Protein Secondary Structure Analysis Research Articles

Impact of different drying methods on physicochemical characteristics and nutritional compositions of bee larvae

This article presents a comprehensive analysis of three distinct drying methods, namely hot air drying (HAD), microwave oven drying (MD), and vacuum freeze drying (VFD), applied to bee larvae. Through rigorous experimentation and analysis, we evaluated various parameters, including moisture content, color, fat, protein, fatty acid composition, aroma components, and protein secondary structure. Our findings reveal distinctive characteristics of bee larvae aroma, notably including E-2-curenal, palmitic acid and 10-undecenal, with palmitic, linolenic, and oleic acids being the dominant fatty acids. Among the drying methods, MD at 10 W/g demonstrated significantly higher levels of volatile components. Noteworthy, VFD-assisted drying closely resembled the composition of fresh bee larvae, with fat and protein contents of 26% and 57%, respectively. Analysis of protein secondary structure unveiled that MD at 10 W/g exhibited the highest β-folding content, 80%, followed closely by VFD at 45 °C, 73%. Remarkably, VFD at 45 °C exhibited as the superior method, yielding dried bee larvae of unparalleled quality among the three techniques investigated. This study provides valuable insights into the impact of different drying methods on the composition and quality of bee larvae, offering significant implications for the processing, preservation and utilization of this valuable resource.

Dry fractionation of Australian mungbean for sustainable production of value‐added protein concentrate ingredients

AbstractBackground and ObjectivesDry fractionation, combining milling and air classification technology, offers an economical and sustainable pathway for the processing of value‐added protein ingredients from Australia's major pulse crops. Leveraging a wider range of pulses will help meet the growing demand for plant‐based protein ingredients. This study demonstrates the efficient processing of protein concentrates from Australian mungbean, which were characterized for key nutritional properties, phytochemical constituents, protein quality, and protein secondary structure.FindingsMilling and air classification of mungbean flour resulted in protein concentrates (fine fraction) with a protein content of 62.2 g/100 g (db), reflecting a two‐fold increase in protein content compared to the original flour (p < .05). Ash, fat, dietary fiber, and free phenolic and antioxidant compounds, also co‐concentrated with protein in the fine fraction (p < .05), imparting enhanced nutritional properties with the potential to deliver health benefits. The protein quality of dry fractionated mungbean protein concentrate was compared to a commercial source of mungbean protein isolate (88 g/100 g, [db]). Amino acid scores highlighted deficiencies in sulfur‐containing amino acids, methionine, and cysteine, as well as tryptophan and threonine. In vitro protein digestibility‐corrected amino acid scores for the mungbean protein concentrate and protein isolate were 63.7% and 59.5%, respectively. SDS‐PAGE protein profiles showed no major differences in protein composition, indicating that no specific types of proteins are lost during the dry fractionation process. Fourier transform infrared analysis of protein secondary structure showed that β‐sheets were the dominant structural component, with relative percentages of 36% and 49%, for the mungbean protein concentrate and isolate, respectively.ConclusionsThere is significant potential for dry fractionation to deliver value‐added opportunities for Australian mungbean, through the production of protein concentrate ingredients with enhanced nutritional properties for use in new and existing foods.Significance and NoveltyNutritional properties, protein quality, and protein secondary structure were compared for protein concentrates and protein isolates processed from Australian‐grown mungbean. Key findings from this study will inform pulse protein processors and pulse‐based food manufacturers.

Application of biological soil crusts for efficient cadmium removal from acidic mine wastewater

Utilizing an acid-resistant biological soil crust (BSC) species that we discovered, we developed a device capable of efficiently removing cadmium (Cd) from mine wastewater with varying levels of acidity. Our research has demonstrated that this particular BSC species adapts to acidic environments by regulating the balance of fatty acids and acid-resistant enzymes. At a Cd concentration of 5 mg/L, the BSC grew well. When the initial Cd concentration was 2 mg/L, and the flow rate was set at 1 mL/min (at pH levels of 3, 4, and 5), BSC had a high removal rate of Cd, and the removal rate increased with the increase of pH (from 90% to 97%). Chemisorption is the primary removal mechanism in the initial stage, where the functional groups and minerals on the surface of the BSC play a significant role. In addition, BSC also adapts to Cd stress by changing bacterial community structure. It was discovered through infrared spectroscopy and two-dimensional correlation analysis that hydrophilic groups, specifically phosphate and carboxyl groups, exhibited the highest reactivity during the Cd binding process. Protein secondary structure analysis confirmed that as the pH increased, the adsorption capacity of the BSC increased; making biofilm formation easier. This study presents a novel approach for the treatment of acidic wastewater.

Enhancement of sewer sediment control and disruption of adhesive gelatinous sediment structure using low-dose calcium peroxide

Large quantities of sediments in urban sewer systems pose significant risk of pipe clogging and corrosion. Owing to their gel-like structure, sewer sediments have strong resistance to hydraulic shear stress. This study proposed a novel approach to weaken the erosion resistance of sewer sediments by destroying viscous gel-like biopolymers in sediments with low doses of calcium peroxide (CaO2). After treatment with 10–50 mg g−1 TS of CaO2, the critical erosion shear stress was significantly reduced by 25.7%–59.9%. The sediment aggregates gradually disintegrated into small diameter particles with increasing CaO2 dosage. Further analysis showed that the strong oxidizing and alkaline environment induced by CaO2 treatment led to cell lysis and changes in the composition and property of extracellular polymeric substances (EPS). After CaO2 treatment, aromatic proteins and humic acid-like substances associated with adhesion translocated from the inner EPS layers to outer layers while being disintegrated into small organic molecules. Concomitantly, CaO2 treatment disrupted the main functional groups (–OH, COO−, C–N, CO, and CN) in inner EPS layers, thus weakening EPS adhesion. Analysis of protein secondary structure and zeta potential reflected the reduced aggregation capacity of sediment microorganisms and loosening of sediment structure after CaO2 treatment. Thus, CaO2 treatment facilitated fragmentation and disaggregation of the gelatinous structure of sewer sediments. Such green strategy decreased the cost of sewer sediment disposal by 42.10–68.95% when compared to water flushing, and it would improve the self-cleaning capacity of sewer system and efficiency of dredging equipment.

Synergistic promotion of sludge reduction by surfactant-producing and lysozyme-producing bacteria: Optimization and effect of Na+

To improve the efficiency of aerobic digestion, this investigation utilized the synergistic effect of lysozyme-producing strain YH14 and surfactant-producing strain ZXY4 to promote sludge hydrolysis, and added NaCl to enhance this promoting effect. The best performance in promoting sludge hydrolysis was achieved when the inoculum of functional bacteria was 12 % (inoculum ratio of strain YH14: strain ZXY4 = 1:3) and the dosage of NaCl was 5 g L-1, which caused an increase of 19.25 % in the SS removal rate and 2588.21 mg L-1 in the SCOD release, as compared with the control. Fluorescence region integral analysis shows that the synergy of two functional bacteria and NaCl can enhance the biodegradability of sludge. Protein secondary structure analysis shows that strain ZXY4 and Na+ cause the EPS structure to loosen, increasing the chances of lysozyme lysis of bacteria. Nucleotide metabolism, metabolism of other amino acids and membrane transport enhanced in a co-processing system.

Insights into the membrane fouling aggravation under polyethylene terephthalate microplastics contamination: From a biochemical point of view

This study evaluated the potential effects of polyethylene terephthalate microplastics (PET-MPs) on a membrane bioreactor. The results showed that 10–30 mg/L PET-MPs exposure showed a minor effect on reactor performances, while 50 mg/L PET-MPs significantly decreased the chemical oxygen demand and NH4+-N removal efficiencies. Long-term PET-MPs exposure resulted in sludge foaming, and significantly increased extracellular polymeric substances (EPS) contents from 463.08 ± 62.42 to 952.54 ± 23.67 mg/m2, which was the main factor in triggering severe membrane fouling. Excitation emission matrix and Fourier transform infrared spectroscopic analysis revealed significant changes in fluorescence properties and functional groups of EPS. Particularly, protein secondary structure analysis indicated that high abundant β-sheet facilitated the exposure of inner hydrophobic groups of bacterial cells and EPS, and consequently enhanced the interfacial interactions of foulants-foulants and membrane-foulants. Long-term PET-MPs exposure significantly shifted the microbial community structures. In particular, the abundances of foam-forming filamentous bacteria and quorum-sensing (QS) bacteria, such as Thiothrix, Kouleothrix and Aeromonas, were constantly increasing with the increasing PET-MPs concentration. Furthermore, PET-MPs exposure significantly up-regulated the abundances of genes encoding QS signaling molecules and exopolysaccharides, such as lasI, lsrA and algZ. Collectively, these findings suggested that PET-MPs exposure stimulated the excessive growth of fouling-causing bacteria, which contained more biofilm formation related genes, that consequently accelerated membrane fouling.

Ultrasonic treatment combined with curdlan improves the gelation properties of low-salt Nemipterus virgatus surimi

In this study, the gel properties of ultrasonic alone, curdlan treatment alone, and the combination of both at low-salt surimi levels were investigated, mainly in terms of textural properties, water holding capacity, water distribution, dynamic rheology, protein secondary structure, microstructure and correlation analysis. The results showed that the springiness, gel strength, water holding capacity and energy storage modulus (G') of the low-salt surimi gels without ultrasonic or curdlan treatment were lower than those of the high-salt concentration surimi gels. Compared with the 1 % low-salt group, the ultrasonic treatment combination with curdlan resulted in a significant improvement (p < 0.05) in the texture, water holding capacity and energy storage modulus (G') of the low-salt surimi at the same salt concentration. The gel strength increased significantly from 3386.360 g·mm to 5457.203 g·mm, but there was no significant improvement in whiteness (p > 0.05). In addition, ultrasonic treatment combined with curdlan promoted the shift of the α-helix to the random coil and the β-turn angle shift, thus exposing the internal groups, enhancing protein intermolecular interactions, and promoting the orderly aggregation of proteins, resulting in a microstructure of dense, and obtained the lowest porosity of 14.534 %. The present study might be necessary for promoting the high-value use of aquatic surimi products and the development of low-salt foods.

Genome-Wide Identification and Characterization of the ANS Gene Family in Pomegranate (Punica granatum L.)

Anthocyanidin Synthase (ANS) is a key enzyme in the later stages of the anthocyanin biosynthetic pathway, and its role is to convert colorless leucoanthocyanidins to colored anthocyanidins. In this study, a total of 75 members of the pomegranate ANS family were identified and divided into four groups (Group I, Group Ⅱ, Group Ⅲ and Group Ⅳ) based on evolutionary relationships. The 75 ANS gene family members were unevenly distributed on seven of the eight chromosomes of pomegranate. The results of the physical and chemical property analysis showed that 93.33% of the proteins were acidic proteins, 6.67% were alkaline proteins, 28% of the proteins were stable proteins and 72% were unstable proteins. Protein secondary structure analysis showed that α-Spiral and irregular curl are the main structural elements. Analysis of the conserved structural domains of the proteins showed that all 75 ANS family members contained one DIOX -N subfamily structural domain and one 2OG-FeII_Oxy subfamily structural domain. The results of subcellular localization showed that all 75 ANS family members of pomegranate were localized in the cytoplasm. Analysis of the transcriptome data showed that the expression of the pomegranate ANS genes were variety-specific and period-specific.

Study of the Molecular Structure of Proteins in Eggs under Different Storage Conditions

The aim of this study is to reveal the relationship between changes in the physical and chemical characterization of eggs during storage and to provide a new way to assess egg freshness at the molecular chemical level. In this study, the Fourier transform infrared (FTIR) spectra of egg albumin from 60 fresh eggs (ISA Brown layer) stored for 1, 10, 20, 30, and 40 days at 4°C and 10°C were measured ( n = 6 ), and the amide I band of the egg albumin spectra was quantified by Fourier deconvolution and curve fitting to obtain the composition of the protein molecular structure. The results showed that different storage temperatures and storage times led to protein denaturation, resulting in changes in the conformation of the protein secondary structure. With increasing storage temperature and storage time, the content of the ordered structures β-sheet and α-helix in the egg protein secondary structure decreased significantly ( p &lt; 0.05 ), and the content of the disordered structure β-turn and random coil increased significantly ( p &lt; 0.05 ). Based on the pattern of protein secondary structure changes during storage, it was found that fresh eggs were better stored at 4°C for up to 15 days. Spearman’s correlation analysis of egg protein height, Haugh unit, egg weight, and protein secondary structure in eggs stored at 4°C showed a significant positive correlation between β-sheet and α-helix and egg weight, protein height, and Haugh unit. And a significant negative correlation between random coil and egg weight, protein height, and Haugh unit. Therefore, a curve fitting method based on Fourier transform infrared spectroscopy of deconvoluted spectra is an effective method for evaluating egg quality and freshness.

Molecular characterization of a teleost-specific toll-like receptor 22 (tlr22) gene from yellow catfish (Pelteobagrus fulvidraco) and its transcriptional change in response to poly I:C and Aeromonas hydrophila stimuli

Toll-like receptors (TLRs) are a class of pattern recognition receptors (PRRs) that can recognize pathogen-associated molecular patterns (PMPs) and play important roles in the innate immune system in vertebrates. In this study, we identified a teleost-specific tlr22 gene from yellow catfish (Pelteobagrus fulvidraco) and its immune roles in response to different pathogens were also determined. The open reading frame (ORF) of the tlr22 was 2892 bp in length, encoding a protein of 963 amino acids. Multiple protein sequences alignment, secondary and three-dimensional structure analyses revealed that TLR22 is highly conserved among different fish species. Phylogenetic analysis showed that the phylogenetic topology was divided into six families of TLR1, TLR3, TLR4, TLR5, TLR7 and TLR11, and TLR22 subfamily was clustered into TLR11 family. Meanwhile, synteny and gene structure comparisons revealed functional and evolutionary conservation of the tlr22 gene in teleosts. Furthermore, tlr22 gene was shown to be widely expressed in detected tissues except barbel and eye, with highest expression level in liver. The transcription of tlr22 was significantly increased in spleen, kidney, liver and gill tissues at different timepoints after Poly I:C infection, suggesting TLR22 plays critical roles in defensing virus invasion. Similarly, the transcription of tlr22 was also dramatically up-regulated in spleen, kidney and gill tissues with different patterns after Aeromonas hydrophila infection, indicating that TLR22 is also involved in resisting bacteria invasion. Our findings will provide a solid basis for the investigation the immune functions of tlr22 gene in teleosts, as well as provide useful information for disease control and treatment for yellow catfish.

Disordered-ordered protein binary classification by circular dichroism spectroscopy.

Intrinsically disordered proteins are abundant in nature and responsible for a plethora of cellular functions. They lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we proposed an automatized binary disorder-order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. To reach the best classification accuracy, CD of the protein should be measurable down to 197 nm in good quality. However, the method can be used even if the spectrum can be recorded down to the wavelength of 212 nm due to the strong absorbance of the samples. The method is implemented on a webserver (https://bestsel.elte.hu/idp_classification.php) and freely available for academic users to help the experimental identification of intrinsically disordered proteins (IDPs) and the verification of the results of bioinformatics tools. This study was supported by the National Research, Development and Innovation Office of Hungary (grants 2017-1.2.1-NKP-2017-00002, PD135510, K120391, K125340, K131702, K138937 and 2019-2.1.11-TÉT-2020-00101). SRCD measurements were supported by SOLEIL (Proposals 20181890, 20191810, and 20200751).

Bioinformatics and Functional Analysis of High Oleic Acid-Related Gene GmSAM22 in Soybean [Glycine max (L.) Merr.

High yield, high quality, stable yield, adaptability to growth period, and modern mechanization are the basic requirements for crops in the 21st century. Soybean oleic acid is a natural unsaturated fatty acid with strong antioxidant properties and stability. Known as a safe fatty acid, it has the ability to successfully prevent cardiovascular and cerebrovascular disorders. Improving the fatty acid composition of soybean seeds, can not only speed up the breeding process of high-quality high-oil and high-oleic soybeans, but also have important significance in human health, and provide the possibility for the development of soybean oil as a new energy source. Hence, the aim of this study was to analyze the high oleic acid elated gene GmSAM22 in soybean. In this research the soybean oleic acid-related gene GmSAM22 was screened out by Genome-wide association analysis, a 662 bp fragment was acquired by specific PCR amplification, and the pMD18T cloning vector was linked by the use of a seamless cloning technique. Bioinformatics analysis of the signal peptide prediction, subcellular localization, protein hydrophobicity, transmembrane region analysis, a phosphorylation site, protein secondary and tertiary structure and protein interaction analysis of the protein encoded by the SAM22 gene was carried out. The plasmid of the gene editing vector is pBK041. The overexpression vector was transformed from pCAMBIA3301 as the base vector, and overexpression vector were designed. Positive plants were obtained by genetic transformation by the pollen tube channel method. Fluorescence quantitative PCR was performed on the T2 generation plants to detect the relative expression levels in different tissues. Southern Blot was used to detect the presence of hybridization signal. Screening genes BAR, 35S, and NOS in plants were identified by conventional PCR. 10 seeds with high and low oleic acid content were chosen for quantitative PCR identification, and finally, the concentration and morphology of soybean fatty acids were identified by near-far infrared spectroscopy. On 10 seeds with an upper and lower oleic acid content, a quantitative fluorescence analysis was done. In Southern blot hybridization, the SAM22 gene was integrated into the recipient soybean plant in hands of a sole copy. Fluorescence quantitative PCR appeared that the average relative expression of the SAM22 gene in roots, stems, leaves, and seeds was 1.70, 1.67, 3.83, and 4.41, respectively. Positive expression seeds had a 4.77% increase in oleic acid content. The level of oleic acid in the altered seeds was reduced by 4.13% when compared to CK, and it was discovered that the GmSAM22 gene could be a regulatory and secondary gene that promotes the conversion of stearic acid to oleic acid in soybean. There has not been a discussion of gene cloning or functional verification. The cloning and genetic transformation of the soybean SAM22 gene can effectively increase the content of oleic acid, which lays a foundation for the study of soybean with high oleic acid.

Beta-galactosidase gene family genome-wide identification and expression analysis of members related to fruit softening in melon (Cucumis melo L.)

BackgroundTexture quality is impotent for melon (Cucumis melo L.) fruit. β-galactosidase (β-Gal, EC 3.2.1.23) is an important cell wall glycosyl hydrolase involved in fruit softening, However, the β-Gal gene (BGALs) family hasn’t been identified genome-wide in melon. Thus, it’s necessary to conduct an in-depth bioinformatic analysis on melon BGALs family and to seek out the key members who participated in melon fruit softening.ResultsA total of 21 BGALs members designated as CmBGAL1-CmBGAL21 were identified genome-wide in melon, clustered into A-G seven clades. Among them, three duplications CmBGAL1:CmBGAL3, CmBGAL19:CmBGAL21, and CmBGAL20:CmBGAL21 happened. For conserved domains, besides the Glyco_hydro_35 domain (PF01301), all the members also contained the GHD domain (PF17834) except for CmBGAL12, and the Gal_Lectin (PF02140) domain existed in most CmBGALs at the C-termini. Motifs, protein secondary and tertiary structure analysis showed that the CmBGAL12 is a unique member. Moreover, protein-protein association network analysis showed that the CmBGAL12 is the only node protein. Furthermore, spatiotemporal expression pattern analysis by quantitative real-time PCR (qRT-PCR) suggested that most of CmBGALs expressed in tissues with vigorous cell wall remodeling/disassembly. In addition, cis-acting regulatory elements analysis in promoters inferred that CmBGALs might participate in diverse responsiveness to phytohormone, biotic and abiotic signaling.ConclusionsA novel clade of CmBGAL members (Clade F) related to melon fruit softening was discovered, since their expression showed a specific surge in the mature fruit of ‘HPM’ with mealy texture (softening sharply), but not in ‘HDB’ with crisp texture (softening bluntly). The homologous CmBGAL7–11 in Clade F exhibited identical spatiotemporal expression patterns may multiple genes leading to melon fruit softening.

Reduced Graphene Oxide-Extracellular Matrix Scaffolds as a Multifunctional and Highly Biocompatible Nanocomposite for Wound Healing: Insights into Characterization and Electroconductive Potential.

The development of novel regenerative technologies based on the implementation of natural extracellular matrix (ECM), or individual components of ECM combined with multifunctional nanomaterials such as graphene oxide and reduced graphene oxide, has demonstrated remarkable results in wound healing and tissue engineering. However, the synthesis of these nanocomposites involves great challenges related to maintaining the biocompatibility with a simultaneous improvement in their functionalities. Based on that, in this research we developed novel nanoengineered ECM-scaffolds formed by mixing small intestinal submucosa (SIS) with graphene oxide (GO)/reduced graphene oxide (rGO) to improve electrical conductivity while maintaining remarkable biocompatibility. For this, decellularized SIS was combined with GO to form the scaffold precursor for subsequent lyophilization, chemically crosslinking and in situ reduction. The obtained GO and rGO were characterized via Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), X-ray diffraction (XRD), electrical conductivity testing and atomic force microscopy (AFM). The results confirm the suitable synthesis of GO, the effective reduction to rGO and the significant increase in the electrical conductivity (more than four orders of magnitude higher than bare GO). In addition, the graphene oxide/reduced graphene oxide-SIS scaffolds were characterized via Raman spectroscopy, FTIR, TGA, SEM, porosity assay (higher than 97.5% in all cases) and protein secondary structural analysis. Moreover, the biocompatibility of scaffolds was studied by standardized assays of hemolysis activity (less than 0.5%), platelet activation and deposition, and cell viability in Vero, HaCat and HFF-1 cells (higher than 90% for all evaluated cell lines on the different scaffolds). The obtained results confirm the remarkable biocompatibility, as supported by high hemocompatibility, low cytotoxicity and no negative impact on platelet activation and deposition. Finally, structural characteristics such as pore size and interconnectivity as well as superior cell attachment abilities also corroborated the potential of the developed nanoengineered ECM-scaffolds as a multifunctional nanoplatform for application in regenerative medicine and tissue engineering.

Identification and functional analysis of Tex11 and Meig1 in spermatogenesis of Hyriopsis cumingii.

: The process of spermatogenesis is complex and controlled by many genes. In mammals, Testis-expressed gene 11 (Tex11) and meiosis expressed gene 1 (Meig1) are typical spermatogenesis-related genes. In this study, we obtained the full length cDNAs for Tex11 (3143bp) and Meig1 (1649bp) in Hyriopsis cumingii by cloning. Among them, Hc-Tex11 contains 930 amino acids and Hc-Meig1 contains 91 amino acids. The protein molecular masses (MW) of Hc-Tex11 and Hc-Meig1 were 105.63 kDa and 10.95 kDa, respectively. Protein secondary structure analysis showed that Hc-TEX11 protein has three TPR domains. The expression of Hc-Tex11 and Hc-Meig1 in different tissues showed higher levels in testes. At different ages, the expression of Hc-Tex11 and Hc-Meig1 was higher levels in 3-year-old male mussels. During spermatogenesis, the mRNA levels of Hc-Tex11, Hc-Meig1 gradually increased with the development of spermatogonia and reached a peak during sperm maturation. Hc-Tex11 and Hc-Meig1 mRNA signals were detected on spermatogonia and spermatocytes by in situ hybridization. In addition, RNA interference (RNAi) experiments of Hc-Tex11 caused a down-regulated of Dmrt1, KinaseX, Tra-2 and Klhl10 genes and an up-regulated of β-catenin gene. Based on the above experimental results, it can be speculated that Hc-Tex11 and Hc-Meig1 are important in the development of the male gonadal and spermatogenesis in H. cumingii, which can provide important clues to better comprehend the molecular mechanism of Tex11 and Meig1 in regulating spermatogenesis of bivalves.

Disordered-Ordered Protein Binary Classification by Circular Dichroism Spectroscopy.

Intrinsically disordered proteins lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. They are abundant in nature and responsible for a large variety of cellular functions. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. It is usable in a wide concentration range under various buffer conditions. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we propose an automatized binary disorder–order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. Moreover, the method can be used even for strong absorbing samples, such as the case of crowded environmental conditions, if the spectrum can be recorded down to the wavelength of 212 nm. We believe the classification method will be useful in identifying disorder and will also facilitate the growth of experimental data in IDP databases. The method is implemented on a webserver and freely available for academic users.

Analysis and comparison of protein secondary structures in the rachis of avian flight feathers.

Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.

Infrared spectrometric biomarkers for ulcerative colitis screening using human serum samples.

This study uses infrared spectrometry coupled with data analysis techniques to understand colitis-induced alterations in the molecular components of serum samples. Using samples from 18 ulcerative colitis patients and 28 healthy volunteers, we assessed features such as absorbance values at wavenumbers of 1033 and 1076 cm-1 , and the ratios at 1121 versus 1020 cm-1 and 1629 versus 1737 cm-1 . Through the deconvolution of the amide I band, protein secondary structure analysis was performed. Colitis-induced alterations are reflected as fluctuations in the vibrational modes, and are used to identify associated spectral signatures. The results of the study show statistically significant differences in five identifying spectral signatures. Among them, the sensitivity and specificity of the spectral signature, I1121 /I1020 , were 100% and 86%, respectively. These findings resemble our earlier proof-of-concept investigations in mouse models and provide preliminary evidence that this could be a reliable diagnostic test for human patients.

Extraction of keratin from sheep wool fibres using aqueous ionic liquids assisted probe sonication technology

Wool derived keratin is a potential biopolymer that can play a vital role as a cheap, sustainable, renewable source of material for designing various speciality products in the field of biomedicine. Unlike conventional methods for keratin extraction, the use of eco-friendly, a recyclable solvent like ionic liquids opens a new perspective for the processing of natural raw materials from livestock industries. In this research work, we develop a technique for rapid dissolution of keratin in ionic liquid assisted by probe sonication without any heating from an external source. The whole process of keratin extraction was optimized concerning the type of ionic liquid, sonication time, initial loading of the sample, and acoustic power of probe sonicator. The properties of regenerated keratin were studied further by using various analytical techniques such as Scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) analysis, thermogravimetric analysis (TGA), Nuclear magnetic resonance (NMR) spectroscopic analysis, Sodium dodecyl sulphate -polyacrylamide gel electrophoresis (SDS-PAGE). FTIR analysis showed the protein secondary structure and TGA analysis further revealed improved thermal properties of regenerated keratin when compared to raw untreated wool. The presence of intermediate filament derived low sulphur keratin along with some fraction of matrix protein in regenerated keratin was confirmed by SDS – PAGE analysis. Thus, further efforts are required to implement this technique at larger industrial scale to make this whole process of keratin extraction economical, quick, and environmentally friendly.

Protein secondary structure analysis of serum from patients with oncohematological diseases

One of the promising approaches for diagnosing oncohematological diseases is infrared spectroscopy of blood serum. In this work secondary structure of blood serum proteins of patients with multiple myeloma, chronic lymphocytic leukemia and healthy donors was studied using IR spectroscopy. As a result of the study, it was found that the secondary structure of blood serum proteins in patients with chronic lymphocytic leukemia does not change in comparison with healthy donors. In contrast, patients with multiple myeloma have significant differences in the secondary structure composition of serum proteins compared to healthy donors. We conclude, that IR spectroscopy makes it possible to distinguish serum of healthy donors and patients with multiple myeloma, leading to the potential applicability of this approach to the diagnosis of multiple myeloma.