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The native conformation of a protein plays a decisive role in ensuring its functionality. It is established that the spatial structure of proteins may exhibit a greater degree of conservation than the corresponding amino acid sequences. This study aims to clarify structural distinctions between homologous and non-homologous proteins with identical topology. The analysis focuses on secondary structures with special emphasis on their fraction, distribution along the polypeptide chain, and chirality. Three different groups of proteins with identical topology were considered according to the CATH database: a homologous group of Globins, a group of Phycocyanins, which is often considered as a potential relative of globins, and a diverse assembly of other globin-like proteins. Some structural patterns in the distribution of secondary structure have been identified within Globins. A similar profile was observed in Phycocyanins, in contrast to the third group. In addition, a distinguishable structural motif, including structures such as 310-helix and irregular structure, has been found in both Globins and Phycocyanins, which can be proposed as an evolutionary imprint.

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Embeddings from protein Language Models (pLMs) are replacing evolutionary information from multiple sequence alignments (MSAs) as the most successful input for protein prediction. Is this because embeddings capture evolutionary information? We tested various approaches to explicitly incorporate evolutionary information into embeddings on various protein prediction tasks. While older pLMs (SeqVec, ProtBert) significantly improved through MSAs, the more recent pLM ProtT5 did not benefit. For most tasks, pLM-based outperformed MSA-based methods, and the combination of both even decreased performance for some (intrinsic disorder). We highlight the effectiveness of pLM-based methods and find limited benefits from integrating MSAs.

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Effective circularization of mRNA molecules is a key step for the efficient initiation of translation. Research has shown that the intrinsic separation of the ends of mRNA molecules is rather small, suggesting that intramolecular arrangements could provide this effective circularization. Considering that the innate proximity of RNA ends might have important unknown biological implications, we aimed to determine whether the close proximity of the ends of mRNA molecules is a conserved feature across organisms and gain further insights into the functional effects of the proximity of RNA ends. To do so, we studied the secondary structure of 274 full native mRNA molecules from 17 different organisms to calculate the contour length (CL) of the external loop as an index of their end-to-end separation. Our computational predictions show bigger variations (from 0.59 to 31.8 nm) than previously reported and also than those observed in random sequences. Our results suggest that separations larger than 18.5 nm are not favored, whereas short separations could be related to phenotypical stability. Overall, our work implies the existence of a biological mechanism responsible for the increase in the observed variability, suggesting that the CL features of the exterior loop could be relevant for the initiation of translation and that a short CL could contribute to the stability of phenotypes.

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We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3'-untranslated region (3'-UTR) of SPINK1 as the cause of severe infantile isolated exocrine pancreatic insufficiency. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here, we aimed to elucidate these mechanisms through a hypothesis-driven approach. Initially, we speculated that, owing to its particular location, Alu_Ins could independently disrupt mRNA 3' end formation and/or affect other post-transcriptional processes such as nuclear export and translation. However, employing a 3'-UTR luciferase reporter assay, Alu_Ins was found to result in only an ∼50% reduction in luciferase activity compared to wild type, which is insufficient to account for the severe pancreatic deficiency in the Alu_Ins homozygote. We then postulated that double-stranded RNA (dsRNA) structures formed between Alu elements, an upstream mechanism regulating gene expression, might be responsible. Using RepeatMasker, we identified two Alu elements within SPINK1's third intron, both oriented oppositely to Alu_Ins. Through RNAfold predictions and full-length gene expression assays, we investigated orientation-dependent interactions between these Alu repeats. We provide compelling evidence to link the detrimental effect of Alu_Ins to extensive dsRNA structures formed between Alu_Ins and pre-existing intronic Alu sequences, including the restoration of SPINK1 mRNA expression by aligning all three Alu elements in the same orientation. Given the widespread presence of Alu elements in the human genome and the potential for new Alu insertions at almost any locus, our findings have important implications for detecting and interpreting Alu insertions in disease genes.

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Common vetch protein, similar to pea protein, offers valuable qualities like being non-GMO, hypoallergenic, and nutritious. However, its strong beany flavor hinders consumer acceptance. This study explores enzymatic deamidation using glutaminase to address this issue. GC-MS analysis identified 54 volatile compounds in the raw material protein, with 2-pentylfuran, hexanal, and several nonenals contributing the most to the undesirable aroma. Principal component analysis (PCA) confirmed the effectiveness of glutaminase deamidation in removing these off-flavors. The study further reveals that deamidation alters the protein's secondary structure, with an increase in α - helix structure and a decrease in ß - sheet structure. The surface hydrophobicity increased from 587.33 ± 2.63 to 1855.63 ± 3.91 exposing hydrophobic clusters that bind flavor compounds. This disruption weakens the interactions that trap these undesirable flavors, ultimately leading to their release and a more pleasant aroma. These findings provide valuable insights for enzymatic deodorization of not only common vetch protein but also pea protein.

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The Ebola delta peptide is an amphipathic, 40-residue peptide encoded by the Ebola virus, referred to as E40. The membrane-permeabilising activity of the E40 delta peptide has been demonstrated in cells and lipid vesicles suggesting the E40 delta peptide likely acts as a viroporin. The lytic activity of the peptide increases in the presence of anionic lipids and a disulphide bond in the C-terminal part of the peptide. Previous in silico work predicts the peptide to show a partially helical structure, but there is no experimental information on the structure of E40. Here, we use circular dichroism spectroscopy to report the secondary structure propensities of the reduced and oxidised forms of the E40 peptide in water, detergent micelles, and lipid vesicles composed of neutral and anionic lipids (POPC and POPG, respectively). Results indicate that the peptide is predominately a random coil in solution, and the disulphide bond has a small but measurable effect on peptide conformation. Secondary structure analysis shows large uncertainties and dependence on the reference data set and, in our system, cannot be used to accurately determine the secondary structure motifs of the peptide in membrane environments. Nevertheless, the spectra can be used to assess the relative changes in secondary structure propensities of the peptide depending on the solvent environment and disulphide bond. In POPC-POPG vesicles, the peptide transitions from a random coil towards a more structured conformation, which is even more pronounced in negatively charged SDS micelles. In vesicles, the effect depends on the peptide-lipid ratio, likely resulting from vesicle surface saturation. Further experiments with zwitterionic POPC vesicles and DPC micelles show that both curvature and negatively charged lipids can induce a change in conformation, with the two effects being cumulative. Electrostatic screening from Na+ ions reduced this effect. The oxidised form of the peptide shows a slightly lower propensity for secondary structure and retains a more random coil conformation even in the presence of PG-PC vesicles.

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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 ß-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. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-024-05973-7.

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Recombinant spider silk protein (RSP) is a promising biomaterial for developing high-performance materials independent of fossil fuels. In this study, we investigated the influence of the initial secondary structure of RSPs on the properties of RSP-based hydrogels. By altering the initial structure of RSP to ß-sheets (ß-RSP), α-helices (α-RSP), and random coils (rc-RSP) through solvent treatment, we compared the structures and mechanical properties of the resulting gels. Solid-state NMR revealed a ß-sheet-rich structure in all gels, with the α-RSP gel exhibiting significantly higher strength and Young's modulus compared to the rc-RSP gel. X-ray diffraction revealed that the α-RSP gel had a unique crystalline structure, distinguishing it from the ß-RSP and rc-RSP gels. The different initial secondary structures possibly lead to variations in the crystalline and network structures of the molecular chains within the gels, explaining the superior mechanical properties observed in the α-RSP gels.

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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.

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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.

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The saline wastewater produced in industrial activities and seawater use would flow into wastewater treatment plants and affect the characteristic of extracellular polymeric substance (EPS) of activated sludge, which could potentially impact the removal of antibiotics via adsorption. Nonetheless, the effect of salinity on trimethoprim adsorption by activated sludge extracellular polymeric substances at trace concentration and the underlying mechanism remain largely unknown. In this study, the effect of salinity on the adsorption removal of a typical antibiotic, i.e., trimethoprim (TMP) at trace concentration (25.0 µg/L) was evaluated. The results showed the content of EPS was decreased significantly from 56.36 to 21.70 mg/g VSS when the salinity was increased from 0 to 10 g/L. Protein fractions occupied the predominant component of EPS, whose concentration was decreased from 38.17 to 12.83 mg/g VSS. The equilibrium adsorption capacity of activated sludge for TMP was decreased by 49.70% (from 4.97 to 2.50 µg/g VSS). The fluorescence quenching results indicated the fluorescence intensity of tryptophan-like substances was decreased by 30% and the adsorption sites of EPS were decreased from 0.51 to 0.21 when the salinity was increased. The infrared spectrum and XPS results showed that the nitrogen-containing groups from protein were decreased significantly. The circular dichroic analysis showed α helix structure of protein in EPS was decreased with the increase of salinity, which was responsible for the decrease of adsorption capacity for TMP.

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BACKGROUND: Ventricular septal defect (VSD) is the most common congenital heart disease. Although a small number of genes associated with VSD have been found, the genetic factors of VSD remain unclear. In this study, we evaluated the association of 10 candidate single nucleotide polymorphisms (SNPs) with isolated VSD in a population from Southwest China. METHODS: Based on the results of 34 congenital heart disease whole-exome sequencing and 1000 Genomes databases, 10 candidate SNPs were selected. A total of 618 samples were collected from the population of Southwest China, including 285 VSD samples and 333 normal samples. Ten SNPs in the case group and the control group were identified by SNaPshot genotyping. The chi-square (χ2) test was used to evaluate the relationship between VSD and each candidate SNP. The SNPs that had significant P value in the initial stage were further analysed using linkage disequilibrium, and haplotypes were assessed in 34 congenital heart disease whole-exome sequencing samples using Haploview software. The bins of SNPs that were in very strong linkage disequilibrium were further used to predict haplotypes by Arlequin software. ViennaRNA v2.5.1 predicted the haplotype mRNA secondary structure. We evaluated the correlation between mRNA secondary structure changes and ventricular septal defects. RESULTS: The χ2 results showed that the allele frequency of FLT4 rs383985 (P = 0.040) was different between the control group and the case group (P < 0.05). FLT4 rs3736061 (r2 = 1), rs3736062 (r2 = 0.84), rs3736063 (r2 = 0.84) and FLT4 rs383985 were in high linkage disequilibrium (r2 > 0.8). Among them, rs3736061 and rs3736062 SNPs in the FLT4 gene led to synonymous variations of amino acids, but predicting the secondary structure of mRNA might change the secondary structure of mRNA and reduce the free energy. CONCLUSIONS: These findings suggest a possible molecular pathogenesis associated with isolated VSD, which warrants investigation in future studies.

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This research examined the impact of defatted coconut flour (DCF)-based oleogels on the quality of surimi. Microscopic analysis indicated that the dietary fiber present in DCF could act as the main structure of the oleogels network. The formation of the oleogels network primarily relies on the tensile intramolecular or intermolecular hydrogen bonds between DCF and corn oil. The oleogels displayed oil binding capacity of up to 96.95% and exhibited favorable mechanical and rheological properties. Efforts were undertaken to integrate the acquired oleogels into silver carp surimi to create oil-fortified surimi products. Adding oleogels significantly enhanced the gel strength, texture, and water-holding capacity of surimi compared to adding corn oil. Especially, oleogels containing 5.0 % (w/v) DCF concentration elevated the lipid content in the surimi and preserved the gel and texture properties. Therefore, incorporating oleogels in surimi presents a potential solution for enhancing the nutritional content of surimi products.

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Secondary structure refers to highly regular local sub-structures formed by the polypeptide backbone through hydrogen bonding. The two main types of secondary structures are α-helices and ß-strands (which can form ß-sheets). The development of a robust circular dichroism (CD) method for structural analysis of biomolecules requires careful consideration of several key factors. Solvent selection plays a crucial role in maintaining the native or desired conformation of the sample while ensuring transparency in the relevant wavelength regions. Aqueous buffers are often preferred for studying proteins in their native state. Optimizing the sample concentration and path length is essential to achieve an optimal absorbance range and maximize the signal-to-noise ratio. Typical concentrations for far-UV CD measurements range from 0.1 to 1 mg/ml, with shorter path lengths (1 mm) allowing for higher concentrations and longer path lengths (5 mm) suitable for dilute solutions. Instrumental parameters, such as scanning speed, accumulations, and nitrogen flow rate, significantly impact the quality and reliability of the acquired CD spectra. Data processing is a critical step in obtaining accurate and interpretable CD spectra. Baseline correction, smoothing, and conversion to mean residue ellipticity are essential for reliable secondary structure analysis.

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G-quadruplexes (G4s) form throughout the genome and influence important cellular processes. Their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected role for the double-stranded DNA (dsDNA) translocase helicase-like transcription factor (HLTF) in responding to G4s. We show that HLTF, which is enriched at G4s in the human genome, can directly unfold G4s in vitro and uses this ATP-dependent translocase function to suppress G4 accumulation throughout the cell cycle. Additionally, MSH2 (a component of MutS heterodimers that bind G4s) and HLTF act synergistically to suppress G4 accumulation, restrict alternative lengthening of telomeres, and promote resistance to G4-stabilizing drugs. In a discrete but complementary role, HLTF restrains DNA synthesis when G4s are stabilized by suppressing primase-polymerase (PrimPol)-dependent repriming. Together, the distinct roles of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.

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Traditionally, the order Ulotrichales comprised green algae of an unbranched, uniseriate, filamentous morphology. However, since the establishment of ultrastructural features, the circumscription of this order has dramatically changed. Some genera and species have been excluded from this order and others with different morphologies (sarcinoid, branched filaments or even parenchymatous taxa) have been included. Phylogenetic analyses have confirmed the monophyly of this order, but its differentiation from the Ulvales and Acrosiphoniales remains difficult because of the lack of synapomorphies at every level (morphology, molecular signatures). To demonstrate the difficulties of placement into genera and orders, we investigated two sarcinoid taxa with the absence of zoospore formation. SSU and ITS rDNA tree topology and the ITS-2/CBC approach revealed that both strains SAG 2661 and CCAP 312/1 belong to Ulosarcina terrestrica and the newly erected genus Caulinema, respectively. The species conception using this approach was evaluated by sequencing the plastid-coding gene tufA, a commonly used barcode marker for green algae. All three molecular markers resulted in similar topologies at the generic and species levels, which is consistent with the ITS-2/CBC approach and tufA for barcoding. The reevaluation of the ultrastructural features revealed that the presence of organic scales on the surfaces of motile cells is characteristic for the order Ulotrichales and can be used for separation from the closely related orders. As a consequence of our study, we propose the new genus Caulinema for strain CCAP 312/1.

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Antifreeze peptide (AFP) including in frozen protein ink is an inevitable trend because AFP can make protein ink suitable for 3D printing after freezing. AFP-based surimi ink (ASI) was firstly investigated, and the AFP significantly enhanced 3D printability of frozen surimi ink. The rheological and textural results of ASI show that the τ0, K, and n values are 321.14 Pa, 2.2259 × 105 Pa·sn, and 0.19, respectively, and the rupture strength of the 3D structure is up to 217.67 g. Circular dichroism, intermolecular force, and differential scanning calorimeter show ASI has more undenatured protein after freezing when compared that surimi ink (SI), which was denatured, and the α-helix changed to a ß-sheet due to the destruction of hydrogen bonds and the exposure of hydrophobic groups. The water distribution, water holding capacity, and microstructure indicate that ASI effectively binds free water after freezing, while SI has weak water binding capacity and a large amount of free water is formed. ASI is suitable for 3D printing, and can print up to 40.0 mm hollow isolation column and 50.0 mm high Wuba which is not possible with SI. The application of AFP provides guidance for 3D printing frozen protein ink in food industry.

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Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

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Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.

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Proteins have recently caught attention as potential excipients for amorphous solid dispersions (ASDs) to improve oral bioavailability of poorly water-soluble drugs. Notably, the studies have highlighted whey protein isolates, particularly ß-lactoglobulin (BLG), as promising candidates in amorphous stabilization, dissolution and solubility enhancement, achieving drug loadings of 50 wt% and higher. Consequently, investigations into the mechanisms underlying the solid-state stabilization of amorphous drugs and the enhancement of drug solubility in solution have been conducted. This graphical review provides a comprehensive overview of recent findings concerning BLG-based ASDs. Firstly, the dissolution performance of BLG-based ASDs is compared to more traditional polymer-based ASDs. Secondly, the drug loading onto BLG and the resulting amorphous stabilization mechanisms is summarized. Thirdly, interactions between BLG and drug molecules in solution are described as the mechanisms governing the improvement of drug solubility. Lastly, we outline the impact of the spray drying process on the secondary structure of BLG, and the resulting differences in amorphous stabilization and drug dissolution performance between α-helix-rich and ß-sheet-rich BLG-based ASDs.

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