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Spike (S) glycoprotein is the largest structural protein of SARS‐CoV‐2 virus and the main one involved in anchoring of the host receptor ACE2 through the receptor binding domain (RBD). S protein secondary structure is of great interest for shedding light on various aspects, from functionality to pathogenesis, finally to spectral fingerprint for the design of optical biosensors. In this paper, the secondary structure of SARS‐CoV‐2 S protein and its constituting components, namely RBD, S1 and S2 regions, are investigated at serological pH by measuring their amide I infrared absorption bands through Attenuated Total Reflection Infrared (ATR‐IR) spectroscopy. Experimental data in combination with MultiFOLD predictions, Define Secondary Structure of Proteins (DSSP) web server and Gravy value calculations, provide a comprehensive understanding of RBD, S1, S2, and S proteins in terms of their secondary structure content, conformational order, and interaction with the solvent. [ABSTRACT FROM AUTHOR]

Summary: Lentil is one of the major pulses consumed in many parts of the world. Lentil proteins comprise primarily three fractions, viz. globulins, albumins and glutelins, each having distinct structural and functional characteristics. The secondary structure of lentil proteins is characterised by a predominance of β‐sheets, which occur in proportions up to 63% in the fractions. Protein isolates, in comparison, have up to 40% random coils, 38% sheets, 36% turns and 33% helix. Lentil proteins contain most essential amino acids, while albumins and glutelins have relatively higher content of lysine, methionine, histidine, threonine and branched‐chain amino acids. Amongst globulin proteins, vicilins have a more balanced amino acid composition than legumins. Lentil proteins also exhibit techno‐functional properties (foaming and emulsification, water and fat absorption and gelation) and may also serve as a potential source of active proteins/peptides, which make them an attractive alternative to conventional protein sources. [ABSTRACT FROM AUTHOR]

The investigation of the central and external zones of ten industrial and artisanal Maroilles cheeses showed differences in their physicochemical parameters, namely fat, pH, moisture content, ash, and color. This difference significantly impacted the rheological properties of the investigated cheeses, which depended on the protein network englobing lipid and water and its interaction with the other components. Overall, Maroilles cheeses had an elastic-like behavior, with the central zones exhibiting the greatest viscoelastic modules (G′ and G″). The mid-infrared (MIR) spectra highlighted the presence of lipids, proteins, and sugars. A significant difference in α-helix and β-sheet levels in the central zones was noted between artisanal and industrial Maroilles cheeses. It is suggested that the difference between artisanal and industrial Maroilles cheeses observed at the macroscopic level, due to the cheese-making procedure and ripening stage, affects the structure at the molecular level, which can be determined by MIR spectroscopy. This trend was confirmed by the FDA when applied to the MIR spectra, since 96.67% correct classification was noted between artisanal and industrial cheeses. The present study indicates that MIR spectroscopy can be used successfully to study Maroilles cheese samples belonging to different production chains. [ABSTRACT FROM AUTHOR]

Hydrodynamic cavitation (HC) is thought weaken the allergenicity of beer gluten proteins. However, the mechanism of action has not been thoroughly studied. In this study, an HC device was used to treat wheat gliadin and two specific celiac-toxic peptides, P1 and P2. FT-IR, MFS, HPLC, and CD were used to monitor the structural characteristics of gliadin and the two peptides. HC reduced the abundance of the coeliac toxic peptides P1 and P2 in solution and the contents of secondary structure β-turns and PPII, which are related to reduced allergen immunoreactivity. This meant that both the primary and secondary structures of P1 and P2 were affected by HC, leading to fewer allergic reactions. This study was focused on the impact of HC on the secondary structures of allergens produced from gluten raw materials, and it has positive implications for reducing product allergenicity. [ABSTRACT FROM AUTHOR]

The gel properties and molecular conformation of Spanish mackerel myofibrillar protein (MP) induced by soy protein isolate–inulin conjugates (SPI–inulin conjugates) were investigated. The addition of SPI–inulin conjugates significantly enhanced the quality of the protein gel. An analysis of different additives was conducted to assess their impact on the gel strength, texture, water-holding capacity (WHC), water distribution, intermolecular force, dynamic rheology, Raman spectrum, fluorescence spectrum, and microstructure of MP. The results demonstrated a substantial improvement in the strength and water retention of the MP gel with the addition of the conjugate. Compared with the control group (MP), the gel strength increased from 35.18 g·cm to 41.90 g·cm, and WHC increased from 36.80% to 52.67% with the inclusion of SPI–inulin conjugates. The hydrogen bond content was notably higher than that of other groups, and hydrophobic interaction increased from 29.30% to 36.85% with the addition of SPI–inulin conjugates. Furthermore, the addition of the conjugate altered the secondary structure of the myofibrillar gel, with a decrease in α-helix content from 62.91% to 48.42% and an increase in β-sheet content from 13.40% to 24.65%. Additionally, the SPI–inulin conjugates led to a significant reduction in the endogenous fluorescence intensity of MP. Atomic force microscopy (AFM) results revealed a substantial increase in the Rq value from 8.21 nm to 20.21 nm. Adding SPI and inulin in the form of conjugates is an effective method to improve the gel properties of proteins, which provides important guidance for the study of adding conjugates to surimi products. It has potential application prospects in commercial surimi products. [ABSTRACT FROM AUTHOR]

The liquid-liquid phase separation of biopolymers in living cells contains multiple interactions and occurs in a dynamic environment. Resolving the regulation mechanism is still a challenge. In this work, we designed a series of peptides (XXLY)6SSSGSS and studied their complexation and coacervation behavior with single-stranded oligonucleotides. The "X" and "Y" are varied to combine known amounts of charged and non-charged amino acids, together with the introduction of secondary structures and pH responsiveness. Results show that the electrostatic interaction, which is described as charge density, controls both the strength of complexation and the degree of chain relaxation, and thus determines the growth and size of the coacervates. The hydrophobic interaction is prominent when the charges are neutralized. Interestingly, the secondary structures of peptides exhibit profound effect on the morphology of the phases, such as solid phase to liquid phase transition. Our study gains insight into the phase separation under physiological conditions. It is also helpful to create coacervates with desirable structures and functions. [ABSTRACT FROM AUTHOR]

The Pearl darter Percina aurora, a member of the species-rich family Percidae, is endemic to the Pearl and Pascagoula river systems in Louisiana and Mississippi, USA. However, this fish is now only found in the Pascagoula River and is listed as threatened under the US Endangered Species Act. This study, for the first time, assembled and characterised in detail the mitochondrial genome of P. aurora. The mitochondrial genome of P. aurora is 16,646 bp in length and comprises 13 protein coding genes (PCGs), 22 transfer RNA genes, and 2 ribosomal RNA genes (rrnS [12s ribosomal RNA] and rrnL [16s ribosomal RNA]). A 33 bp long region was identified as the origin of replication for the light strand (OL), and a putative non-coding control region (CR), 987 bp in length, contains the origin of replication for the heavy strand (OH). The two ribosomal RNA genes, the majority of the PCGs, and the majority of the tRNA genes are encoded on the positive, or heavy, strand. The gene order in P. aurora is identical to that previously reported for confamilial species. All tRNAs exhibit a cloverleaf secondary structure except tRNA-Serine 1 which lacked the D-arm loop. An analysis of selective pressure (Ka/Ks ratios) for all the PCGs showed Ka/Ks values ≤1, suggesting that all these PCGs experience strong purifying selection. This new genomic resource will aid with bioprospecting and biomonitoring of P. aurora using environmental DNA. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization of its nucleotides. The formation of large stem-length secondary structures makes the sequences chemically inactive towards synthesis and sequencing processes. Furthermore, in DNA computing, other constraints like homopolymer run length also introduce complications. In this paper, our goal is to tackle the problems due to the creation of secondary structures in DNA sequences along with constraints such as not having a large homopolymer run length. This paper presents families of DNA codes with secondary structures of stem length at most two and homopolymer run length at most four. We identified Z 11 as an ideal structure to construct DNA codes to avoid the above problems. By mapping the error-correcting codes over Z 11 to DNA nucleotides, we obtained DNA codes with rates 0.5765 times the corresponding code rate over Z 11 , including some new secondary structure-free and better-performing codes for DNA-based data storage and DNA computing purposes. [ABSTRACT FROM AUTHOR]

In this study, we probed the secondary structure of a soluble Aβ (25-35) peptide in water solution by applying a molecular mechanics method as well as infrared spectroscopy. We have used Fourier Transformed Infrared Spectroscopy (FTIR) to examine the secondary structure of this peptide. The amide I bands of A (25-35) obtained from transmission-FTIR spectra consists of one main band at 1658 cm-1, at both concentrations used (200 M and 1 mM). This band shows us that A (25-35) in aqueous solution was mostly organized into a -helical structure (48 %). The contribution of the unordered structure was found to be about 12 %. The proportion of -sheet and -turn structures are slightly lower, 12-15 % and 13-14 %, respectively for both concentrations. FTIR spectra of the peptide in water solution (100 μM) after incubation for 12h showed Aβ peptide conformation is critically dependent on the environmental conditions used. The simulation approach reveals that the C-terminal octapeptide of this molecule preferably adopts an α-helical structure, while the N-terminal tripeptide may exist as a β-turn and unordered structures. [ABSTRACT FROM AUTHOR]

Beta turns, in which the protein backbone abruptly changes direction over four amino acid residues, are the most common type of protein secondary structure after alpha helices and beta sheets and play key structural and functional roles. Previous work has produced classification systems for turn geometry at multiple levels of precision, but these operate in backbone dihedral‐angle (Ramachandran) space, and the absence of a local Euclidean‐space coordinate system and structural alignment for turns, or of any systematic Euclidean‐space characterization of turn backbone shape, presents challenges for the visualization, comparison and analysis of the wide range of turn conformations and the design of turns and the structures that incorporate them. This work derives a turn‐local coordinate system that implicitly aligns turns, together with a set of geometric descriptors that characterize the bulk BB shapes of turns and describe modes of structural variation not explicitly captured by existing systems. These modes are shown to be meaningful by the demonstration of clear relationships between descriptor values and the electrostatic energy of the beta‐turn H‐bond, the overrepresentations of key side‐chain motifs, and the structural contexts of turns. Geometric turn descriptors complement Ramachandran‐space classifications, and they can be used to select turn structures for compatibility with particular side‐chain interactions or contexts. Potential applications include protein design and other tasks in which an enhanced Euclidean‐space characterization of turns may improve understanding or performance. The web‐based tools ExploreTurns, MapTurns, and ProfileTurn, available at www.betaturn.com, incorporate turn‐local coordinates and turn descriptors and demonstrate their utility. [ABSTRACT FROM AUTHOR]

While protein aggregation is a hallmark of many neurodegenerative diseases, acquiring structural information on protein aggregates inside live cells remains challenging. Traditional microscopy does not provide structural information on protein systems. Routinely used fluorescent protein tags, such as Green Fluorescent Protein (GFP), might perturb native structures. Here, we report a counter‐propagating mid‐infrared photothermal imaging approach enabling mapping of secondary structure of protein aggregates in live cells modeling Huntington's disease. By comparing mid‐infrared photothermal spectra of label‐free and GFP‐tagged huntingtin inclusions, we demonstrate that GFP fusions indeed perturb the secondary structure of aggregates. By implementing spectra with small spatial step for dissecting spectral features within sub‐micrometer distances, we reveal that huntingtin inclusions partition into a β‐sheet‐rich core and a ɑ‐helix‐rich shell. We further demonstrate that this structural partition exists only in cells with the [RNQ+] prion state, while [rnq−] cells only carry smaller β‐rich non‐toxic aggregates. Collectively, our methodology has the potential to unveil detailed structural information on protein assemblies in live cells, enabling high‐throughput structural screenings of macromolecular assemblies. [ABSTRACT FROM AUTHOR]

Nanostructuration of dynamic helical polymers such as poly(phenylacetylene)s (PPAs) depends on the secondary structure adopted by the polymer and the functional group used to connect the chiral pendant to the PPA backbone. Thus, while PPAs with dynamic and flexible scaffolds (para‐ and meta‐substituted, ω1<165°) generate by nanoprecipitation low polydisperse nanospheres with controllable size at different acetone/water mixtures, those with a quasi‐static behavior and the presence of an extended, almost planar structure (ortho‐substituted, ω1>165°), aggregate into a mixture of spherical and oval nanostructures whose size is not controlled. Photostability studies show that poly(phenylacetylene) particles are more stable to light irradiation than when dissolved macromolecularly. Moreover, the photostability of the particle depends on the secondary structure of the PPA and its screw sense excess. This fact, in combination with the encapsulation ability of these polymer particles, allows the creation of light stimuli‐responsive nanocarriers, whose cargo can be delivered by light irradiation. [ABSTRACT FROM AUTHOR]

Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage. [ABSTRACT FROM AUTHOR]

To reveal the structural mechanism by which the low‐complexity domain of the fused in sarcoma protein (FUS‐LC) mediates liquid–liquid phase separation (LLPS), we conducted a vacuum‐ultraviolet circular dichroism (VUV‐CD) spectroscopic study, a technique to analyze the secondary structures of proteins. The VUV‐CD measurements were performed at the BL12 VUV‐CD station at the Hiroshima Synchrotron Radiation Center (HiSOR) in Japan. CD spectra were measured between 180 and 260 nm while controlling the temperature of samples from 37°C to 5°C to obtain the LLPS of FUS‐LC. The CD spectrum obtained at 37°C exhibited a large negative peak at 195 nm and a small negative shoulder near 220 nm. The peak intensity around 195 nm decreased as the sample temperature decreased. The spectral changes originated from the LLPS formation. [ABSTRACT FROM AUTHOR]

ITS sections, which are situated inside the ribosomal DNA operon, are recognized for their high levels of diversity and slow rate of evolution, which makes them important for plant phylogenetic studies. The objective of this work is to use the internal transcribed spacer (ITS) regions of 18 alfalfa (Medicago sativa) genotypes/varieties to determine their genetic relationships and to verify possible genetic markers for variety identification and classification. This has been done by validating the secondary structures of the ITS regions and observing the effects of the relationships among the lowest energy state, the total number of possible secondary structure hairpins, and (GC) content. The results indicated that the length of the ITS sequences varied between 426 and 629 nucleotides and that the G + C content of the ITS region varied between 46.6 and 50%. In this study, the analysis of molecular variance (AMOVA) was used to validate the effectiveness of configuration analysis and revealed that fluctuations in the data accounted for a substantial amount of the observed total variance. Moreover, 94 percent of the genotypes analyzed exhibited a significant degree of variety. This shows that a large fraction of the observed variation is likely attributable to genetic variables. Population four, comprising Bilensoy80, Emily, Quin, Vendor, and Felicia, had the highest degree of heterozygosity at 68.8%, whereas population two, including Gozlu1, Prosementi, Nimet and Local (Van), had the lowest level at 37.5%. The original Shannon's approach as an unbiased estimator employed in population genetics research validated the differences among alfalfa genotypes with the AMOVA analysis results of this study. Individual differences were found to be 59%, whereas population differences were found to be 41%. There have been a few ITS studies on Medicago sativa that have utilized ITS as a phylogenetic marker to estimate connections and define new taxonomic categories (e.g., tribes). However, our research also includes an analysis of the secondary structure of these sequences and the results of this study imply that ITS sequence and secondary structure data can be utilized to understand the intraspecific genetic makeup of different alfalfa varieties. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Different forms of integration into the European Union (EU) call for studies of the consequences of multilevel access structures. Similar to EU member-states, government officials from associated states interact closely with EU-level administrative institutions, notably the European Commission (Commission) and EU agencies. Benefiting from a large-N survey, this study demonstrates that bureaucrats from "third-countries", such as Norway, may exert sectoral policy influence in the EU, and that organizational features of the public administration may systematically shape such patterns. The study offers two distinct contributions to the extant literature: First, it presents original survey data on how domestic agency officials perceive their influence vis-à-vis the EUs executive branch. Secondly, it probes the effects of two distinct drivers of policy influence—bureaucrats' access to secondary structures and requisite administrative capacities. [ABSTRACT FROM AUTHOR]

To meet the different functional needs for soybean protein isolate (SPI) in different food applications, this study utilized infrared spectroscopy to rapidly analyze 70 SPI samples subjected to different pH treatments, and explored the effect of pH changes on the secondary structure content of SPI. Mean centralization (MC), multivariate scattering correction (MSC), standard normal variate transformation, and normalization were used for infrared data preprocessing. Feature wavebands were identified based on two-dimensional correlation infrared spectra, and predictive modeling of the secondary structure content of SPI against pH was performed using partial least squares (PLS) and arithmetic optimization algorithm-random forests (AOA-RF). The results showed that the relative standard deviations of the α-helix, β-sheet, β-turn, and random coil prediction models developed by the combined use of MC and MSC were 1.29%, 1.60%, 1.37%, and 7.28%, respectively, indicating their combination to be the best spectral pre-processing method. The optimal model for predicting α-helix and β-sheet contents was AOA-RF (characteristic wavebands), with calibration determination coefficients of 0.935 0 and 0.926 6 and prediction determination coefficients of 0.856 8 and 0.870 1, respectively. The optimal model for predicting β-turn and random coil contents was PLS (characteristic wavebands), with calibration determination coefficients of 0.915 4 and 0.881 7 and prediction determination coefficients of 0.891 3 and 0.784 3, respectively. The results of this study provide a theoretical basis for product quality detection and processing condition control in industrial settings.

To elucidate the influence of different concentrations of carrageenan (CA, 0.4%, 0.8%, 1.2%, 1.6%, 2.0%, w/w) on the gelation properties and structure of hemp protein isolate (HPI), with the hemp protein isolate without adding CA as the control, the water-holding capacity, texture, rheological properties of the composite gels were determined. Meanwhile, the effect of CA addition on the water distribution, protein structure and intermolecular forces in the composite gels was also investigated. The results showed that the addition of CA significantly (P

In order to explore the effects of cooking pressure and holding time on the structure of chicken myofibrillar protein eggs, in this study, chicken breast meat was used as the main raw material, and atmospheric pressure, micro-pressure (4 kPa) and high-pressure (70 kPa) were selected to cook for 15~35 min. The changes of carbonyl content, sulfhydryl content, microstructure and protein secondary structure of myofibrillar protein during cooking were studied. The results showed that with the extension of holding time, the carbonyl content showed an upward trend, and the carbonyl content increased by 1.22 times, 1.38 times and 1.19 times respectively with normal pressure, micro pressure and high pressure cooking. The content of sulfhydryl group showed a downward trend, and the content of sulfhydryl group decreased by 29.6%, 29.8% and 31.4% respectively after normal pressure, micro pressure and high pressure cooking. With the extension of holding time, the content of β-sheet and random coil in the secondary structure of myofibrillar protein increased, and the content of α-helix decreased. The degree of damage to the structure of chicken breast protein was high pressure>micro pressure>normal pressure. The results of this study would provide data reference and technical support for the production of sauced chicken prefabricated products.

Abstract Objective The eukaryotic tree of life has been subject of numerous studies ever since the nineteenth century, with more supergroups and their sister relations being decoded in the last years. In this study, we reconstructed the phylogeny of eukaryotes using complete 18S rDNA sequences and their individual secondary structures simultaneously. After the sequence-structure data was encoded, it was automatically aligned and analyzed using sequence-only as well as sequence-structure approaches. We present overall neighbor-joining trees of 211 eukaryotes as well as the respective profile neighbor-joining trees, which helped to resolve the basal branching pattern. A manually chosen subset was further inspected using neighbor-joining, maximum parsimony, and maximum likelihood analyses. Additionally, the 75 and 100 percent consensus structures of the subset were predicted. Results All sequence-structure approaches show improvements compared to the respective sequence-only approaches: the average bootstrap support per node of the sequence-structure profile neighbor-joining analyses with 90.3, was higher than the average bootstrap support of the sequence-only profile neighbor-joining analysis with 73.9. Also, the subset analyses using sequence-structure data were better supported. Furthermore, more subgroups of the supergroups were recovered as monophyletic and sister group relations were much more comparable to results as obtained by multi-marker analyses.

Motivation Mirtrons, a vital category of non-canonical microRNAs (miRNAs) originating from exon-intron boundaries through splicing mechanisms, play crucial roles in cellular processes. However, existing databases lack the latest data and structural information, hindering understandings of mirtron formation and functions. Results We introduce MirtronStructDB, an online database addressing these gaps by incorporating over 350 novel mirtrons. Significantly, it provides corresponding predicted RNA secondary structures, offering a deeper understanding of the functional roles and mechanisms of all mirtrons. This enhances previous repositories, offering a total of 4,209 mirtron records spanning 25 species from 46 publications. Our database contributes for unraveling patterns and functions in mirtrons across species and diverse structural features. MirtronStructDB allows users to freely browse, search, visualize, and download data via a user-friendly interface. Availability MirtronStructDB is accessible at: http://www.bio8.cs.hku.hk/msdb/. Contact lishumin@connect.hku.hk, rbluo@cs.hku.hk

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. [ABSTRACT FROM AUTHOR]

The effect of β-sheet ratio and chain length on all-β proteins was investigated by MD simulations. Protein samples composed of different repeating units with various β-sheet ratios or a different number of repeating units were simulated under a broad temperature range. The simulation results show that the smaller radius of gyration was achieved by the protein with the higher proportion of β-sheet secondary structure, which had the lower nonbonded energy with more HBs within the protein. The root mean square deviation (RMSD) and the root mean square fluctuation (RMSF) both increased with temperature, especially in the case of a longer chain. The visible period was also shown according to the repeated secondary structure. Several minimum values of RMSF were located on the skeleton of Cα atoms participating in the β-sheet, indicating that it is a kind of stable secondary structure. We also concluded that proteins with a short chain or a lower ratio of β-sheet could easily transform their oriented and compact structures to other ones, such as random coils, turns, and even α-helices. These results clarified the relationship from the primary level to the 3D structure of proteins and potentially predicted protein folding [ABSTRACT FROM AUTHOR]

The microalgal genus known as Picochlorum, belonging to the green algae family Trebouxiophyceae, is recognized for its rapid growth and high lipid productivity. A Picochlorum strain (GJ210610) was recently established from the waters off Geoje, South Sea of Korea. Picochlorum sp. GJ210610 was a single, green ellipsoidal cell with an average size ranging from 1 to 2 µm. Its reproduction occurred through autosporulation. A phylogenetic tree based on nuclear small-subunit rDNA sequences revealed that this strain formed a unique branch, distinct from other Picochlorum species. Furthermore, the secondary structure of the ITS2 sequences was revealed for the first time within Picochlorum. The newly discovered Picochlorum sp. grew between 15°C and 25°C, with survival ceasing at 30°C. The maximum specific growth rate was measured at 0.91 d−1 at 25°C. The fatty acids of Picochlorum sp. GJ210610 were palmitic acid, oleic acid, linoleic acid, and alpha-linolenic acid. Based on morphological and phylogenetic analyses, we propose Picochlorum geojense sp. nov. (GJ210610) as a new species. The results of the present study may enhance our knowledge of the taxonomy and ecological characteristics of Picochlorum. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Chinese Institute of Food Science & Technology is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Food Research & Development is the property of Food Research & Development Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This study emphasized the alpha-amylase gene from Bacillus licheniformis as this species has been witnessed as the most prolific bio-factories for the alpha amylase production on industrial scales with particular reference to its wide commercial applicability. In the present study, a gene encoding alpha-amylase from an indigenously isolated B. licheniformis 208 strain was PCR amplified and sequenced. The obtained 1313 bp long nucleotide sequence (GenBank KM27230) exhibited the closest match with its homologous genes in B. licheniformis ATCC 9945A and ATCC 14580 strains. Gene translation retrieved 437 amino acid long enzyme sequence and exhibits a molecular weight of 50231.8 KDa. Other computed parameters include isoelectric point (5.95), aliphatic index (67.4), instability index (27.45), and GRAVY (-0.627) values. The structure of alphaamylase 208 was found to exhibit a 17 residues long active site, a conserved catalytic site with 3 residues, and a ligand-binding site comprised of 3 residues. Secondary structure configuration in the alpha-amylase 208 was predominated with a-helix and random coils followed by extended strands. The number of ß-turns was found comparatively less. ITASSER assigned E.C number to the BLA 208 sequence was 3.2.1.1 with extracellular origin. Deduced tertiary structure of BLA 208 showed the 7 residues long active site comprising of histidine, arginine, aspartic acid, glutamic acid, tryptophan, histidine, and aspartic acid at position 122, 246, 248, 278, 280, 344, 345 respectively. Na, K, and Ca were observed as the ligand-binding sites existing as a metal triad. Natural selection analysis explains that the alpha-amylase gene in B. licheniformis species is under purifying or negative selection i.e. it stabilizes itself by removing the deleterious mutation. Recombination event analysis was done using GARD (Genetic algorithm for recombination detection). Although, it rather inferred the presence of two break points which were found insignificant when validated via Kishino-Hasegawa test which demonstrates topological incongruence. [ABSTRACT FROM AUTHOR]

Prolamins, proteins derived from plants, have extensive applications in pharmaceutics and food science. Jiuzao is a byproduct of the Baijiu brewing industry, and is a great source of prolamin. Despite its importance, knowledge regarding the extraction techniques and the properties of prolamin derived from Baijiu Jiuzao (PBJ) remains limited. Reverse micelles (RMs) extraction offers an efficient and cost-effective method for purifying proteins. In the present study, prolamin was extracted from Baijiu Jiuzao using RMs extraction and subsequently characterized in terms of its secondary structure, morphology, and particle size distribution. Our findings indicate that the purified prolamin extracted using further RMs extraction possessed higher α-helix content (+13.25%), forming a large-scale protein network, and narrower particle size distributions compared to the crude prolamin obtained by NaOH-ethanol method. This research suggests that RMs extraction has potential applications in extracting prolamin from brewing industry byproducts, offering an environmentally friendly approach to Baijiu Jiuzao recycling. [ABSTRACT FROM AUTHOR]

Copyright of Science & Technology of Food Industry is the property of Science & Technology of Food Industry Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

N-capping (N-cap) and C-capping (C-cap) in biologically active peptides, including specific amino acids or unconventional group motifs, have been shown to modulate activity against pharmacological targets by interfering with the peptide's secondary structure, thus generating unusual scaffolds. The insertion of capping motifs in linear peptides has been shown to prevent peptide degradation by reducing its susceptibility to proteolytic cleavage, and the replacement of some functional groups by unusual groups in N- or C-capping regions in linear peptides has led to optimized peptide variants with improved secondary structure and enhanced activity. Furthermore, some essential amino acid residues that, when placed in antimicrobial peptide (AMP) capping regions, are capable of complexing metals such as Cu2+, Ni2+, and Zn2+, give rise to the family known as metallo-AMPs, which are capable of boosting antimicrobial efficacy, as well as other activities. Therefore, this review presents and discusses the different strategies for creating N- and C-cap motifs in AMPs, aiming at fine-tuning this class of antimicrobials. [ABSTRACT FROM AUTHOR]

The paper discusses experimental results concerning the probable inheritance of the secondary structure of the polypeptide chain of wool keratin used as a biotemplate by titanium dioxide through topochemical reaction and crystal nucleation during crystallization under hydrothermal conditions. Sheep wool fibers were impregnated with a solution containing titanium hydroxocomplexes. Samples of native wool, wool-TiO2 hybrid material, and TiO2 crystalline powders were characterized using X-ray diffraction, IR spectroscopy, thermal analysis (DSC and TG), and scanning electron microscopy. X-ray studies revealed that diffuse halos characteristic of the secondary structure of wool (containing α-spiral and β-folded keratin configurations) at 2θ = 8.7° and 19.6° are preserved both for hydrothermally impregnated wool and after annealing at 600°C and 800°C, albeit with a shift towards smaller angles of 2θ = 6.3° and 13.2°. This suggests stretching of keratin fibers during hydrothermal impregnation and preservation of crystallinity domains of the secondary structure in annealed samples, representing a mixture of well-crystallized phases of anatase and rutile. The interpretation of this effect is based on the assumption that TiO2 crystallization centers are located along the turns of the α-helix or folds of the β-structure, replicating these structures in a certain spatial arrangement. Nucleation is attributed to the interaction of monomeric forms of titanium hydroxocomplexes with carbonyl and carboxyl groups of the polypeptide chain, followed by growth of anatase and rutile crystallites via olation/oxolation reactions under hydrothermal conditions. [ABSTRACT FROM AUTHOR]

Terrestrial cyanobacteria are extremely diverse. In urban areas, they can be found as black stains on the surface of building walls, stone monuments, or man-made structures. Many of the terrestrial cyanobacteria are still understudied. To expand knowledge of terrestrial cyanobacterial diversity, a polyphasic characterization was performed to identify 12 strains isolated from campus of University of the Ryukyus, Okinawa, Japan. Multigene phylogenetic analyses based on 16S rRNA gene and 16S-23S rRNA internal transcribed spacer (ITS) region showed that the isolated strains formed two independent subclades within Nodosilinea, and were distantly related to all described Nodosilinea species. The 16S-23S rRNA ITS secondary structures showed variations for D1-D1' and Box B domain, while V3 domain was almost identical among entire species of Nodosilinea, including the studied strains. In addition, a unique morphological character, i.e. forming nodule or spiral shape, was also observed in certain studied strains. According to polyphasic characterization, Nodosilinea coculeatus sp. nov. and Nodosilinea terrestrialis sp. nov., were proposed as two new species of terrestrial cyanobacteria from Okinawa. [ABSTRACT FROM AUTHOR]

To enhance the value proposition of sweet potato and oat while broadening their applicability in further processing, this study systematically investigated the impact of oat flour incorporation ratios (5%–25% of sweet potato dry weight) on the quality attributes of sweet potato–oat composite dough and its resulting steamed cake products. The results showed that the addition of oat flour could promote the rheological, water retention, and thermomechanical properties of the composite dough and improve the internal microstructure, specific volume, texture, and other processing properties of the steamed cake products. The rheology, water retention, and protein stability of the dough were maximized when the proportion of oat flour was 25%. The textural properties of steamed cakes, hardness, elasticity, cohesion, adhesion, chewiness, and recovery significantly increased (p < 0.05) and viscosity significantly decreased (p < 0.05) with the addition of oat flour. It is noteworthy that thermodynamic properties, internal structure of the dough, and air holding capacity, which are critical for processing, showed the best results at 20% oat flour addition. Therefore, the addition of 20%–25% oats is recommended to produce composite doughs with optimal quality and processing characteristics. Practical Application: As living standards improve, traditional cereals may no longer able to meet people's health needs. Therefore, there is an urgent consumer demand for nutritious, tasty alternatives to staple foods. In this study, oat flour and sweet potato mash were mixed to make sweet potato–oat cake, and the effect of ingredient ratio on the performance and quality of composite dough containing sweet potato–oat flour was analyzed, thus proposing an innovative approach to the research, development, and industrial production of sweet potato and oat food products. [ABSTRACT FROM AUTHOR]

The effects of tea polyphenols (TPs) and antioxidant of bamboo leaves (AOB) on quinoa polypeptides (QPs) properties were investigated. Polyphenols induced structural changes, affected antioxidant and antibacterial properties of the polypeptides. The structural changes of QPs with polyphenols in all the composite samples were studied by Fourier transform infrared and fluorescence spectroscopy. ANS probe was used to analyze the surface hydrophobicity of QPs, particle size and potential were used to characterize the QPs-polyphenol particles. The fluorescence results showed that the intrinsic fluorescence of QPs was quenched and decreased with the increase of the number of polyphenols added, and the maximum emission wavelength was red-shifted. Secondary structure analysis showed that the percentage of /3-fold, a-helix and random coil of QPs decreased, while the percentage of /3-turn increased in all composite samples. When the ratio of QPs to TPs was 1"2, the percentages of /3-fold, a-spiral, random crimp and /3-corner were 43.58%, 17.20%, 12.92% and 26.30%, respectively. When the ratio of QPs to AOB was 1 #2, the percentages of /3-folding, "-helix, random curling and (3-corner were 49.60%, 14.99%, 9.79% and 25.62%, respectively. TPs significantly reduced the surface hy-drophobicity of QPs (P<0.05), When the ratio of QPs # TPs was 1 # 2, the fluorescence intensity of ANS decreased from 74.131.67AU to 62.141.36AU; but AOB had no significant effect on the surface hydrophobicity of QPs (P>0.05). In addition, the combination of QPs with TPs or AOB significantly improve the antioxidant activity and inhibitory activity of QPs against Escherichia coli and Staphylococcus aureus (P<0.05). These findings demonstrate the feasible application of TPs and AOB to improve the functional properties of QPs and the potential use of QPs -polyphenol composites in food ingredients and functional food systems' [ABSTRACT FROM AUTHOR]

The conjugation of proteins with polymers offers immense biotechnological potential by creating novel macromolecules. This article presents experimental findings on the structural properties of maltose‐binding protein (MBP) conjugated with linear biodegradable polyphosphoester polymers with different molecular weights. We studied isotopic effects on both proteins and polymers. Circular dichroism and fluorescence spectroscopy and small‐angle neutron scattering reveal that the conjugation process destabilizes the protein, affecting the secondary more than the tertiary structure, even at room temperature, and that the presence of two domains in the MBP may contribute to its observed instability. Notably, unfolding temperatures differ between native MBP and the conjugates. In particular, this study sheds light on the complex interplay of factors such as the deuteration influencing protein stability and conformational changes in the conjugation processes. The perdeuteration influences the hydrogen bond network and hydrophobic interactions in the case of the MBP protein. The perdeuteration of the protein influences the hydrogen bond network and hydrophobic interactions. This is evident in the decreased thermal stability of deuterated MBP protein, in the conjugate, especially with high‐molecular‐mass polymers. [ABSTRACT FROM AUTHOR]

Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated "rarity" measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with "Highway" versus "Meander" versus "Ambiguous" transitions and to design algorithms that can identify these same folding pathways and critical protein-water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein-water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape. [ABSTRACT FROM AUTHOR]

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RAMOSA1 (RA1) is a Cys2-His2-type (C2H2) zinc finger transcription factor that controls plant meristem fate and identity and has played an important role in maize domestication. Despite its importance, the origin of RA1 is unknown, and the evolution in plants is only partially understood. In this paper, we present a well-resolved phylogeny based on 73 amino acid sequences from 48 embryophyte species. The recovered tree topology indicates that, during grass evolution, RA1 arose from two consecutive SUPERMAN duplications, resulting in three distinct grass sequence lineages: RA1-like A, RA1-like B, and RA1; however, most of these copies have unknown functions. Our findings indicate that RA1 and RA1-like play roles in the nucleus despite lacking a traditional nuclear localization signal. Here, we report that copies diversified their coding region and, with it, their protein structure, suggesting different patterns of DNA binding and protein–protein interaction. In addition, each of the retained copies diversified regulatory elements along their promoter regions, indicating differences in their upstream regulation. Taken together, the evidence indicates that the RA1 and RA1-like gene families in grasses underwent subfunctionalization and neofunctionalization enabled by gene duplication. [ABSTRACT FROM AUTHOR]

Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation have been extensively researched. Although obtaining a protein in three-dimensional structure through experimental or computational methods enhances the accuracy of function prediction, the sheer volume of proteins sequenced by high-throughput technologies presents a significant challenge. To address this issue, we introduce a deep neural network model DeepSS2GO (Secondary Structure to Gene Ontology). It is a predictor incorporating secondary structure features along with primary sequence and homology information. The algorithm expertly combines the speed of sequence-based information with the accuracy of structure-based features while streamlining the redundant data in primary sequences and bypassing the time-consuming challenges of tertiary structure analysis. The results show that the prediction performance surpasses state-of-the-art algorithms. It has the ability to predict key functions by effectively utilizing secondary structure information, rather than broadly predicting general Gene Ontology terms. Additionally, DeepSS2GO predicts five times faster than advanced algorithms, making it highly applicable to massive sequencing data. The source code and trained models are available at https://github.com/orca233/DeepSS2GO. [ABSTRACT FROM AUTHOR]

Summary: This research was designed to examine the effects of activated carbon dosage and pH on various attributes of corn protein hydrolysate, including decolourization efficiency, nitrogen component, amino acid (AA) composition, protein secondary structure, and antioxidant activity. Optimal pigment elimination of occurred within the pH range of 2.0–4.0, utilising the hydrolysate as the control. Remarkably, the removal of trichloroacetic acid (TCA) insoluble peptide was evident at pH 4.0. The decolourization process elicited considerable reduction of the aromatic AA, exhibiting pronounced decreases of acidic AA (Glu and Asp) within the pH range of 2.0–4.0, and basic AA (His, Lys, and Arg) within the range of 6.0–8.0. Meanwhile, infrared spectroscopy analyses indicated that a dosage of 0.5% activated carbon at pH 4.0, effectively preserved the secondary structure and ratios of the control, maintaining its antioxidant activity. These results provide insights into optimisation strategies for decolourization in the food industry. [ABSTRACT FROM AUTHOR]

Peptides with antimicrobial activity or protease inhibitory activity are potential candidates to supplement traditional antibiotics or cancer chemotherapies. However, the potential of many peptides are limited by drawbacks such as cytotoxicity or susceptibility to hydrolysis. Therefore, strategies to modify the structure of promising peptides may represent an effective approach for developing more promising clinical candidates. In this study, the mature peptide OSTI−1949, a Kunitz-type inhibitor from Odorrana schmackeri, and four designed analogues were successfully synthesised. In contrast to the parent peptide, the analogues showed impressive multi-functionality including antimicrobial, anticancer, and trypsin inhibitory activities. In terms of safety, there were no obvious changes observed in the haemolytic activity at the highest tested concentration, and the analogue OSTI−2461 showed an increase in activity against cancer cell lines without cytotoxicity to normal cells (HaCaT). In summary, through structural modification of a natural Kunitz-type peptide, the biological activity of analogues was improved whilst retaining low cytotoxicity. The strategy of helicity enhancement by forming an artificial α-helix and ß-sheet structure provides a promising way to develop original bioactive peptides for clinical therapeutics. [ABSTRACT FROM AUTHOR]

Objective: The eukaryotic tree of life has been subject of numerous studies ever since the nineteenth century, with more supergroups and their sister relations being decoded in the last years. In this study, we reconstructed the phylogeny of eukaryotes using complete 18S rDNA sequences and their individual secondary structures simultaneously. After the sequence-structure data was encoded, it was automatically aligned and analyzed using sequence-only as well as sequence-structure approaches. We present overall neighbor-joining trees of 211 eukaryotes as well as the respective profile neighbor-joining trees, which helped to resolve the basal branching pattern. A manually chosen subset was further inspected using neighbor-joining, maximum parsimony, and maximum likelihood analyses. Additionally, the 75 and 100 percent consensus structures of the subset were predicted. Results: All sequence-structure approaches show improvements compared to the respective sequence-only approaches: the average bootstrap support per node of the sequence-structure profile neighbor-joining analyses with 90.3, was higher than the average bootstrap support of the sequence-only profile neighbor-joining analysis with 73.9. Also, the subset analyses using sequence-structure data were better supported. Furthermore, more subgroups of the supergroups were recovered as monophyletic and sister group relations were much more comparable to results as obtained by multi-marker analyses. [ABSTRACT FROM AUTHOR]

The effects of different types of acid coagulants and nano fish bone (NFB) additives on the characteristics of tofu were investigated using texture analyzers, SEM, FT‐IR, and other techniques. The breaking force and penetration distance, in descending order, were found in the tofu induced by glucono‐d‐lactone (GDL) (180.27 g and 0.75 cm), citric acid (152.90 g and 0.74 cm), lactic acid (123.33 g and 0.73 cm), and acetic acid (69.84 g and 0.58 cm), respectively. The syneresis of these tofu samples was in the reverse order (35.00, 35.66, 39.66, and 44.50%). Lightness and whiteness were not significantly different among the different samples. Regardless of the acid type, the soluble calcium content in the soybean milk was significantly increased after adding NFB. As a result, the breaking force and penetration distance of all tofu samples increased significantly, but the syneresis decreased. Compared with tofu coagulated by other acids, GDL tofu formed a more uniform and dense gel network maintained by the highest intermolecular forces (especially hydrophobic interactions). Regarding the secondary structure, the lowest percentage of α‐helix (22.72%) and, correspondingly, the highest β‐sheet (48.32%) and random coil (18.81%) were noticed in the GDL tofu. The effects of NFB on the tofu characteristics can be explained by the changes in the gel network, intermolecular forces, and secondary structure, which were in line with the acid type. The characteristics of acid‐induced tofu can be most synergistically improved by coagulation with GDL and NFB. [ABSTRACT FROM AUTHOR]

Content: Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. Methods: All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm. [ABSTRACT FROM AUTHOR]

There is a need to increase the consumption of whole wheat bread (WWB) due to its health benefits by overcoming its poor technological quality and improving its sensory characteristics. In this study, sourdough bread-making and frozen dough technology were combined to provide fresh WWB at any time with better quality. Also, it was aimed to investigate the effects of three types of sourdough (type I, II, and IV) on the final quality of WWB during frozen storage (−30 °C, 14 and 28 days). The tan δ of WWB with type I sourdough was highest at the end of the frozen storage. Freezable water content was lower on day 0 for WWB with type II and IV sourdough than other bread types. No significant effect of frozen storage was observed in bread types in terms of an α helix structure, except for WWB with type I sourdough. A lower hardness increment was shown in WWB with baker's yeast and WWB with type II sourdough over 14 days of frozen storage when compared to other bread types. WWB with type I sourdough and WWB with type IV sourdough were differentiated from other bread samples in volatile compound (VC) analysis on frozen storage days 28 and 0, respectively. The frozen storage of WWB with baker's yeast and WWB with type II sourdough caused no notable changes in the VCs profile. These results suggest that a less detrimental effect of frozen storage was observed in WWB with type II sourdough, indicating a more favorable choice for producing WWB with sourdough. [ABSTRACT FROM AUTHOR]

Abstract Spike (S) glycoprotein is the largest structural protein of SARS‐CoV‐2 virus and the main one involved in anchoring of the host receptor ACE2 through the receptor binding domain (RBD). S protein secondary structure is of great interest for shedding light on various aspects, from functionality to pathogenesis, finally to spectral fingerprint for the design of optical biosensors. In this paper, the secondary structure of SARS‐CoV‐2 S protein and its constituting components, namely RBD, S1 and S2 regions, are investigated at serological pH by measuring their amide I infrared absorption bands through Attenuated Total Reflection Infrared (ATR‐IR) spectroscopy. Experimental data in combination with MultiFOLD predictions, Define Secondary Structure of Proteins (DSSP) web server and Gravy value calculations, provide a comprehensive understanding of RBD, S1, S2, and S proteins in terms of their secondary structure content, conformational order, and interaction with the solvent.