Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy

The binding of different model membranes with PKCε C2 domain is not dependent on membrane curvature but affects the sequence of events during unfolding

The C2 domain of novel protein kinases C (nPKC) binds to membranes in a Ca2+-independent way contributing to the activation of these enzymes. We have studied the C2 domain of one of these nPKCs, namely PKCε, and confirmed that it establishes a strong interaction with POPA, which is clearly visible through changes in chemical shifts detected through 31P-MAS-NMR and the protection that it exerts on the domain against thermal denaturation seen through DSC and FT-IR. In this study, using two-dimensional correlation analysis (2D-COS) applied to infrared spectra, we determined the sequence of events that occur during the thermal unfolding of the domain and highlighted some differences when phosphatidic acid or cardiolipin are present. Finally, by means of FRET and DLS experiments, we wanted to determine the effect of membrane curvature on the domain/membrane interaction by using lysophosphatidylcholine to introduce positive curvature as a control and we observed that the effect of these phospholipids on the protein binding is not exerted through the change of membrane curvature.

Normal mode calculation and infrared spectroscopy of proteins in water solution: Relationship between amide I transition dipole strength and secondary structure

Dipole Strength (DS) of the amides has gained a renewed interest in chemical physics since it provides an important tool to disclose the on-site vibrational energy distributions. Apart from earlier experimental efforts on polypeptides, little is still known about DS in complex proteins. We accurately measured the Fourier Transform Infrared absorption spectra of nine proteins in water solution obtaining their Molar Extinction Coefficient in the amide I and II spectral region. Our results show that the amide I DS value depends on the protein secondary structure, being that of the α-rich and unstructured proteins lower by a factor of 2 than that of the β-rich proteins. The average DS for amino acids in α and β secondary structures confirms this finding. Normal Mode calculation and Molecular Dynamics were performed and used as tools for data analysis and interpretation. The present outcomes corroborate the hypothesis that antiparallel β-sheet environment is more prone to delocalize the on-site CO stretching vibration through coupling mechanisms between carbonyl groups, whereas α-helix structures are energetically less stable to permit vibrational mode delocalization.

Divergicin M35-Chitosan Film: Development and Characterization

Chitosan films loaded with bacteriocin were examined by FTIR spectroscopy, tested for color, puncture strength, water vapor permeability, and as antimicrobials of Listeria innocua HPB13. Divergicin M35, a bacteriocin produced by Carnobacterium divergens, was incorporated into films made with chitosan of molecular mass 2 kDa, 20 kDa, or 100 kDa and de-acetylated either 87% or 95%. Only 100 kDa chitosan yielded films that could be peeled and handled easily. The higher degree of de-acetylation increased the total color factor (ΔE) of bacteriocin-loaded films, their permeability, and puncture strength. Incorporation of divergicin M35 into the films increased amide I peak intensity but otherwise did not induce significant structural change. The FTIR spectra of divergicin M35 shed from the films did not differ from those of the original free bacteriocin, except in overall peak intensity. The release of active divergicin M35 from the film was faster into the buffer than into tryptic soy broth and peaked at 10-12 h in both cases. Chitosan 95% de-acetylated and loaded with divergicin M35 was the most active, producing a six-log drop in Listeria innocua HPB13 viable count within 24 h. These results suggest that the biocompatible and biodegradable films developed here have the potential for application as antimicrobials of Listeria spp. in foods, especially ready-to-eat, minimally processed products.

Application of ultraviolet, visible, and infrared light imaging in protein-based biopharmaceutical formulation characterization and development studies

Imaging is increasingly more utilized as analytical technology in biopharmaceutical formulation research, with applications ranging from subvisible particle characterization to thermal stability screening and residual moisture analysis. This review offers a comprehensive overview of analytical imaging for scientists active in biopharmaceutical formulation research and development, where it presents the unique information provided by the ultraviolet (UV), visible (Vis), and infrared (IR) sections in the electromagnetic spectrum. The main body of this review consists of an outline of UV, Vis, and IR imaging techniques for several (bio)physical properties that are commonly determined during protein-based biopharmaceutical formulation characterization and development studies. The review concludes with a future perspective of applied imaging within the field of biopharmaceutical formulation research.

Conformational distortion in a fibril-forming oligomer arrests alpha-Synuclein fibrillation and minimizes its toxic effects

The fibrillation pathway of alpha-Synuclein, the causative protein of Parkinson's disease, encompasses transient, heterogeneous oligomeric forms whose structural understanding and link to toxicity are not yet understood. We report that the addition of the physiologically-available small molecule heme at a sub-stoichiometric ratio to either monomeric or aggregated α-Syn, targets a His50 residue critical for fibril-formation and stabilizes the structurally-heterogeneous populations of aggregates into a minimally-toxic oligomeric state. Cryo-EM 3D reconstruction revealed a 'mace'-shaped structure of this monodisperse population of oligomers, which is comparable to a solid-state NMR Greek key-like motif (where the core residues are arranged in parallel in-register sheets with a Greek key topology at the C terminus) that forms the fundamental unit/kernel of protofilaments. Further structural analyses suggest that heme binding induces a distortion in the Greek key-like architecture of the mace oligomers, which impairs their further appending into protofilaments and fibrils. Additionally, our study reports a novel mechanism of prevention as well as reclamation of amyloid fibril formation by blocking an inter-protofilament His50 residue using a small molecule.

Binding of tyrosine kinase inhibitor to epidermal growth factor receptor: surface-enhanced infrared absorption microscopy reveals subtle protein secondary structure variations

Surface-Enhanced Infrared Absorption (SEIRA) has been proposed as a valuable tool for protein binding studies, but its performances have been often proven on model proteins undergoing severe secondary structure rearrangements, while ligand binding only marginally involves the protein backbone in the vast majority of the biologically relevant cases. In this study we demonstrate the potential of SEIRA microscopy for highlighting the very subtle secondary structure modifications associated with the binding of Lapatinib, a tyrosine kinase inhibitor (TKI), to epidermal growth factor receptor (EGFR), a well-known driver of tumorigenesis in pathological settings such as lung, breast and brain cancers. By boosting the performances of Mid-IR plasmonic devices based on nanoantennas cross-geometry, accustoming the protein purification protocols, carefully tuning the protein anchoring methodology and optimizing the data analysis, we were able to detect EGFR secondary structure modification associated with few amino acids. A nano-patterned platform with this kind of sensitivity bridges biophysical and structural characterization methods, thus opening new possibilities in studying of proteins of biomedical interest, particularly for drug-screening purposes.

Trimethylamine N-oxide alters structure-function integrity of β-casein: Structural disorder co-regulates the aggregation propensity and chaperone activity

Intrinsically disordered proteins (IDPs), involved in the regulation and function of various cellular processes like transcription, translation, cell cycle etc., exist as ensembles of rapidly interconverting structures with functional plasticity. Among numerous cellular regulatory mechanisms involved in structural and functional regulation of IDPs, osmolytes are emerging as promising regulatory agents due to their ability to affect the structure-function integrity of IDPs. The present study investigated the effect of methylamine osmolytes on β-casein, an IDP essential for maintaining the overall stability of casein complex in milk. It was observed that trimethylamine N-oxide induces a compact structural state in β-casein with slightly decreased chaperone activity and insignificant aggregation propensity. However, the other two osmolytes from this group, i.e., sarcosine and betaine, had no significant effect on the overall structure and chaperone activity of the IDP. The present study hints towards the possible evolutionary selection of higher structural disorder in β-casein, compared to α-casein, for stability of the casein complex and prevention of amyloidosis in the mammary gland.

Doxycycline Interferes With Tau Aggregation and Reduces Its Neuronal Toxicity

Tauopathies are neurodegenerative disorders with increasing incidence and still without cure. The extensive time required for development and approval of novel therapeutics highlights the need for testing and repurposing known safe molecules. Since doxycycline impacts α-synuclein aggregation and toxicity, herein we tested its effect on tau. We found that doxycycline reduces amyloid aggregation of the 2N4R and K18 isoforms of tau protein in a dose-dependent manner. Furthermore, in a cell free system doxycycline also prevents tau seeding and in cell culture reduces toxicity of tau aggregates. Overall, our results expand the spectrum of action of doxycycline against aggregation-prone proteins, opening novel perspectives for its repurposing as a disease-modifying drug for tauopathies.

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.

Developability Assessment of an Isolated CH2 Immunoglobulin Domain

The IgG C_H2 domain continues to hold promise for the development of new therapeutic entities because of its bifunctional role as a biomarker and effector protein. The need for further understanding of molecular stability and aggregation in therapeutic proteins has led to the development of a breakthrough quantum cascade laser microscope to allow for real-time comparability assessment of an array of related proteins in solution upon thermal perturbation. Our objective was to perform a comprehensive developability assessment of three similar monoclonal antibody (mAb) fragments: C_H2, C_H2s, and m01s. The C_H2 construct consists of residues Pro238 to Lys340 of the IgG1 heavy chain sequence. C_H2s has a 7-residue deletion at the N-terminus and a 16-residue C-terminal extension containing a histidine tag. The m01s construct is identical to C_H2s, except for two cysteines introduced at positions 242 and 334. A series of hyperspectral images was acquired during thermal perturbation from 28 to 60 °C for all three proteins in an array. Co-distribution and two-dimensional infrared correlation spectroscopies yielded the mechanism of aggregation and stability for these three proteins. The level of detail is unprecedented, identifying the regions within C_H2 and C_H2s that are prone to self-association and establishing the differences in stability. Furthermore, C_H2 helical segments, β-sheets, β-turns, and random coil regions were less stable than in C_H2s and m01s because of the presence of the N-terminal 3₁₀-helix and β-turn type III. The engineered disulfide bridge in m01s eliminated the self-association process and rendered this mAb fragment the most stable.

Effect of green tea extract on gelatin-based films incorporated with lemon essential oil

The use of natural polymers, such as gelatin and other proteins, has increased in an attempt to replace part of the consumption of petroleum-based packaging. This study evaluated the influence of green tea extract and lemon nanoemulsion on mechanical, thermal and permeability properties of gelatin matrix. The results showed that green tea increased the gelatin tensile strength (TS) from 86 ± 7 MPa to 101 ± 5 MPa, on the other hand, the nanoemulsion decreases to 78 ± 8 MPa. The incorporation of green tea and nanoemulsion enhanced the water vapor permeability of gelatin film; this could be due to the interacting with the hydrophobic domains of gelatin. This was indicated by melting point (Tm) in differential scanning calorimetry (DSC) and degradation temperatures in the thermogravimetric analysis (TG), respectively. Changes in FTIR spectra of gelatin film were observed when the green tea and nanoemulsion were incorporated. Therefore, this study showed a new characterization and formulation of gelatin films incorporated by green tea extract and lemon nanoemulsion and their potential for edible film.

Protaetia brevitarsis seulensis Derived Protein Isolate with Enhanced Osteomodulatory and Antioxidative Property

The osteogenic differentiation of stem cells is profoundly affected by their microenvironmental conditions. The differentiation behavior of stem cells can be tuned by changing the niche environments. The proteins or peptides that are derived by living organisms facilitate the osteogenic differentiation of stem cells. Here, we have evaluated the osteoinductive and antioxidative potential of the Protaetia brevitarsis seulensis insect-derived protein for human bone marrow-derived mesenchymal stem cells (hBMSCs). The amino acid contents in the isolated protein were determined by an amino acid analyzer. Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) were used to analyze the extract’s functional groups and surface morphology. The extracted protein exhibited 51.08% β-sheet conformation. No adverse effects were observed in extract-treated cells, indicating their biocompatibility. The protein isolate showed an excellent antioxidative property. Besides this, an enhancement in the hBMSCs’ mineralization has been observed in the presence of treated protein isolates. Notably, osteogenic marker genes and proteins were effectively expressed in the treated cells. These results indicated that the P. brevitarsis-derived protein isolate can be used as a potential antioxidative biomaterial for bone tissue engineering applications.

Extraction and Characterization of Collagen from Elasmobranch Byproducts for Potential Biomaterial Use

With the worldwide increase of fisheries, fish wastes have had a similar increase, alternatively they can be seen as a source of novel substances for the improvement of society's wellbeing. Elasmobranchs are a subclass fished in high amounts, with some species being mainly bycatch. They possess an endoskeleton composed mainly by cartilage, from which chondroitin sulfate is currently obtained. Their use as a viable source for extraction of type II collagen has been hypothesized with the envisaging of a biomedical application, namely in biomaterials production. In the present work, raw cartilage from shark (Prionace glauca) and ray (Zeachara chilensis and Bathyraja brachyurops) was obtained from a fish processing company and submitted to acidic and enzymatic extractions, to produce acid-soluble collagen (ASC) and pepsin-soluble collagen (PSC). From all the extractions, P. glauca PSC had the highest yield (3.5%), followed by ray ASC (0.92%), ray PSC (0.50%), and P. glauca ASC (0.15%). All the extracts showed similar properties, with the SDS-PAGE profiles being compatible with the presence of both type I and type II collagens. Moreover, the collagen extracts exhibited the competence to maintain their conformation at human basal temperature, presenting a denaturation temperature higher than 37 °C. Hydrogels were produced using P. glauca PSC combined with shark chondroitin sulfate, with the objective of mimicking the human cartilage extracellular matrix. These hydrogels were cohesive and structurally-stable at 37 °C, with rheological measurements exhibiting a conformation of an elastic solid when submitted to shear strain with a frequency up to 4 Hz. This work revealed a sustainable strategy for the valorization of fisheries' by-products, within the concept of a circular economy, consisting of the use of P. glauca, Z. chilensis, and B. brachyurops cartilage for the extraction of collagen, which would be further employed in the development of hydrogels as a proof of concept of its biotechnological potential, ultimately envisaging its use in marine biomaterials to regenerate damaged cartilaginous tissues.

Determination of Gossypol in Hamid and Bt (Seeni 1) Cottonseed Oil using Fourier Transform Infrared Spectroscopy

This study was conducted to determine the gossypol content in Bt cottonseed (Seeni-1) oil by using Fourier Transform Infrared (FTIR) spectroscopy with an Attenuated Total Reflectance (ATR) element. The wavelengths used were selected by spiking refined, bleached deodorized palm oil (RBDPO) to gossypol concentrations of 0-5% and noting the regions of maximal absorbance. Absorbance values of the wavelength regions 3700-2400 & 1900-750 cm-1 and a partial least squares (PLS) method were used to derive calibration models for Hamid cottonseed oil, Seeni-1 cottonseed oil, and gossypol-spiked RBDPO. The coefficients of determination (R2) for the calibration models were computed for the FTIR spectroscopy results against those found by using the wet chemical method AOCS method Ba 8�78. The R2 was 0.8916, 0.9581, and 0.9374 for Hamid cottonseed oil, Seeni-1 cottonseed oil, and gossypol-spiked RBDPO, respectively. The standard error (SE) of the calibration was 0.053, 0.078, and 0.062, respectively. The calibration models were validated using the cross-validation technique within the same set of oil samples. The results of FTIR spectroscopy as a useful technique determining gossypol content in crude cottonseed oil showed that there is a significant difference (p <0.05) in the amount of gossypol content in Hamid and Bt Seeni-1 cottonseed oils.

The extent of protein hydration dictates the preference for heterogeneous or homogeneous nucleation generating either parallel or antiparallel β-sheet α-synuclein aggregates

α-Synuclein amyloid self-assembly is the hallmark of a number of neurodegenerative disorders, including Parkinson's disease, although there is still very limited understanding about the factors and mechanisms that trigger this process. Primary nucleation has been observed to be initiated in vitro at hydrophobic/hydrophilic interfaces by heterogeneous nucleation generating parallel β-sheet aggregates, although no such interfaces have yet been identified in vivo. In this work, we have discovered that α-synuclein can self-assemble into amyloid aggregates by homogeneous nucleation, without the need of an active surface, and with a preference for an antiparallel β-sheet arrangement. This particular structure has been previously proposed to be distinctive of stable toxic oligomers and we here demonstrate that it indeed represents the most stable structure of the preferred amyloid pathway triggered by homogeneous nucleation under limited hydration conditions, including those encountered inside α-synuclein droplets generated by liquid-liquid phase separation. In addition, our results highlight the key role that water plays not only in modulating the transition free energy of amyloid nucleation, and thus governing the initiation of the process, but also in dictating the type of preferred primary nucleation and the type of amyloid polymorph generated depending on the extent of protein hydration. These findings are particularly relevant in the context of in vivo α-synuclein aggregation where the protein can encounter a variety of hydration conditions in different cellular microenvironments, including the vicinity of lipid membranes or the interior of membraneless compartments, which could lead to the formation of remarkably different amyloid polymorphs by either heterogeneous or homogeneous nucleation.

CMT-3 targets different α-synuclein aggregates mitigating their toxic and inflammogenic effects

Parkinson's disease (PD) is a neurodegenerative disorder for which only symptomatic treatments are available. Repurposing drugs that target α-synuclein aggregation, considered one of the main drivers of PD progression, could accelerate the development of disease-modifying therapies. In this work, we focused on chemically modified tetracycline 3 (CMT-3), a derivative with reduced antibiotic activity that crosses the blood–brain barrier and is pharmacologically safe. We found that CMT-3 inhibited α-synuclein amyloid aggregation and led to the formation of non-toxic molecular species, unlike minocycline. Furthermore, CMT-3 disassembled preformed α-synuclein amyloid fibrils into smaller fragments that were unable to seed in subsequent aggregation reactions. Most interestingly, disaggregated species were non-toxic and less inflammogenic on brain microglial cells. Finally, we modelled the interactions between CMT-3 and α-synuclein aggregates by molecular simulations. In this way, we propose a mechanism for fibril disassembly. Our results place CMT-3 as a potential disease modifier for PD and possibly other synucleinopathies.

Exploring polar headgroup interactions between sphingomyelin and ceramide with infrared spectroscopy

Ceramide is a major actor in the sphingolipid signaling pathway elicited by various kinds of cell stress. Under those conditions ceramide (Cer) is produced in the plasma membrane as a product of sphingomyelin (SM) hydrolysis, and this may lead to apoptosis. Thus, SM and Cer coexist in the membrane for some time, and they are known to separate laterally from the (more abundant) glycerolipids, giving rise to highly rigid domains or platforms. The properties of these domains/platforms are rather well understood, but the underlying SM:Cer molecular interactions have not been explored in detail. Infrared (IR) spectroscopy is a powerful analytical technique that provides information on all the chemical groupings in a molecule, and that can be applied to membranes and lipid bilayers in aqueous media. IR spectra can be conveniently retrieved as a function of temperature, thus revealing the thermotropic transitions of SM and its mixtures with Cer. Four regions of the IR spectrum of these sphingolipids have been examined, two of them dominated by the hydrophobic regions in the molecules, namely the C–H stretching vibrations (2800–3000 cm⁻¹), and the CH₂ scissoring vibrations (1455–1485 cm⁻¹), and two others arising from chemical groups at the lipid-water interface, the sphingolipid amide I band (1600–1680 cm⁻¹), and the phosphate vibrations in the 1000–1110 cm⁻¹ region. The latter two regions have been rarely studied in the past. The IR data from the hydrophobic components show a gel (or ripple)-fluid transition of SM at 40 °C, that is shifted up to about 70 °C when Cer is added to the bilayers, in agreement with previous studies using a variety of techniques. IR information concerning the polar parts is more interesting. The amide I (carbonyl) band of pure SM exhibits a maximum at 1638 cm⁻¹ at room temperature, and its position is shifted by about 10 cm⁻¹ in the presence of Cer. Cer causes also a change in the overall band shape, but no signs of band splitting are seen, suggesting that SM and Cer carbonyl groups are interacting tightly, presumably through H-bonds. The 1086 cm⁻¹ band, corresponding to PO₂⁻ vibrations, appears more stable in SM than in DPPC, and it is further stabilized by Cer, again suggesting an important role of H-bonds in the formation of SM:Cer clusters. Thus, SM and Cer can interact through their polar headgroups, in a way that is not accessible to other lipid classes.

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.

Ultrastable Plasmonic Bioink for Printable Point-Of-Care Biosensors

Point-of-care biosensors are critically important for early disease diagnosis and timely clinical intervention in resource-limited settings. The real-world application of these biosensors requires the use of stable biological reagents and cost-effective fabrication approaches. To meet these stringent requirements, we introduce a generic encapsulation strategy to realize ultrastable plasmonic bioink by encapsulating antibodies with an organosiloxane polymer through in situ polymerization. Plasmonic nanostructures serve as sensitive nanotransducers, allowing for label-free biochemical detection. The plasmonic bioink with encapsulated antibodies exhibits excellent thermal, biological, and colloidal stabilities making it compatible with printing process. As a proof-of-concept, we demonstrate the printability of the ultrastable plasmonic bioinks on different types of substrates with direct writing techniques. The organosiloxane polymer preserves the biorecognition capabilities of the biosensors under harsh conditions, including elevated temperature, exposure to chemical/biological denaturants, and ultrasonic agitation. Plasmonic biochips fabricated with the ultrastable ink exhibit superior stability compared to the biochips with unencapsulated antibodies.

Conjugative Coupling Proteins and the Role of Their Domains in Conjugation, Secondary Structure and in vivo Subcellular Location

Type IV Coupling Proteins (T4CPs) are essential elements in many type IV secretion systems (T4SSs). The members of this family display sequence, length, and domain architecture heterogeneity, being the conserved Nucleotide-Binding Domain the motif that defines them. In addition, most T4CPs contain a Transmembrane Domain (TMD) in the amino end and an All-Alpha Domain facing the cytoplasm. Additionally, a few T4CPs present a variable domain at the carboxyl end. The structural paradigm of this family is TrwB_R388, the T4CP of conjugative plasmid R388. This protein has been widely studied, in particular the role of the TMD on the different characteristics of TrwB_R388. To gain knowledge about T4CPs and their TMD, in this work a chimeric protein containing the TMD of TraJ_pKM101 and the cytosolic domain of TrwB_R388 has been constructed. Additionally, one of the few T4CPs of mobilizable plasmids, MobB_CloDF13 of mobilizable plasmid CloDF13, together with its TMD-less mutant MobBΔTMD have been studied. Mating studies showed that the chimeric protein is functional in vivo and that it exerted negative dominance against the native proteins TrwB_R388 and TraJ_pKM101. Also, it was observed that the TMD of MobB_CloDF13 is essential for the mobilization of CloDF13 plasmid. Analysis of the secondary structure components showed that the presence of a heterologous TMD alters the structure of the cytosolic domain in the chimeric protein. On the contrary, the absence of the TMD in MobB_CloDF13 does not affect the secondary structure of its cytosolic domain. Subcellular localization studies showed that T4CPs have a unipolar or bipolar location, which is enhanced by the presence of the remaining proteins of the conjugative system. Unlike what has been described for TrwB_R388, the TMD is not an essential element for the polar location of MobB_CloDF13. The main conclusion is that the characteristics described for the paradigmatic TrwB_R388 T4CP should not be ascribed to the whole T4CP family. Specifically, it has been proven that the mobilizable plasmid-related MobB_CloDF13 presents different characteristics regarding the role of its TMD. This work will contribute to better understand the T4CP family, a key element in bacterial conjugation, the main mechanism responsible for antibiotic resistance spread.

Automated, High-Throughput Infrared Spectroscopy for Secondary Structure Analysis of Protein Biopharmaceuticals

Protein higher order structure (HOS) is an important product quality attribute that governs the structure-function characteristics, safety, and efficacy of therapeutic proteins. Infrared (IR) spectroscopy has long been recognized as a powerful biophysical tool in determining protein secondary structure and monitoring the dynamic structural changes. Such biophysics analyses help establish process and product knowledge, understand the impact of upstream (cell culture) and downstream (purification) process conditions, create stable formulations, monitor product stability, and assess product comparability when process improvements are implemented (or establish biosimilarity to originator products). This paper provides an overview of a novel automated mid-IR spectroscopic technique called microfluidic modulation spectroscopy (MMS) for the characterization of protein secondary structure. The study demonstrates that MMS secondary structure analysis of therapeutic monoclonal antibodies (mAb) is comparable with a conventional Fourier transform infrared (FTIR) method. More importantly the study shows MMS exhibits higher sensitivity and repeatability for low concentration samples over FTIR, as well as provides automated operation and superior robustness with simplified data analysis, increasing the utility of the instrument in determination of mAb secondary structure. Therefore, we propose that the MMS method can be widely applied in characterization and comparability/biosimilarity studies for biopharmaceutical process and product development.

On the Secondary Structure of Silk Fibroin Nanoparticles Obtained Using Ionic Liquids: An Infrared Spectroscopy Study

Silk fibroin from Bombyx mori caterpillar is an outstanding biocompatible polymer for the production of biomaterials. Its impressive combination of strength, flexibility, and degradability are related to the protein’s secondary structure, which may be altered during the manufacture of the biomaterial. The present study looks at the silk fibroin secondary structure during nanoparticle production using ionic liquids and high-power ultrasound using novel infrared spectroscopic approaches. The infrared spectrum of silk fibroin fibers shows that they are composed of 58% β-sheet, 9% turns, and 33% irregular and/or turn-like structures. When fibroin was dissolved in ionic liquids, its amide I band resembled that of soluble silk and no β-sheet absorption was detected. Silk fibroin nanoparticles regenerated from the ionic liquid solution exhibited an amide I band that resembled that of the silk fibers but had a reduced β-sheet content and a corresponding higher content of turns, suggesting an incomplete turn-to-sheet transition during the regeneration process. Both the analysis of the experimental infrared spectrum and spectrum calculations suggest a particular type of β-sheet structure that was involved in this deficiency, whereas the two other types of β-sheet structure found in silk fibroin fibers were readily formed.

Hydroxyapatite nanoparticles derived from mussel shells for in vitro cytotoxicity test and cell viability

Hydroxyapatite (HA) nanoparticles derived from mussel shells were prepared using the wet precipitation method and were tested on human mesenchymal and epithelial cells. Shells and HA powder were characterized via X-ray diffraction analysis (XRD) and scanning electron microscopy along with energy dispersive X-ray spectroscopy (SEM/EDX), high resolution transmission electron microscopy (HR-TEM) and Fourier transform infrared spectroscopy (FTIR). The in vitro cytotoxic properties of HA and mussel shells were determined using sulphorhodamine B (SRB) assays for MCF-7 cells (HepG2) and colon (Caco-2) cells. Cell viability tests confirmed the nontoxic effects of synthesized HA and mussel shells on human mesenchymal stem cells (h-MSCs) and epithelial cells. Toxicity values were less than 50% of the cell's validity ratio based on analyses using different concentrations (from 0.01 to 1,000 μg). The results indicate that MSC and epithelial cell attachment and proliferation in the presence of both HA and shell occurred. The proliferation capability was established after 3 and 7 days. SEM images revealed that stem cells and epithelial cells attached to the scaffold indicated full and complete integration between the cells and the material. It seems that due to the ion exchange between bovine serum albumin solutions (BSA) and HA, the FTIR data confirmed an increase in the amide I and amide II bands, which indicates the compatibility of the BSA helix structure. This study sheds light on the importance of merging stem cells and nanomaterials that may lead to improvements in tissue engineering to develop novel treatments for various diseases.

Spectral Analysis and Deconvolution of the Amide I Band of Proteins Presenting with High-Frequency Noise and Baseline Shifts

The challenge of deriving quantitative information from the infrared spectra of proteins arises from the large number of secondary structures and amino acid side-chain functional groups that all contribute to the spectral intensity, such as within the amide I band (1600-1700 cm^-1). The band is invariably heavily convoluted from overlapping spectral features, thereby making interpretation difficult such that deconvolution is usually required. This work critically examines the methods available to deconvolute the spectra and assesses the commonly used methods and algorithms applied to vibrational spectra for smoothing and peak identification. We show that unless their spectra have very high signal-to-noise ratios, quantitative analysis to decipher protein constituents is not feasible. The advantages and disadvantages of spectral smoothing using adjacent averaging, the Savitzky-Golay filter and the fast Fourier transform filter are examined in detail. The use of derivative spectra to identify peaks is described with particular reference to the influence and reduction of interfering water bands in the amide I region. The reliability of band narrowing techniques such as second-derivative analysis or Fourier deconvolution that lead to the identification of the contributing protein peaks is investigated. Both methods are shown to be limited in their capacity to resolve features with very similar frequencies. Additionally, the presence of narrow bands arising from high-frequency noise whether from atmospheric water vapor, acoustic vibrations, or electrical interference results in both methods becoming increasingly unusable as narrow bands are preferentially enhanced at the expense of broad ones such as the amide I bands. An optimal strategy is critically developed to allow accurate determination and quantification of protein constituents and their conformations. Additionally, quantitative methods are proposed to account for baseline shifts, which would otherwise introduce significant errors in similarity indices.

Natural flagella-templated Au nanowires as a novel adjuvant against Listeria monocytogenes

A simple method was developed for the extraction and purification of bacterial flagella with a yield of a concentration of 113.22 ± 5.64 mg mL^-1. Gold (Au) nanowires were synthesized using the bacterial flagella as the template. Transmission Electron Microscopy (TEM) analysis showed that the nanowires were scarcely clustered as stiff (no tendency to bend or fold) and straight nanorods with homogeneous surface and a uniform aspect ratio over 60. Fourier Transform Infrared (FT-IR) spectroscopic studies revealed the deep involvement of the functional groups located within and on the surface of flagellin, including C-N, N-H, O-H, and C[double bond, length as m-dash]O. The profound transformation observed in the absorption profiles of these groups supported the notion that both chemical (reduction) reaction and physical (electrostatic) binding of Au occurred during the formation of Au nanowires. Verbascoside, oleuropein, and olive leaf extract (OLE) have been shown to inhibit the growth of Listeria monocytogenes completely at their respective Minimal Inhibitory Concentrations (MICs) of 20, 64, and 64 mg mL^-1. In contrast, the synthesized Au nanowires demonstrated high electrocatalytic activity and reduced the MICs of the three antibacterial compounds by half. Moreover, results from the AMES assays indicated that the synthesized Au nanowires had no mutagenic activities at the catalytic concentration used, 128 μg mL^-1. Therefore, the Au nanowires fabricated in this work have the potential to be used as new antimicrobial food packaging materials to enhance food safety.

The Binding of Aβ42 Peptide Monomers to Sphingomyelin/Cholesterol/Ganglioside Bilayers Assayed by Density Gradient Ultracentrifugation

The binding of Aβ42 peptide monomers to sphingomyelin/cholesterol (1:1 mol ratio) bilayers containing 5 mol% gangliosides (either GM1, or GT1b, or a mixture of brain gangliosides) has been assayed by density gradient ultracentrifugation. This procedure provides a direct method for measuring vesicle-bound peptides after non-bound fraction separation. This centrifugation technique has rarely been used in this context previously. The results show that gangliosides increase by about two-fold the amount of Aβ42 bound to sphingomyelin/cholesterol vesicles. Complementary studies of the same systems using thioflavin T fluorescence, Langmuir monolayers or infrared spectroscopy confirm the ganglioside-dependent increased binding. Furthermore these studies reveal that gangliosides facilitate the aggregation of Aβ42 giving rise to more extended β-sheets. Thus, gangliosides have both a quantitative and a qualitative effect on the binding of Aβ42 to sphingomyelin/cholesterol bilayers.

The allergen Mus m 1.0102: Cysteine residues and molecular allergology

Mus m 1.0102 is a member of the mouse Major Urinary Protein family, belonging to the Lipocalins superfamily. Major Urinary Proteins (MUPs) are characterized by highly conserved structural motifs. These include a disulphide bond, involved in protein oxidative folding and protein structure stabilization, and a free cysteine residue, substituted by serine only in the pheromonal protein Darcin (MUP20). The free cysteine is recognized as responsible for the onset of inter- or intramolecular thiol/disulphide exchange, an event that favours protein aggregation. Here we show that the substitution of selected cysteine residues modulates Mus m 1.0102 protein folding, fold stability and unfolding reversibility, while maintaining its allergenic potency. Recombinant allergens used for immunotherapy or employed in allergy diagnostic kits require, as essential features, conformational stability, sample homogeneity and proper immunogenicity. In this perspective, recombinant Mus m 1.0102 might appear reasonably adequate as lead molecule because of its allergenic potential and thermal stability. However, its modest resistance to aggregation renders the protein unsuitable for pharmacological preparations. Point mutation is considered a winning strategy. We report that, among the tested mutants, C138A mutant acquires a structure more resistant to thermal stress and less prone to aggregation, two events that act positively on the protein shelf life. Those features make that MUP variant an attractive lead molecule for the development of a diagnostic kit and/or a vaccine.

A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII

Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe–S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm⁻¹) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe–S (sulfide) and Fe–S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe–S bond lengths upon DNA binding, both of the Fe–S (sulfide) and Fe–S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.

Understanding the structural degradation of South American historical silk: A Focal Plane Array (FPA) FTIR and multivariate analysis

Silk artifacts constitute an invaluable heritage, and to preserve such patrimony it is necessary to correlate the degradation of silk fibroin with the presence of dyes, pollutants, manufacturing techniques, etc. Fourier Transform Infrared Spectroscopy with a Focal plane array detector (FPA FTIR) provides structural information at the micron scale. We characterized the distribution of secondary structures in silk fibers for a large set of South American historical textiles, coupling FTIR with multivariate statistical analysis to correlate the protein structure with the age of the samples and the presence of dyes. We found that the pressure applied during attenuated total reflectance (ATR) measurements might induce structural changes in the fibers, producing similar spectra for pristine and aged samples. Reflectance spectra were thus used for the rigorous characterization of secondary structures. Some correlation was highlighted between the age of the samples (spanning over five centuries) and specific changes in their secondary structure. A correlation was found between the color of the samples and structural alterations, in agreement with the chemical nature of the dyes. Overall, we demonstrated the efficacy of reflectance FPA µ-FTIR, combined with multivariate analysis, for the rigorous and non-invasive description of protein secondary structures on large sets of samples.

Spectral and Photochemical Properties of Rhodobacter sphaeroides R-26 Reaction Center Films in Vacuum

Using absorption spectroscopy in the visible/near-IR and mid-IR regions, spectral and photochemical properties of isolated reaction centers (RCs) from Rhodobacter sphaeroides R-26 were studied in dried films on the inorganic support surface (quartz or CaF₂ plates) under vacuum dehydration conditions (10^-2 or 7·10^-5 mm Hg). Three detergents, N,N-dimethyldodecylamine N-oxide (LDAO), Triton X-100 (TX100), and n-dodecyl-β-D-maltoside (DM), were tested for their ability to stabilize the RC-detergent complexes in the vacuum-dried state. It was shown that in the presence of LDAO, RC complexes underwent destruction in vacuum. In contrast, DM provided an environment that minimized irreversible disruptive changes in the RCs in vacuum. The effects of vacuum dehydration on the RC-DM films included a small increase in the content of α-helices in the RC protein, a short-wavelength reversible shift in the optical transitions of pigments, and minor changes in the electronic structure of the P⁺ dimer. The films retained their photochemical activity upon excitation with high-intensity light (200 mW/cm²). TX100 also helped to maintain spectral and functional properties of the RCs in vacuum; however, in this case, the stabilizing effect was less pronounced than in the presence of DM, especially, at high detergent concentrations. The results are discussed within the framework of a model suggesting that the detergent-protein interactions and the properties of detergent micelles play a dominant role in maintaining the structure of the RCs upon vacuum dehydration of the RC complexes. The obtained data can be useful for developing hybrid photoconverting systems based on bacterial RCs.

Microstructure Transitions and Dry-Wet Spinnability of Silk Fibroin Protein from Waste Silk Quilt

With excellent biocompatibility and biodegradability, silk fibroin has been developed into many protein materials. For producing regenerated silk fibroin (RSF) fibers, the conformation transition of silk fibroin needs to be thoroughly studied during the spinning process. Since the many silk fabrics that are discarded comprise an increasing waste of resources and increase the pressure on the environment, in this paper, waste silk fiber was recycled in an attempt to prepare regenerated fibroin fiber by dry-wet spinning. Ethanol was the coagulation bath. The rheological properties of all the RSF solutions were investigated to acquire rheology curves and non-Newtonian indexes for spinnability analysis. Four stages of the spinning process were carried out to obtain RSF samples and study their conformation transitions, crystallization, and thermal properties by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction, and differential scanning calorimetry. Quantitative analysis of the FTIR results was performed to obtain specific data regarding the contents of the secondary structures. The results showed that higher concentration spinning solutions had better spinnability. As the spinning process progressed, random coils were gradually converted into β-sheets and crystallization increased. Among the different influencing factors, the ethanol coagulation bath played a leading role in the conformation transitions of silk fibroin.

Studies on the Interaction of Alyteserin 1c Peptide and Its Cationic Analogue with Model Membranes Imitating Mammalian and Bacterial Membranes

Antimicrobial peptides (AMPs) are effector molecules of the innate immune system and have been isolated from multiple organisms. Their antimicrobial properties are due to the fact that they interact mainly with the anionic membrane of the microorganisms, permeabilizing it and releasing the cytoplasmic content. Alyteserin 1c (+2), an AMP isolated from Alytes obstetricans and its more cationic and hydrophilic analogue (+5) were synthesized using the solid phase method, in order to study the interaction with model membranes by calorimetric and spectroscopic assays. Differential scanning calorimetry (DSC) showed that both peptides had a strong effect when the membrane contained phosphatidylcholine (PC) alone or was mixed with phosphatidylglycerol (PG), increasing membrane fluidization. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to study the secondary structure of the peptide. Peptide +2 exhibited a transition from β-sheet/turns to β-sheet/α-helix structures after binding with model membranes, whereas peptide +5 had a transition from aggregation/unordered to β-sheet/α-helix structures after binding with membrane-contained PC. Interestingly, the latter showed a β-sheet structure predominantly in the presence of PG lipids. Additionally, molecular dynamics (MD) results showed that the carboxy-terminal of the peptide +5 has the ability to insert into the surface of the PC/PG membranes, resulting in the increase of the membrane fluidity.

A Spectroscopic Study on Secondary Structure and Thermal Unfolding of the Plant Toxin Gelonin Confirms Some Typical Structural Characteristics and Unravels the Sequence of Thermal Unfolding Events

Gelonin from the Indian plant Gelonium multiflorum belongs to the type I ribosome-inactivating proteins (RIPs). Like other members of RIPs, this toxin glycoprotein inhibits protein synthesis of eukaryotic cells; hence, it is largely used in the construction of immunotoxins composed of cell-targeted antibodies. Lysosomal degradation is one of the main issues in targeted tumor therapies, especially for type I RIP-based toxins, as they lack the translocation domains. The result is an attenuated cytosolic delivery and a decrease of the antitumor efficacy of these plant-derived toxins; therefore, strategies to permit their release from endosomal vesicles or modifications of the toxins to make them resistant to degradation are necessary to improve their efficacy. Using infrared spectroscopy, we thoroughly analyzed both the secondary structure and the thermal unfolding of gelonin. Moreover, by the combination of two-dimensional correlation spectroscopy and phase diagram method, it was possible to deduce the sequence of events during the unfolding, confirming the typical characteristic of the RIP members to denature in two steps, as a sequential loss of tertiary and secondary structure was detected at 58 °C and at 65 °C, respectively. Additionally, some discrepancies in the unfolding process between gelonin and saporin-S6, another type I RIP protein, were detected.

Secondary Structural Changes in Proteins as a Result of Electroadsorption at Aqueous-Organogel Interfaces

The electroadsorption of proteins at aqueous-organic interfaces offers the possibility to examine protein structural rearrangements upon interaction with lipophilic phases, without modifying the bulk protein or relying on a solid support. The aqueous-organic interface has already provided a simple means of electrochemical protein detection, often involving adsorption and ion complexation; however, little is yet known about the protein structure at these electrified interfaces. This work focuses on the interaction between proteins and an electrified aqueous-organic interface via controlled protein electroadsorption. Four proteins known to be electroactive at such interfaces were studied: lysozyme, myoglobin, cytochrome c, and hemoglobin. Following controlled protein electroadsorption onto the interface, ex situ structural characterization of the proteins by FTIR spectroscopy was undertaken, focusing on secondary structural traits within the amide I band. The structural variations observed included unfolding to form aggregated antiparallel β-sheets, where the rearrangement was specifically dependent on the interaction with the organic phase. This was supported by MALDI ToF MS measurements, which showed the formation of protein-anion complexes for three of these proteins, and molecular dynamic simulations, which modeled the structure of lysozyme at an aqueous-organic interface. On the basis of these findings, the modulation of protein secondary structure by interfacial electrochemistry opens up unique prospects to selectively modify proteins.