Secondary Structure Determination by Means of ATR-FTIR Spectroscopy

Effects of Various Decellularization Methods for the Development of Decellularized Extracellular Matrix from Tilapia (Oreochromis niloticus) Viscera

Tilapia, a widely farmed aquaculture fish, produces substantial waste, including viscera that contain extracellular matrix (ECM) utilized as a biomaterial for tissue regeneration applications. Extracting ECM from viscera requires a specific decellularization method, as no standardized protocol exists. This study performed three decellularization methods: sonication, orbital shaking at room temperature, and agitation at 4°C, using SDS and TX100 at concentrations of 0.1% and 0.3%. The effectiveness of each method was assessed through H&E staining, dsDNA quantification, and SEM imaging to verify cellular content removal and ECM structure preservation. Additional analyses, including ATR-FTIR, SDS-PAGE, protein quantification, HPLC, and detergent residue tests, were performed to examine functional groups, collagen composition, protein content, amino acid profiles, and detergent residues in the decellularized samples. The results of H&E staining showed a significant reduction in cellular components in all samples, which was confirmed through DNA quantification. Sonication with 0.3% SDS achieved the highest DNA removal rate (96.5 ± 1.1%), while SEM images revealed that agitation at 4°C with 0.3% TX100 better preserved ECM structure. Collagen was present in all samples, as confirmed by ATR-FTIR analysis, which revealed pronounced spectral peaks in the amide I, II, III, A, and B regions. Samples treated with agitation at 4°C using 0.1% SDS exhibited the highest protein content (875 ± 15 µg/mg), whereas those treated with TX100 had lower detergent residue. Overall, the decellularization methods effectively reduced DNA content while preserving ECM structure and components, highlighting the potential of tilapia viscera as bioscaffolds and offering insights into utilizing fish waste for high-value products.

Exploring keratin composition variability for sustainable thermal insulator design

In pursuing sustainable thermal insulation solutions, this study explores the integration of human hair and feather keratin with alginate. The aim is to assess its potential in thermal insulation materials, focusing on the resultant composites' thermal and mechanical characteristics. The investigation uncovers that the type and proportion of keratin significantly influence the composites' porosity and thermal conductivity. Specifically, higher feather keratin content is associated with lesser sulfur and reduced crosslinking due to shorter amino acids, leading to increased porosity and pore sizes. This, in turn, results in a decrease in β-structured hydrogen bond networks, raising non-ordered protein structures and diminishing thermal conductivity from 0.044 W/(m·K) for pure alginate matrices to between 0.033 and 0.038 W/(m·K) for keratin-alginate composites, contingent upon the specific ratio of feather to hair keratin used. Mechanical evaluations further indicate that composites with a higher ratio of hair keratin exhibit an enhanced compressive modulus, ranging from 60 to 77 kPa, demonstrating the potential for tailored mechanical properties to suit various applications. The research underscores the critical role of sulfur content and the crosslinking index within keratin's structures, significantly impacting the thermal and mechanical properties of the matrices. The findings position keratin-based composites as environmentally friendly alternatives to traditional insulation materials.

Exploring the effect of protein secondary structure on the solid state and physical stability of protein-based amorphous solid dispersions

Amorphous solid dispersions (ASDs) using proteins as carriers have emerged as a promising strategy for stabilizing amorphous drug molecules. Proteins possess diverse three-dimensional structures that significantly influence their own properties and may also impact the properties of ASDs. We prepared β-lactoglobulin (BLG) with different contents of β-sheet and α-helical secondary structures by initially dissolving BLG in different mixed solvents, containing different ratios of water, methanol/ethanol, and acetic acid, followed by spray drying of the solutions. Our findings revealed that an increase in α-helical content resulted in a decrease in the glass transition temperature (Tg) of the protein. Subsequently, we utilized the corresponding mixed solvents to dissolve both BLG and the model drug celecoxib (CEL), allowing the preparation of ASDs containing either β-sheet-rich or α-helix/random coil-rich BLG. Using spray drying, we successfully developed BLG-based ASDs with drug loadings ranging from 10 wt% to 90 wt%. At drug loadings below 40 wt%, samples prepared using both methods exhibited single-phase ASDs. However, heterogeneous systems formed when the drug loading exceeded 40 wt%. At higher drug loadings, physical stability assessments demonstrated that the α-helix/random coil-rich BLG structure exerted a more pronounced stabilizing effect on the drug-rich phase compared to the β-sheet-rich BLG. Overall, our results highlight the importance of considering protein secondary structure in the design of ASDs.

Optimizing the Metal Bioreduction Process in Recombinant Shewanella azerbaijanica Bacteria: A Novel Approach via mtrC Gene Cloning and Nitrate-Reducing Pathway Destruction

Environmental pollution is growing every day in terms of the increase in population, industrialization, and urbanization. Shewanella azerbaijanica is introduced as a highly potent bacterium in metal bioremediation. The mtrC gene was selected as a cloning target to improve electron flux chains in the EET (extracellular electron transfer) pathway. Using the SDM (site-directed mutagenesis) technique, the unique gene assembly featured the mtrC gene sandwiched between two napD/B genes to disrupt the nitrate reduction pathway, which serves as the primary metal reduction competitor. Shew-mtrC gene construction was transferred to expression plasmid pET28a (+) in the expression host bacteria (E. coli BL21 and S. azerbaijanica), in pUC57, cloning plasmid, which was transferred to the cloning host bacteria E. coli Top10 and S. azerbaijanica. All cloning procedures (i.e., synthesis, insertion, transformation, cloning, and protein expression) were verified and confirmed by precise tests. ATR-FTIR analysis, CD, western blotting, affinity chromatography, SDS-PAGE, and other techniques were used to confirm the expression and structure of the MtrC protein. The genome sequence and primers were designed according to the submitted Shewanella oneidensis MR-1 genome, the most similar bacteria to this native species. The performance of recombinant S. azerbaijanica bacterium in metal bioremediation, as sustainable strategy, has to be verified by more research.

Human Albumin-Based Hydrogels for Their Potential Xeno-Free Microneedle Applications

Nowadays, hydrogels-based microneedles (MNs) have attracted a great interest owing to their outstanding qualities for biomedical applications. For the fabrication of hydrogels-based microneedles as tissue engineering scaffolds and drug delivery carriers, various biomaterials have been tested. They are required to feature tunable physiochemical properties, biodegradability, biocompatibility, nonimmunogenicity, high drug loading capacity, and sustained drug release. Among biomaterials, human proteins are the most ideal biomaterials for fabrication of hydrogels-based MNs; however, they are mechanically weak and poorly processible. To the best of the knowledge, there are no reports of xeno-free human protein-based MNs so far. Here, human albumin-based hydrogels and microneedles for tissue engineering and drug delivery by using relatively new processible human serum albumin methacryloyl (HSAMA) are engineered. The resultant HSAMA hydrogels display tunable mechanical properties, biodegradability, and good biocompatibility. Moreover, the xeno-free HSAMA microneedles display a sustained drug release profile and significant mechanical strength to penetrate the model skin. In vitro, they also show good biocompatibility and anticancer efficacy. Sustainable processible human albumin-based biomaterials may be employed as a xeno-free platform in vivo for tissue engineering and drug delivery in clinical trials in the future.

Evaluating Subtle Pathological Changes in Early Myocardial Ischemia Using Spectral Histopathology

Early myocardial ischemia (EMI) is morphologically challenging, and the results from conventional histological staining may be subjective, imprecise, or even silent. The size of myocardial necrosis determines the acute and long-term mortality of EMI. The precise diagnosis of myocardial ischemia is critical for both clinical management and forensic investigation. Fourier transform infrared (FTIR) spectroscopic imaging is a highly sensitive tool for detecting protein conformations and imaging protein profiles. The aim of this study was to evaluate the application of FTIR imaging with multivariate analysis to detect biochemical changes in the protein conformation in the early phase of myocardial ischemia and to visually classify different disease states. The spectra and curve fitting results revealed that the total protein content decreased significantly in the EMI group and that the α-helix content of the secondary protein structure continuously decreased as ischemia progressed, while the β-sheet content increased. Differences in the control and EMI groups and perfused and ischemic myocardium were confirmed using principal component analysis and partial least squares discriminant analysis. Next, two support vector machine classifiers were effectively created. The accuracy, recall, and precision were 99.98, 99.96, and 100.00%, respectively, to differentiate the EMI group from the control group and 99.25, 98.95, and 99.54%, respectively, to differentiate perfused and ischemic myocardium. Ultimately, high EMI diagnostic accuracy was achieved with 100.00% recall and 100.00% precision, and ischemic myocardium diagnostic accuracy was achieved with 99.30% recall and 99.53% precision for the test set. This pilot study demonstrated that FTIR imaging is a powerful automated quantitative analysis tool to detect EMI without morphological changes and will improve diagnostic accuracy and patient prognosis.

Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure

Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H₂O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H₂O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.

Lubricin-Inspired Loop Zwitterionic Peptide for Fabrication of Superior Antifouling Surfaces

Biofouling represents great challenges in many applications, and zwitterionic peptides have been a promising candidate due to their biocompatibility and excellent antifouling performance. Inspired by lubricin, we designed a loop-like zwitterionic peptide and investigated the effect of conformation (linear or loop) on the antifouling properties using a combination of surface plasma resonance (SPR), surface force apparatus (SFA), and all atomistic molecular dynamics (MD) simulation techniques. Our results demonstrate that the loop-like zwitterionic peptides perform better in resisting the adsorption of proteins and bacteria. SFA measurements show that the loop-like peptides reduce the adhesion between the modified surface and the modeling foulant lysozyme. All atomistic MD simulations reveal that the loop-like zwitterionic peptides are more rigid than the linear-like zwitterionic peptides and avoid the penetration of the terminus into the foulants, which lower the interaction between the zwitterionic peptides and foulants. Besides, the loop-like zwitterionic peptides avoid the aggregation of the chains and bind more water, improving the hydrophilicity and antifouling performance. Altogether, this study provides a more comprehensive understanding of the conformation effect of zwitterionic peptides on their antifouling properties, which may contribute to designing novel antifouling materials in various biomedical applications.

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.

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.

Design and Synthesis of Bio-Inspired Polyurethane Films with High Performance

In the present work, the synthesis of segmented polyurethanes functionalized with catechol moieties within the hard or the soft segment is presented. For this purpose, a synthetic route of a new catechol diol was designed. The direct insertion of this catechol-free derivative into the rigid phase led to segmented polyurethanes with low performance (σmax ≈ 4.5 MPa). Nevertheless, when the derivative was formally located within the soft segment, the mechanical properties of the corresponding functionalized polyurethane improved considerably (σmax ≈ 16.3 MPa), owing to a significant increase in the degree of polymerization. It is proposed that this difference in reactivity could probably be attributed to a hampering effect of this catecholic ring during the polyaddition reaction. To corroborate this hypothesis, a protection of the aromatic ring was carried out, blocking the hampering effect and avoiding secondary reactions. The polyurethane bearing the protected catechol showed the highest molecular weight and the highest stress at break described to date (σmax ≈ 66.1 MPa) for these kind of catechol-functionalized polyurethanes. Therefore, this new approach allows for the obtention of high-performance polyurethane films and can be applied in different sectors, benefiting from the molecular adhesion introduced by the catechol ring.

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.

The Next Generation of IR Spectroscopy: EC-QCL-Based Mid-IR Transmission Spectroscopy of Proteins with Balanced Detection

We report a mid-IR transmission setup for the analysis of the protein amide I and amide II band in aqueous solutions that achieves a limit of detection as low as 0.0025 mg mL-1 (outperforming our previous results and other state-of-the-art mid-IR-based techniques by almost an order of magnitude). This large improvement is made possible by combining the latest-generation external cavity-quantum cascade laser (EC-QCL) operated at room temperature with an optimized double-beam optical setup that adjusts the path length (26 μm) to ensure robust sample handling. For minimizing the noise introduced by the high-intensity laser light source, a thermoelectrically cooled mercury cadmium telluride balanced detection module was employed. In this way, noise levels better by a factor of up to 20 were achieved compared with single-channel measurements. Characteristic spectral features of proteins with different secondary structures were successfully identified at concentrations as low as 0.1 mg mL-1. Furthermore, a highly linear response was demonstrated for concentrations between 0.05 and 10 mg mL-1. The total acquisition time of the setup can be adapted to fulfill the required sensitivity of the protein measurements and to ensure maximum flexibility for future applications. The presented setup combines high sensitivity, large optical path lengths, and short measurement times and thus outperforms previous research type EC-QCL setups as well as commercially available instruments. This opens a wide range of future applications including protein-ligand interaction studies as well as qualitative and quantitative analyses of proteins in complex matrices such as those found in up- and downstream bioprocess monitoring and similar challenging applications which can not be readily met by conventional FT-IR spectroscopy.

Elevated amyloidoses of human IAPP and amyloid beta by lipopolysaccharide and their mitigation by carbon quantum dots

Type 2 diabetes (T2D) and Alzheimer's disease (AD) represent two most prevalent amyloid diseases with a significant global burden. Pathologically, T2D and AD are characterized by the presence of amyloid plaques consisting primarily of toxic human islet amyloid polypeptide (IAPP) and amyloid beta (Aβ). It has been recently revealed that the gut microbiome plays key functions in the pathological progression of neurological disorders through the production of bacterial endotoxins, such as lipopolysaccharide (LPS). In this study, we examined the catalytic effects of LPS on IAPP and Aβ amyloidoses, and further demonstrated their mitigation with zero-dimensional carbon quantum dots (CQDs). Whereas LPS displayed preferred binding with the N-terminus of IAPP and the central hydrophobic core and C-terminus of Aβ, CQDs exhibited propensities for the amyloidogenic and C-terminus regions of IAPP and the N-terminus of Aβ, accordingly. The inhibitory effect of CQDs was verified by an embryonic zebrafish model exposed to the peptides and LPS, where impaired embryonic hatching was rescued and production of reactive oxygen species in the organism was suppressed by the nanomaterial. This study revealed a robust synergy between LPS and amyloid peptides in toxicity induction, and implicated CQDs as a potential therapeutic against the pathologies of T2D and AD.

Systematic FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin under Various Denaturation Conditions

Human serum albumin (HSA) is the most abundant protein in blood plasma. HSA is involved in the transport of hormones, fatty acids, and some other compounds, maintenance of blood pH, osmotic pressure, and many other functions. Although this protein is well studied, data about its conformational changes upon different denaturation factors are fragmentary and sometimes contradictory. This is especially true for FTIR spectroscopy data interpretation. Here, the effect of various denaturing agents on the structural state of HSA by using FTIR spectroscopy in the aqueous solutions was systematically studied. Our data suggest that the second derivative deconvolution method provides the most consistent interpretation of the obtained IR spectra. The secondary structure changes of HSA were studied depending on the concentration of the denaturing agent during acid, alkaline, and thermal denaturation. In general, the denaturation of HSA in different conditions is accompanied by a decrease in α-helical conformation and an increase in random coil conformation and the intermolecular β-strands. Meantime, some variation in the conformational changes depending on the type of the denaturation agent were also observed. The increase of β-structural conformation suggests that HSA may form amyloid-like aggregates upon the denaturation.