differences in the chemical interactions between 1,3-β-D-glucan units and N-glucosamine in chitosan, resulting in surface polarity changes. The second order derivatives and deconvolution revealed the alterations in the secondary structure of studied matrices, along with different sized grain-like structures revealed by AFM. Since surface physicochemical properties of biomaterials have great impact on cell behavior, abovementioned techniques may allow to optimize and modify the preparation of polymeric matrices with desired features.

A hybrid of two major Blomia tropicalis allergens as an allergy vaccine candidate

Introduction

Allergen‐specific immunotherapy (AIT) represents a curative approach for treating allergies. In the tropical and subtropical regions of the world, Blomia tropicalis (Blo t 5 and Blo t 21) is the likely dominant source of indoor allergens.

Aim

To generate a hypoallergenic Blo t 5/Blo t 21 hybrid molecule that can treat allergies caused by B tropicalis.

Methods

Using in silico design of B tropicalis hybrid proteins, we chose two hybrid proteins for heterologous expression. Wild‐type Blo t 5/Blo t 21 hybrid molecule and a hypoallergenic version, termed BTH1 and BTH2, respectively, were purified by ion exchange and size exclusion chromatography and characterized by physicochemical, as well as in vitro and in vivo immunological, experiments.

Results

BTH1, BTH2 and the parental allergens were purified to homogeneity and characterized in detail. BTH2 displayed the lowest IgE reactivity that induced basophil degranulation using sera from allergic rhinitis and asthmatic patients. BTH2 essentially presented the same endolysosomal degradation pattern as the shortened rBlo t 5 and showed a higher resistance towards degradation than the full‐length Blo t 5. In vivo immunization of mice with BTH2 led to the production of IgG antibodies that competed with human IgE for allergen binding. Stimulation of splenocytes from BTH2‐immunized mice produced higher levels of IL‐10 and decreased secretion of IL‐4 and IL‐5. In addition, BTH2 stimulated T‐cell proliferation in PBMCs isolated from allergic patients, with secretion of higher levels of IL‐10 and lower levels of IL‐5 and IL‐13, when compared to parental allergens.

Conclusions and Clinical Relevance

BTH2 is a promising hybrid vaccine candidate for immunotherapy of Blomia allergy. However, further pre‐clinical studies addressing its efficacy and safety are needed.

Hybrid polymers bearing oligo-l-lysine(carboxybenzyl)s: synthesis and investigations of secondary structure

Hybrid polymers of peptides resembling (partially) folded protein structures are promising materials in biomedicine, especially in view of folding-interactions between different segments. In this study polymers bearing repetitive peptidic folding elements, composed of N-terminus functionalized bis-ω-ene-functional oligo-l-lysine(carboxybenzyl(Z))s (Lys_n) with repeating units (n) of 3, 6, 12, 24 and 30 were successfully synthesized to study their secondary structure introduced by conformational interactions between their chains. The pre-polymers of ADMET, narrowly dispersed Lys_ns, were obtained by ring opening polymerization (ROP) of N-carboxyanhydride (NCA) initiated with 11-amino-undecene, following N-terminus functionalization with 10-undecenoyl chloride. The resulting Lys_ns were subsequently polymerized via ADMET polymerization by using Grubbs’ first generation (G1) catalyst in 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) generating the ADMET polymers (A-[Lys_n]_m) (m = 2–12) with molecular weights ranging from 3 to 28 kDa, displaying polydispersity (Đ) values in the range of 1.5–3.2. After chemical analyses of Lys_ns and A-[Lys_n]_ms by ¹H-NMR, GPC and MALDI-ToF MS, secondary structural investigations were probed by CD spectroscopy and IR spectroscopy in 2,2,2-trifluoroethanol (TFE). In order to study A-[Lys_n]_ms with defined molecular weights and low polydispersity values (Đ = 1.03–1.48), the ADMET polymers A-[Lys_n=3]_m=3 and A-[Lys_n=24]_m=4 were fractionated by preparative GPC, and subsequently analysed by ¹H-NMR, analytical GPC, MALDI-ToF MS and CD spectroscopy. We can demonstrate the influence of chain length of the generated polymers on the formation of secondary structures by comparing Lys_ns with varying n values to the ADMET-polymers with the help of spectroscopic techniques such as CD and FTIR-spectroscopy in a helicogenic solvent.

We demonstrate the influence of chain length of segmented polymers bearing dynamic folding elements onto the formation of secondary structures with the help of spectroscopic techniques such as CD and FTIR-spectroscopy in a helicogenic solvent.

Photodegradation of porphyrin-bound hIAPP(1–37) fibrils

Amyloid deposits in pancreatic islets of type 2 diabetes mellitus (T2DM) are mainly comprised of human islet amyloid polypeptide (hIAPP), the degradation of hIAPP fibrils by photoactive porphyrin could be a preventive strategy against T2DM.

Label-free metabolic imaging by mid-infrared optoacoustic microscopy in living cells

We develop mid-infrared optoacoustic microscopy (MiROM) for label-free, bond-selective, live-cell metabolic imaging, enabling spatiotemporal monitoring of carbohydrates, lipids and proteins in cells and tissues. Using acoustic detection of optical absorption, MiROM converts mid-infrared sensing into a positive-contrast imaging modality with negligible photodamage and high sensitivity. We use MiROM to observe changes in intrinsic carbohydrate distribution from a diffusive spatial pattern to tight co-localization with lipid droplets during adipogenesis.

Estimating the Level of Carbamoylated Plasma Non-High-Density Lipoproteins Using Infrared Spectroscopy

BACKGROUND

The increased cardiovascular morbidity and mortality observed in chronic kidney disease (CKD) patients can be partly explained by the presence of carbamoylated lipoproteins. Lipid profiles can be determined with infrared spectroscopy. In this paper, the effects of carbamoylation on spectral changes of non-high-density lipoproteins (non-HDL) were studied.

METHODS

In the present study, fasting serum samples were obtained from 84 CKD patients (CKD stage 3-5: n = 37 and CKD stage 5d (hemodialysis): n = 47) and from 45 healthy subjects. In vitro carbamoylation of serum lipoproteins from healthy subjects was performed using increasing concentrations of potassium cyanate. Lipoprotein-containing pellets were isolated by precipitation of non-HDL. The amount of carbamoylated serum non-HDL was estimated using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, followed by soft independent modelling by class analogy analysis.

RESULTS

Carbamoylation resulted in a small increase of the amide I band (1714-1589 cm^-1) of the infrared spectroscopy (IR) spectrum. A significant difference in the amide II/amide I area under the curves (AUC) ratio was observed between healthy subjects and CKD patients, as well as between the two CKD groups (non-dialysis versus hemodialysis patients).

CONCLUSIONS

ATR-FTIR spectroscopy can be considered as a novel method to detect non-HDL carbamoylation.

Effects of Lysozyme on the Activity of Ionic of Fluoroquinolone Species

Fluoroquinolones (FQs) constitute an important class of biologically active broad-spectrum antibacterial drugs that are which are in contact with many biological fluids under different acidity conditions. We studied the reactivity of ciprofloxacin (Cpx) and levofloxacin (Lev) and their interaction with lysozyme (Lyz) at different pH values, using UV-visible absorption, fluorescence, infrared spectroscopies supported by DFT calculation and docking. In addition, by antimicrobial assays, the biological consequences of the interaction were evaluated. DFT calculation predicted that the FQ cationic species present at acid pH have lower stabilization energies, with an electric charge rearrangement because of their interactions with solvent molecules. NBO and frontier orbital calculations evidenced the role of two charged centers, NH₂⁺ and COO-, for interactions by electronic delocalization effects. Both FQs bind to Lyz via a static quenching with a higher interaction in neutral medium. The interaction induces a structural rearrangement in β-sheet content while in basic pH a protective effect against the denaturation of Lyz was inferred. The analysis of thermodynamic parameters and docking showed that hydrophobic, electrostatic forces and hydrogen bond are the responsible of Cpx-Lyz and Lev-Lyz associations. Antimicrobial assays evidenced an antagonist effect of Lyz in acid medium while in neutral medium the FQs' activities were not modified by Lyz.

Gene expression data and FTIR spectra provide a similar phenotypic description of breast cancer cell lines in 2D and 3D cultures

Gene expression patterns and FTIR spectral data are strongly correlated. Both identified the genotypes and phenotypes of breast cancer cell lines.

Application of MCR-ALS to reveal intermediate conformations in the thermally induced α-β transition of poly-l-lysine monitored by FT-IR spectroscopy

Temperature-induced conformational transitions of poly-l-lysine were monitored with Fourier-transform infrared (FT-IR) spectroscopy between 10°C and 70°C. Chemometric analysis of dynamic IR spectra was performed by multivariate curve analysis-alternating least squares (MCR-ALS) of the amide I' and amide II' spectral region. With this approach, the pure spectral and concentration profiles of the conformational transition were obtained. Beside the initial α-helical, the intermediate random coil/extended helices and the final β-sheet structure, an additional intermediate PLL conformation was identified and attributed to a transient β-sheet structure.

Secondary Structure Determination by Means of ATR-FTIR Spectroscopy

Specialized infrared spectroscopic techniques have been developed that allow studying the secondary structure of membrane proteins and the influence of crucial parameters like lipid content and detergent. Here, we focus on an ATR-FTIR spectroscopic study of Af-Amt1 and the influence of LDAO/glycerol on its structural integrity. Our results clearly indicate that infrared spectroscopy can be used to identify the adapted sample conditions.