Secondary structure of proteins in the context of molecular interactions

Effect of physicochemical properties and secondary structure conformation, on the functional properties of protein concentrates prepared from grain legumes was investigated using response surface methodology. Appropriate models were built on the basis of the best subset technique. Oil-holding capacity was mainly influenced by the secondary structure of proteins, particularly unordered structure, β-sheet, and β-turn. Protein solubility depended on secondary structure and surface hydrophobicity of proteins, and solubility decreased with increasing hydrophobicity. Interaction between solubility and hydrophobicity was significant for emulsifying activity, and EA increased with increasing solubility and hydrophobicity. High emulsion stability of legume proteins necessitated high β-turn secondary structure proportion, solubility, and hydrophobicity. Protein unfolding, particularly high unordered, and β-turn structures and high solubility were required for high foaming ability of legume proteins. In summary, the importance of this study was to increase the utilization of grain legume proteins in the food and non-food industry. Practical applications It is important during food processing or when using an underutilized grain legume protein source as ingredient or supplement in the formulation of food products, to predict the functional properties of the protein. Functional properties are important for the consumer acceptance of food product. The physicochemical properties of protein such as surface hydrophobicity and secondary structure could be used as a basis to predict functionality. In this connection, this study provided effects of the variation of physicochemical properties and secondary structure of grain legume proteins on oil-holding capacity, solubility, emulsifying and foaming properties. The aim of this study was to enhance the utilization of grain legume proteins as nutritional and functional ingredient.

This study applies multivariate data analysis to deconvolute the spectral profiles of the Amide III region in the infrared spectra of gingival crevicular fluid (GCF). This reveals the impact of major oral diseases, such as dental caries and periodontal diseases, on the transformation of the secondary structure of GCF proteins. A two-stage analytical approach was employed: first, principal component analysis (PCA) was performed to establish the main factors of variation in the data, followed by pairwise comparisons of the samples based on the results of the Amide III profile deconvolution. The analysis also accounted for comorbidities, such as oncological and gastrointestinal diseases. This approach allowed for the identification of subtle differences in the composition and conformation of the secondary structure of GCF proteins while accounting for the superposition of multiple influencing factors. This methodology was effective in identifying biomarkers of oral diseases in GCF. For the first time, it has been demonstrated that the relative content of the β-sheet-associated component in the spectral profile of the secondary structure element of the protein fraction of GCF serves as a statistically significant marker for dental caries, regardless of the presence or absence of other diseases. Additionally, a significant decrease in the relative content of α-helix structures was observed in GCF from patients with oncological diseases. The changes in the spectral profile of the Amide III band of GCF identified in this study have not been previously detected using molecular spectroscopy, correlated with the secondary structure of proteins, or analyzed using multivariate analysis methods.

The secondary structure of a hydrophobic myelin protein (lipophilin), reconstituted with dimyristoylphosphatidylcholine or dimyristoylphosphatidylglycerol, was investigated by Fourier-transform infrared spectroscopy. Protein infrared spectra in the amide I region were analyzed quantitatively using resolution enhancement and band fitting procedures. Lipophilin in a phospholipid environment adopts a highly ordered secondary structure which at room temperature consists predominantly of alpha-helix (approximately 55%) and beta-type conformations (36%). The secondary structure of the protein is not affected by the lipid gel to liquid crystalline phase transition. Heating of the lipid-protein complex above approximately 35 degrees C results in a gradual decrease in alpha-helical content, accompanied by an increase in the amount of beta-structures. Lipophilin dissolved in 2-chloroethanol is, compared to the protein in a lipid environment, richer in the alpha-helical conformation but still contains a sizable amount of beta-structure.

The secondary structure of a 38 kDa core protein from pig skin proteodermatan sulfate (PDS), was investigated in solution using CD and Fourier transform (FT) ir spectroscopy. Both techniques generally have provided complementary data on the secondary structures of proteins. CD spectral analysis has shown that the core protein contains 60% beta-turn and alpha-helical structures, the rest being "unordered" structure. FT ir data do not permit calculation of quantitative contributions of substructures, at the present time, to the overall secondary structure of the core protein. CD spectrum of the intact PDS is similar to the core protein CD spectrum.

Native-Like Structure of Proteins at a Planar PAA Brush

Applying ATR-FTIR (attenuated total reflection Fourier transform infrared) and TIRF (total internal reflection fluorescence) spectroscopy, we have studied the secondary structure and aggregation properties of different proteins which are adsorbed at a poly(acrylic acid) (PAA) brush that covers a macroscopically large, planar surface. The PAA brush has been prepared on the surface of an ATR silicon crystal or a quartz plate. The preparation includes the deposition of a thin poly(styrene) film by spin-coating and the transfer of the diblock copolymer poly(styrene)-poly(acrylic acid) onto the hydrophobic film using the Langmuir-Schafer technique. It has been found that the proteins hen egg white lysozyme, bovine serum albumin, bovine alpha-lactalbumin, and bovine insulin adsorb spontaneously at a PAA brush at neutral pD values, albeit to different degrees. The secondary structure of the proteins was estimated from a decomposition of the amide I'-band in the observed ATR-FTIR spectra. Generally, the fractions of secondary structure elements recovered in this way were almost identical to those found when the proteins are native in solution. In addition, the tendency of insulin to form amyloid fibrils has also been tested when the protein is adsorbed at a planar PAA brush. Insulin is known to form amyloid fibrils in solution at low pH values and elevated temperatures. The experiments performed in this study suggest that a PAA brush does not promote fibril formation of insulin. Rather, insulin that is adsorbed at a PAA brush seems to be excluded from fibril formation pathways even at pD = 2 and 60 degrees C, where fibril formation of insulin is triggered in solution. Overall, the results of this study demonstrate that a planar PAA brush may serve as a mild environment for immobilized proteins.

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein. An understanding of the structure of the whole protein is often vital to understanding its digestive behavior in animals and nutritive quality. Usually protein secondary structures include alpha-helix and beta-sheet. The percentages of these two structures in protein secondary structures may influence feed protein quality and digestive behavior. Feathers are widely available as a potential protein supplement. They are very high in protein (84%), but the digestibility of the protein is very low (5%). The objective of this study was to use synchrotron-based Fourier transform infrared (FTIR) microspectroscopy to reveal chemical features of feather protein secondary structure within amide I at ultraspatial resolution (pixel size = 10 x 10 microm), in comparison with other protein sources from easily digested feeds such as barley, oat, and wheat tissue at endosperm regions (without destruction of their inherent structure). This experiment was performed at beamline U2B of the Albert Einstein Center for Synchrotron Biosciences at the National Synchrotron Light Source (NSLS) in Brookhaven National Laboratory (BNL), U.S. Dept of Energy (NSLS-BNL, Upton, NY). The results showed that ultraspatially resolved chemical imaging of feed protein secondary structure in terms of beta-sheet to alpha-helix peak height ratio by stepping in pixel-sized increments was obtained. Using synchrotron FTIR microspectroscopy can distinguish structures of protein amide I among the different feed protein sources. The results show that the secondary structure of feather protein differed from those of other feed protein sources in terms of the line-shape and position of amide I. The feather protein amide I peaked at approximately 1630 cm(-1). However, other feed protein sources showed a peak at approximately 1650 cm(-1). By using multicomponent peak modeling, the relatively quantitative amounts of alpha-helix and beta-sheet in protein secondary structure were obtained, which showed that feather contains 88% beta-sheet and 4% alpha-helix, barley contains 17% beta-sheet and 71% alpha-helix, oat contains 2% beta-sheet and 92% alpha-helix, and wheat contains 42% beta-sheet and 50% alpha-helix. The difference in percentage of protein secondary structure may be part of the reason for different feed protein digestive behaviors. These results demonstrate the potential of highly spatially resolved infrared microspectroscopy to reveal feed protein secondary structure. Information from this study by the infrared probing of feed protein secondary structure may be valuable as a guide for feed breeders to improve and maintain protein quality for animal use.

Secondary structure and folding stability of proteins adsorbed on silica particles – Pressure versus temperature denaturation

To analyze the pathogenic variants of the KIF1A gene and its corresponding protein structure in an autism spectrum disorder (ASD) family trio carrying harmful missense variants in the KIF1A gene. The peripheral blood DNA of the patient and his parents was extracted and sequenced using whole exome sequencing (WES) technology and verified by Sanger sequencing. Bioinformatics software SIFT, PolyPhen-2, Mutation Taster, and CADD software were used to analyze the harmfulness and conservation of variants. The Human Brain Transcriptome (HBT) database was used to analyze the expression of the KIF1A gene in the brain. PredictProtein and SWISS-MODEL were further used to predict the secondary structure and tertiary structure of KIF1A wild-type protein and variant protein. PyMOL V2.4 was utilized to investigate the change of hydrogen bond connection after protein variant. The WES sequencing revealed a missense variant c.664A>C (p.Asn222His) in the child's KIF1A gene, and this variant was a de novo variant. The harmfulness prediction results suggest that this variant is harmful. By analyzing expression level of KIF1A gene in the brain. It is found that KIF1A gene widely expressed in various brain regions during embryonic development. By analyzing the variant protein structure, the missense variant of KIF1A will cause many changes in the secondary structure of protein, such as alpha-helix, beta-strand, and protein binding domain. The connection of hydrogen bond and spatial structure will also change, thereby changing the original biological function. The KIF1A gene may be a risk gene for ASD.

Infrared and circular dichroism spectroscopic characterisation of secondary structure components of a water treatment coagulant protein extracted from Moringa oleifera seeds

Protein secondary structure prediction by using deep learning method

The aim of the present study was to predict the secondary structure and the T- and B-cell epitopes of the Echinococcus multilocularis Emy162 antigen, in order to reveal the dominant epitopes of the antigen. The secondary structure of the protein was analyzed using the Gamier-Robson method, and the improved self-optimized prediction method (SOPMA) server. The T- and B-cell epitopes of Emy162 were predicted using Immune Epitope Database (IEDB), Syfpeithi, Bcepred and ABCpred online software. The characteristics of hydrophilicity, flexibility, antigenic propensity and exposed surface area were predicted. The tertiary structure of the Emy162 protein was predicted by the 3DLigandSite server. The results demonstrated that random coils and β sheets accounted for 34.64 and 21.57% of the secondary structure of the Emy162 protein, respectively. This was indicative of the presence of potential dominant antigenic epitopes in Emy162. Following bioinformatic analysis, numerous distinct antigenic epitopes of Emy162 were identified. The high-scoring T-cell epitopes were located at positions 16–29, 36–39, 97–103, 119–125 and 128–135, whilst the likely B-cell epitopes were located at positions 8–10, 19–25, 44–50, 74–81, 87–93, 104–109 and 128–136. In conclusion, five T-cell and seven B-cell dominant epitopes of the Emy162 antigen were revealed by the bioinformatic methods, which may be of use in the development of a dominant epitope vaccine.

Secondary structure composition of two homologous proteins, alpha-fetoprotein and serum albumin, has been compared using circular dichroism and Fourier-transform infrared spectroscopy. CD-only analysis gives an accurate a-helical content for SA, but underestimates the predicted value for AFP. In contrast, FTIR-only analysis underestimates the helical content of SA. However, analysis of hybrid IR-CD spectra gives more accurate values for secondary structure composition for both AFP and SA and shows that the secondary structures of these proteins are the same.

Amino-acid protein composition plays an important role in biology, medicine, and nutrition. Here, a groundbreaking protein analysis technique that quickly estimates amino acid composition and secondary structure across various protein sizes, while maintaining their natural states is introduced and validated. This method combines multivariate statistics and the thermostable Raman interaction profiling (TRIP) technique, eliminating the need for complex preparations. In order to validate the approach, the Raman spectra are constructed of seven proteins of varying sizes by utilizing their amino acid frequencies and the Raman spectra of individual amino acids. These constructed spectra exhibit a close resemblance to the actual measured Raman spectra. Specific vibrational modes tied to free amino and carboxyl termini of the amino acids disappear as signals linked to secondary structures emerged under TRIP conditions. Furthermore, the technique is used inversely to successfully estimate amino acid compositions and secondary structures of unknown proteins across a range of sizes, achieving impressive accuracy ranging between 1.47% and 5.77% of root mean square errors (RMSE). These results extend the uses for TRIP beyond interaction profiling, to probe amino acid composition and structure.

Secondary structures of proteins adsorbed onto aluminum hydroxide: Infrared spectroscopic analysis of proteins from low solution concentrations