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A substantial body of literature, including our own, points to a connection between hepatitis B virus (HBV) infection and the development of drug resistance in hepatocellular carcinoma (HCC), particularly against sorafenib. However, the influence of HBV on resistance to regorafenib, another therapeutic agent, has been less studied. In this study, we used the GEO database (GSE87630) and clinical samples to demonstrate that C‐C motif chemokine receptor 9 (CCR9) was highly expressed in HBV‐related HCC and predicted poor overall survival. Its overexpression correlated with HBsAg‐positive HCC patients. Both univariate and multivariable Cox regression analysis elucidated CCR9 was an independent risk factor for poor overall survival in HCC patients. Our in vitro findings further revealed that HBV structural proteins, small HBV surface antigen (SHBs), triggered an upregulation of CCR9. Functional assays showed that SHBs enhanced HCC cell proliferation, migration, and invasion, increased ABCB1 and ABCC1 expression, and promoted regorafenib resistance via CCR9. Intriguingly, overexpression of HBV plasmid and an AAV‐HBV mouse model both exhibited a significant elevation in global N6‐methyladenosine (m6A) levels. Further investigations revealed that SHBs elevated these m6A levels, upregulated CCR9 and stabilized CCR9 mRNA through KIAA1429‐mediated m6A modification, with sites 1373 and 1496 on CCR9 mRNA being critical for modification. In conclusion, SHBs promoted HCC progression and regorafenib resistance via KIAA1429‐mediated m6A modification of CCR9. Our findings suggested that CCR9 could be a potential prognostic biomarker and a valuable molecular therapeutic target of regorafenib resistance in HBV‐related HCC. [ABSTRACT FROM AUTHOR]

This study investigates the influences and environmental preferences of amide–π interactions, a relatively unexplored class of charge-free interactions, in oligomeric phycocyanins. In a data set of 20 proteins, we observed 2086 amide–π interactions, all of which were part of the protein backbone. Phe and Tyr residues were found to be involved in amide–π interactions more frequently than Trp or His. The most favorable amide–π interactions occurred within a pair distance range of 5–7 Å, with a distinct angle preference for T-shaped ring arrangements. Multiple interaction patterns suggest that approximately 76% of the total interacting residues participate in multiple amide–π interactions. Our ab initio calculations revealed that most amide–π interactions have energy from 0 to −2 kcal/mol. Stabilization centers of phycocyanins showed that all residues in amide–π interactions play a crucial role in locating one or more such centers. Around 78% of the total interacting residues in the dataset contribute to creating hot-spot regions. Notably, the amide–π interacting residues were found to be highly evolutionarily conserved. These findings enhance our understanding of the structural stability and potential for protein engineering of phycocyanins used as bioactive natural colorants in various industries, including food and pharmaceuticals. [ABSTRACT FROM AUTHOR]

[Display omitted] Folded protein hydrogels are emerging as promising new materials for medicine and healthcare applications. Folded globular proteins can be modelled as colloids which exhibit site specific cross-linking for controlled network formation. However, folded proteins have inherent mechanical stability and unfolded in response to an applied force. It is not yet understood how colloidal network theory maps onto folded protein hydrogels and whether it models the impact of protein unfolding on network properties. To address this, we study a hybrid system which contains folded proteins (patchy colloids) and unfolded proteins (biopolymers). We use a model protein, bovine serum albumin (BSA), to explore network architecture and mechanics in folded protein hydrogels. We alter both the photo-chemical cross-linking reaction rate and the mechanical properties of the protein building block, via illumination intensity and redox removal of robust intra-protein covalent bonds, respectively. This dual approach, in conjunction with rheological and structural techniques, allows us to show that while reaction rate can 'fine-tune' the mechanical and structural properties of protein hydrogels, it is the force-lability of the protein which has the greatest impact on network architecture and rigidity. To understand these results, we consider a colloidal model which successfully describes the behaviour of the folded protein hydrogels but cannot account for the behaviour observed in force-labile hydrogels containing unfolded protein. Alternative models are needed which combine the properties of colloids (folded proteins) and biopolymers (unfolded proteins) in cross-linked networks. This work provides important insights into the accessible design space of folded protein hydrogels without the need for complex and costly protein engineering, aiding the development of protein-based biomaterials. [ABSTRACT FROM AUTHOR]

Disulfide bonds in proteins are strong chemical bonds forming the secondary and tertiary structure like in the dairy protein β -lactoglobulin. We hypothesize that the partial or complete removal of disulfide bonds affects the structural rearrangement of proteins caused by intra- and intermolecular interactions that in turn define the interfacial activity of proteins at oil/water interfaces. The experimental and numerical investigations contribute to the mechanistic understanding of the structure-function relationship, especially for the interfacial adsorption behavior of proteins. Systematically, the 5 cysteines of β -lactoglobulin were recombinantly exchanged by alanine. First, the protein structure of the variants in bulk was analyzed with Fourier-transform-infrared-spectroscopy and molecular dynamic simulations. Second, the structural changes after adsorption to the interface have been also analyzed by molecular dynamic simulations. The adsorption behavior was investigated by pendant drop analysis and the interfacial film properties by dilatational rheology. The structural flexibility of β -lactoglobulin with no cysteines encourages its unfolding at the interface, and accelerates the interfacial protein film formation that results in more visco-elastic films in comparison to the reference.   • Partial deletion of disulfide bonds weakens the protein structure. • Partial deletion of surface disulfide bonds accelerates adsorption and increases film stability. • Complete deletion of disulfide bonds increases α -helix and unfolding at the interface. • Complete deletion of disulfide bonds increases flexibility and promotes adsorption at the interface. • Deletion of a single cysteine that contributes to a disulphide bond creates new stabilization mechanisms. [ABSTRACT FROM AUTHOR]

Background: Nephronophthisis (NPH) comprises a heterogeneous group of inherited renal ciliopathies clinically characterized by progressive kidney failure. So far, definite diagnosis is based on molecular testing only. Here, we studied the feasibility of NPHP1 and NPHP4 immunostaining of nasal epithelial cells to secure and accelerate the diagnosis of NPH. Methods: Samples of 86 individuals with genetically determined renal ciliopathies were analyzed for NPHP1 localization using immunofluorescence microscopy (IF). A sub-cohort of 35 individuals was also analyzed for NPHP4 localization. Western blotting was performed to confirm IF results. Results: NPHP1 and NPHP4 were both absent in all individuals with disease-causing NPHP1 variants including one with a homozygous missense variant (c.1027G > A; p.Gly343Arg) formerly classified as a "variant of unknown significance." In individuals with an NPHP4 genotype, we observed a complete absence of NPHP4 while NPHP1 was severely reduced. IF results were confirmed by immunoblotting. Variants in other genes related to renal ciliopathies did not show any impact on NPHP1/NPHP4 expression. Aberrant immunostaining in two genetically unsolved individuals gave rise for a further genetic workup resulting in a genetic diagnosis for both with disease-causing variants in NPHP1 and NPHP4, respectively. Conclusions: IF of patient-derived respiratory epithelial cells may help to secure and accelerate the diagnosis of nephronophthisis—both by verifying inconclusive genetic results and by stratifying genetic diagnostic approaches. Furthermore, we provide in vivo evidence for the interaction of NPHP1 and NPHP4 in a functional module. [ABSTRACT FROM AUTHOR]

Dr. Harish Chandra Pant was Chief of the Section on Neuronal Cytoskeletal Protein Regulation within the National Institute of Neurological Disorders and Stroke at the NIH. A main focus of his group was understanding the mechanisms regulating neuronal cytoskeletal phosphorylation. Phosphorylation of neurofilaments can increase filament stability and confer resistance to proteolysis, but aberrant hyperphosphorylation of neurofilaments can be found in the neurofibrillary tangles that are seen with neurodegenerative diseases like Alzheimer disease (AD). Through his work, Harish would inevitably come across cyclin dependent kinase 5 (Cdk5), a key kinase that can phosphorylate neurofilaments at KSPXK motifs. Cdk5 differs from other Cdks in that its activity is mainly in post-mitotic neurons rather than being involved in the cell cycle in dividing cells. With continued interest in Cdk5, Harish and his group were instrumental in identifying important roles for this neuronal kinase in not only neuronal cytoskeleton phosphorylation but also in neuronal development, synaptogenesis, and neuronal survival. Here, we review the accomplishments of Harish in characterizing the functions of Cdk5 and its involvement in neuronal health and disease. [ABSTRACT FROM AUTHOR]

The generalized Langevin mode analysis (GLMA) is applied to chemical reactions in biomolecules in solution. The theory sees a chemical reaction in solution as a barrier-crossing process, similar to the Marcus theory. The barrier is defined as the crossing point of two free-energy surfaces that are attributed to the reactant and product of the reaction. It is assumed that both free-energy surfaces are quadratic or harmonic. The assumption is based on the Kim-Hirata theory of structural fluctuation of protein, which proves that the fluctuation around an equilibrium structure is quadratic with respect to the structure or atomic coordinates. The quadratic surface is a composite of many harmonic functions with different modes or frequencies. The height of the activation barrier will be dependent on the mode or frequency—the less the frequency, the lower the barrier. Hence, it is essential to decouple the fluctuational modes into a hierarchical order. GLMA is impeccable for this purpose. It is essential for a theoretical study of chemical reactions to choose a reaction coordinate along which the reaction proceeds. We suppose that the mode whose center of coordinate and/or the frequency changes most before and after the reaction is the one relevant to the chemical reaction and choose the coordinate as the reaction coordinate. The rate of reaction along the reaction coordinate is k rate = ν ⁡ exp − Δ F (†) / k B T , which is similar to the Marcus expression for the electron transfer reaction. In the equation, ΔF(†) is the activation barrier defined by Δ F (†) ≡ F (r) Q † − F (r) ( Q e q (r) ) , where F (r) ( Q e q (r) ) and F (r) Q † denote the free energies at equilibrium Q e q (r) and the crossing point Q†, respectively, both on the free energy surface of the reactant. [ABSTRACT FROM AUTHOR]

Introduction Methods and Results Conclusion The filamins are cytoskeletal binding proteins that dynamically crosslink actin into orthogonal networks or bundle it into stress fibres. The domain structure of filamin proteins is very well characterised, with an N‐terminal actin‐binding region, followed by 24 immunoglobulin‐like repeat units. The repeat domains are separated into distinct segments by two regions of low‐complexity known as hinge‐1 and hinge‐2. The role of hinge‐1 especially has been proposed to be essential for protein function as it provides flexibility to the otherwise rigid protein, and is a target for cleavage by calpain. Hinge‐1 protects cells from otherwise destructive forces, and the products of calpain cleavage are involved in critical cellular signalling processes, such as survival during hypoxia. Pathogenic variants in FLNA encoding Filamin A, including those that remove the hinge‐1 domain, cause a wide range of survivable developmental disorders. In contrast, complete loss of function of this gene is embryonic lethal in human and mouse.In this study, we show that removing filamin A hinge‐1 from mouse (FlnaΔH1), while preserving its expression level leads to no obvious developmental phenotype. Detailed characterisation of the skeletons of FlnaΔH1 mice showed no skeletal phenotype reminiscent of that found in the FLNA‐causing skeletal dysplasia. Furthermore, nuclear functions of FLNA are maintained with loss of Filamin A hinge‐1.We conclude that hinge‐1 is dispensable for filamin A protein function during development over the murine lifespan. [ABSTRACT FROM AUTHOR]

Ubiquitination is a crucial post-translational modification of proteins that mediates the degradation or functional regulation of specific proteins. This process participates in various biological processes such as cell growth, development, and signal transduction. E3 ubiquitin ligases play both positive and negative regulatory roles in osteogenesis and differentiation by ubiquitination-mediated degradation or stabilization of transcription factors, signaling molecules, and cytoskeletal proteins. These activities affect the proliferation, differentiation, survival, and bone formation of osteoblasts (OBs). In recent years, advances in genomics, transcriptomics, and proteomics have led to a deeper understanding of the classification, function, and mechanisms of action of E3 ubiquitin ligases. This understanding provides new insights and approaches for revealing the molecular regulatory mechanisms of bone formation and identifying therapeutic targets for bone metabolic diseases. This review discusses the research progress and significance of the positive and negative regulatory roles and mechanisms of E3 ubiquitin ligases in the process of osteogenic differentiation. Additionally, the review highlights the role of E3 ubiquitin ligases in bone-related diseases. A thorough understanding of the role and mechanisms of E3 ubiquitin ligases in osteogenic differentiation could provide promising therapeutic targets for bone tissue engineering based on stem cells. [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]

Background: Increasing evidence shows the pivotal significance of miRNAs in the pathogenesis of osteoporosis. miR-381-3p has been identified as an inhibitor of osteogenesis. This study explored the role and mechanism of miR-381-3p in postmenopausal osteoporosis (PMOP), the most common type of osteoporosis. Methods: Bilateral ovariectomy (OVX) rat model was established and miR-381-3p antagomir was administrated through the tail vein in vivo. The pathological changes in rats were assessed through the evaluation of serum bone turnover markers (BALP, PINP, and CTX-1), hematoxylin and eosin (H&E) staining, as well as the expression of osteoblast differentiation biomarkers. Moreover, isolated bone marrow mesenchymal stem cells from OVX-induced rats (OVX-BMMSCs) were utilized to explore the impact of miR-381-3p on osteoblast differentiation. In addition, the target gene and downstream pathway of miR-381-3p were further investigated both in vivo and in vitro. Results: miR-381-3p expression was elevated, whereas KLF5 was suppressed in OVX rats. miR-381-3p antagomir decreased serum levels of bone turnover markers, improved trabecular separation, promoted osteoblast differentiation biomarker expression in OVX rats. ALP activity and mineralization were suppressed, and levels of osteoblast differentiation biomarkers were impeded after miR-381-3p overexpression during osteoblast differentiation of OVX-BMMSCs. While contrasting results were found after inhibition of miR-381-3p. miR-381-3p targets KLF5, negatively affecting its expression as well as its downstream Wnt/β-catenin pathway, both in vivo and in vitro. Silencing of KLF5 restored Wnt/β-catenin activation induced by miR-381-3p antagomir. Conclusion: miR-381-3p aggravates PMOP by inhibiting osteogenic differentiation through targeting KLF5/Wnt/β-catenin pathway. miR-381-3p appears to be a promising candidate for therapeutic intervention in PMOP. [ABSTRACT FROM AUTHOR]

Human hair is a filament rich in protein that grows from the follicles present in the scalp. It is considered to be a notable biomaterial consisting of β-keratin, which shows excellent catalytic activity in organic transformation. Keratin is a family of structural fibrous proteins rich in cysteine, which are abundantly present in human hair. Based on the template synthesis strategy, human-hair Keratin was used as a platform template to synthesise metal oxide nanoparticles. Here the aim was to synthesis hair protein supported CuO nanoparticles (HHP/CuONPs) and study their catalytic applications. Protein is extracted from the hair sample using the Shindai method. The HHP/CuONPs sample has been scrutinised using various characterisation techniques such as UV, FT-IR, SEM, TEM, EDX, Raman, XPS, and zeta potential. The synthesised HHP/CuONPs show photo-catalytic efficiency against coloured organic pollutants, 2,4-Dinitrophenol (DNP), and amaranth dye. The degradation level has been found to be 96% in DNP and 94% in amaranth dye. Optimisation and reusability of hair protein-mediated copper oxide have been tested under various conditions. [ABSTRACT FROM AUTHOR]

Caveolin is a structural protein within caveolae that may be involved in transmembrane molecular transport and/or various intercellular interactions within cells. Specific mutations of caveolin-3 in muscle fibers are well known to cause limb–girdle muscular dystrophy. Altered expression of caveolin-3 has also been detected in Duchenne muscular dystrophy, which may be a part of the pathological process leading to muscle weakness. Interestingly, it has been shown that the renovation of nitric oxide synthase (NOS) in sarcolemma with muscular dystrophy could improve muscle health, suggesting that NOS may be involved in the pathology of muscular dystrophy. Here, we summarize the notable function of caveolin and/or NOS in skeletal muscle fibers and discuss their involvement in the pathology as well as possible tactics for the innovative treatment of muscular dystrophies. [ABSTRACT FROM AUTHOR]

Human cancers express altered levels of actin-binding cytoskeletal filamin A (FLNA) protein. FLNA in mammals consists of an actin-binding domain at its N-terminus that is followed by 24 immunoglobulin-like repeat modules interrupted by two hinge regions between repeats 15–16 and 23–24. Cleavage of these hinge regions produces a naturally occurring C-terminal 90 kDa fragment of FLNA (FLNACT) that physically interacts with multiple proteins with diverse functions. This cleavage leads to actin cytoskeleton remodeling, which in turn contributes to cellular signaling, nucleocytoplasmic shuttling of transcriptional factors and nuclear receptors, and regulation of their transcriptional activities that are important for initiation and progression of cancers. Therefore, recent studies have proposed blocking FLNA cleavage as a means of cancer therapy. Here, we update how FLNA cleavage has been targeted by different approaches and their potential implications for future treatment of human cancers. [ABSTRACT FROM AUTHOR]

The SP/KLF family of transcription factors harbour three C-terminal C2H2 zinc fingers interspersed by two linkers which confers DNA-binding to a 9-10 bp motif. Mutations in KLF1, the founding member of the family, are common. Missense mutations in linker two result in a mild phenotype. However, when co-inherited with loss-of-function mutations, they result in severe non-spherocytic hemolytic anemia. We generate a mouse model of this disease by crossing Klf1+/− mice with Klf1H350R/+ mice that harbour a missense mutation in linker-2. Klf1H350R/− mice exhibit severe hemolysis without thalassemia. RNA-seq demonstrate loss of expression of genes encoding transmembrane and cytoskeletal proteins, but not globins. ChIP-seq show no change in DNA-binding specificity, but a global reduction in affinity, which is confirmed using recombinant proteins and in vitro binding assays. This study provides new insights into how linker mutations in zinc finger transcription factors result in different phenotypes to those caused by loss-of-function mutations. Mutations in linker 2 of KLF1 are identified in cases of non-spherocytic hemolytic anemia. Here, the authors show the molecular mechanisms of disease due to linker 2 mutation in mice using ChIPseq and RNAseq. [ABSTRACT FROM AUTHOR]

The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore's electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A'α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A'α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs. Here, the authors provide mechanistic insight into light-induced dimerization of a Light-Oxygen-Voltage (LOV) domain using time-resolved X-ray liquidography, furthering our understanding LOV domain photoactivation and protein-protein interaction-driven oligomerization. [ABSTRACT FROM AUTHOR]

Viral infections usually induce the rearrangement of cellular cytoskeletal proteins and organelle membrane structures, thus creating independent compartments [termed replication organelles (ROs)] to facilitate viral genome replication. Within the ROs, viral replicases, including polymerases, helicases, and ligases, play functional roles during viral replication. These viral replicases are pivotal in the virus life cycle, and numerous studies have demonstrated that the viral replicases could be the potential targets for drugs development. Here, we summarize primarily the key replicases within viral ROs and emphasize the advancements of antiviral drugs targeting crucial viral replicases, providing novel insights into the future development of antiviral strategies. [ABSTRACT FROM AUTHOR]

Transglutaminase 2 (TG2) is a GTP-binding, protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that bind and stabilize the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotides bind and stabilize a monomeric closed conformation while calcium binds to an open state that can form higher order oligomers. SAXS analysis suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time resolved SAXS to show that LM11 increases the ability of calcium to bind and stabilize an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state. A structural study of the protein crosslinking enzyme tissue transglutaminase (TG2), combining time-resolved SAXS and cryo-EM approaches, details the mechanisms by which TG2 responds to activating calcium ions or to a small-molecule inhibitor. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION The objective of this experiment was to investigate the role of endogenous proteins and lipids in the structural and physicochemical properties of starch in heat‐moisture treatment (HMT) rice flour and to reveal their effect on starch digestibility under heat.The findings indicate that, in the absence of endogenous proteins and lipids acting as a physical barrier, especially proteins, the interaction between rice flour and endogenous proteins and lipids diminished. This reduction led to fewer starch–protein inclusion complexes and starch–lipid complexes, altering the granule aggregation structure of rice flour. It resulted in a decrease in particle size, an increase in agglomeration between starch granules, and more surface cracking on rice granules. Under HMT conditions with a moisture content of 30%, slight gelatinization of the starch granules occurred, contributing to an increased starch hydrolysis rate. In addition, the elevated thermal energy effect of HMT enhanced interactions between starch molecular chains. These resulted in a decrease in crystallinity, short‐range ordering, and the content of double‐helix structure within starch granules. These structural transformations led to higher pasting temperatures, improved hot and cold paste stability, and a decrease in peak viscosity, breakdown, setback, and enthalpy of pasting of the starch granules.The combined analysis of microstructure, physicochemical properties, and in vitro digestion characteristics has enabled us to further enhance our understanding of the interaction mechanisms between endogenous proteins, lipids, and starches during HMT. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Chikungunya virus (CHIKV), a single-stranded RNA virus transmitted by Aedes mosquitoes, poses a significant global health threat, with severe complications observed in vulnerable populations. The only licensed vaccine, IXCHIQ, approved by the US FDA, is insufficient to address the growing disease burden, particularly in endemic regions lacking herd immunity. Monoclonal antibodies (mAbs), explicitly targeting structural proteins E1/E2, demonstrate promise in passive transfer studies, with mouse and human-derived mAbs showing protective efficacy. This article explores various vaccine candidates, including live attenuated, killed, nucleic acid-based (DNA/RNA), virus-like particle, chimeric, subunit, and adenovirus vectored vaccines. RNA vaccines have emerged as promising candidates due to their rapid response capabilities and enhanced safety profile. This review underscores the importance of the E1 and E2 proteins as immunogens, emphasizing their antigenic potential. Several vaccine candidates, such as CHIKV/IRES, measles vector (MV-CHIK), synthetic DNA-encoded antibodies, and mRNA-lipid nanoparticle vaccines, demonstrate encouraging preclinical and clinical results. In addition to identifying potential molecular targets for antiviral therapy, the study looks into the roles played by Toll-like receptors, RIG-I, and NOD-like receptors in the immune response to CHIKV. It also offers insights into novel tactics and promising vaccine candidates. This article discusses potential antiviral targets, the significance of E1 and E2 proteins, monoclonal antibodies, and RNA vaccines as prospective Chikungunya virus vaccine candidates. [ABSTRACT FROM AUTHOR]

Astragaloside IV (AS-IV), a natural triterpenoid isolated from Astragalus membranaceus, has been used traditionally in Chinese medicine. Previous studies have highlighted its benefits against carcinoma, but its interaction with the gut microbiota and effects on adenomatous polyps are not well understood. This present study investigates the effects of AS-IV on colonic adenomatous polyp (CAP) development in high-fat-diet (HFD) fed A p c Min ∕ + mice. A p c Min ∕ + mice were fed an HFD with or without AS-IV or Naringin for 8 weeks. The study assessed CAP proliferation and employed 16S DNA-sequencing and untargeted metabolomics to explore correlations between microbiome and metabolome in CAP development. AS-IV was more effective than Naringin in reducing CAP development, inhibiting colonic proinflammatory cytokines (IL-1β, IL-6, and TNF-α), tumor associated biomarkers (c-Myc, Cyclin D1), and Wnt/β-catenin pathway proteins (Wnt3a, β-catenin). AS-IV also inhibited the proliferative capabilities of human colon cancer cells (HT29, HCT116, and SW620). Multiomics analysis revealed AS-IV increased the abundance of beneficial genera such as Bifidobacteriumpseudolongum and significantly modulated serum levels of certain metabolites including linoleate and 2-trans,6-trans-farnesal, which were significantly correlated with the number of CAP. Finally, the anti-adenoma efficacy of AS-IV alone was significantly suppressed post pseudoaseptic intervention in HFD-fed A p c Min ∕ + mice but could be reinstated following a combined with Bifidobacteriumpseudolongum transplant. AS-IV attenuates CAP development in HFD-fed A p c Min ∕ + mice by regulating gut microbiota and metabolomics, impacting the Wnt3a/β-catenin signaling pathway. This suggests a potential new strategy for the prevention of colorectal cancer, emphasizing the role of gut microbiota in AS-IV's antitumor effects. [ABSTRACT FROM AUTHOR]

Climate change is accelerating the increase of temperatures across the planet and resulting in the warming of oceans. Ocean warming threatens the survival of many aquatic species, including squids, and has introduced physiological, behavioral, and developmental changes, as well as physical changes in their biological materials composition, structure, and properties. Here, we characterize and analyze how the structure, morphology, and mechanical properties of European common squid Loligo vulgaris sucker ring teeth (SRT) are affected by temperature. SRT are predatory teethed structures located inside the suction cups of squids that are used to capture prey and are composed of semicrystalline structural proteins with a high modulus (GPa-range). We observed here that this biological material reversibly softens with temperature, undergoing a glass transition at ∼35°C, to a MPa-range modulus. We analyzed the SRT protein nanostructures as a function of temperature, as well as microscale and macroscale morphological changes, to understand their impact in the material properties. The results suggested that even small deviations from their habitat temperatures can result in significant softening of the material (up to 40% in modulus loss). Temperature changes following recent global climate trends and predictions might affect environmental adaptation in squid species and pose emerging survival challenges to adapt to increasing ocean temperatures. [ABSTRACT FROM AUTHOR]

The giant cytoskeletal protein obscurin contains multiple cell signaling domains that influence cell migration. Here, we follow each of these pathways, examine how these pathways modulate epithelial cell migration, and discuss the cross-talk between these pathways. Specifically, obscurin uses its PH domain to inhibit phosphoinositide-3-kinase (PI3K)-dependent migration and its RhoGEF domain to activate RhoA and slow cell migration. While obscurin's effect on the PI3K pathway agrees with the literature, obscurin's effect on the RhoA pathway runs counter to most other RhoA effectors, whose activation tends to lead to enhanced motility. Obscurin also phosphorylates cadherins, and this may also influence cell motility. When taken together, obscurin's ability to modulate three independent cell migration pathways is likely why obscurin knockout cells experience enhanced epithelial to mesenchymal transition, and why obscurin is a frequently mutated gene in several types of cancer. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N), and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and the N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular, and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Fish species of the genus Amphiprion (Perciformes: Pomacentridae) seek protection from predators among the tentacles of sea anemones as their natural habitat, where they live essentially unharmed from stinging by the host's nematocysts. The skin mucus of these anemonefish has been suggested as a protective mechanism that prevents the discharge of the nematocysts upon contact. Whereas some anemonefish species seem to produce their own protective mucous coating, others may acquire mucus (or biomolecules within) from the sea anemone during an acclimation period. In controlled experiments, we show that Amphiprion ocellaris acclimated successfully to their natural host anemone species Stichodactyla gigantea, and also to Stichodactyla haddoni, and in some cases Heteractis crispa, neither of which are natural host species. No symbiosis was observed for three other anemone species tested, Entacmaea quadricolor, Macrodactyla doreensis, and Heteractis malu. We explored the skin mucous protein profile from naive and experienced A. ocellaris during their acclimation to natural and unnatural host anemones. We confidently report the presence of metabolic and structural proteins in the skin mucus of all samples, likely involved in immunological defense, molecular transport, stress response, and signal transduction. For those anemonefish that established symbiosis, there was a clear increase in ribosomal‐type proteins. We additionally provide evidence for the presence of anemone proteins only in the skin mucus of individuals that established symbiosis. Our results support previous speculation of the role of skin mucous–associated proteins in anemonefish–anemone symbiosis. Further exploration of these mucosal proteins could reveal the mechanism of anemonefish acclimation to host anemones. [ABSTRACT FROM AUTHOR]

The present study assessed the impact of glycyrrhizin on the mechanisms of progression and metastasis in cervical cancer cells. To this end, cell proliferation, migration, and invasion and protein/mRNA expression levels of protein kinase B, glycogen synthase kinase-3 β and β-catenin were measured in three groups of cells: normal cervical epithelial cell line End1/E6E7 (Group A), human cervical squamous cell carcinoma cell line C33a (group B), and human cervical squamous cell carcinoma cell line C33a treated with 50μmol/L glycyrrhizin (Group C). Results showed that glycyrrhizin treatment decreased the proliferation, migration, and invasion of C33a cells and increased apoptosis compared to the cervical cancer control cells. Expression levels of proteins associated with apoptosis such as FS-7-associated surface antigen, Bcl-2-associated X protein and Fas ligand were higher, while protein kinase B pathway activity was attenuated in the glycyrrhizin-treated group compared to the cervical cancer control group. These results suggest that glycyrrhizin may impair cervical cancer cell viability and impede their progression and metastasis by modulating the protein kinase B/glycogen synthase kinase-3β/β-catenin signaling pathway. [ABSTRACT FROM AUTHOR]

The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive. A correlation, based on published data and crystallisation conditions for several proteins, is proposed here between some thermodynamic properties of proteins and the position in the Hofmeister series of the salts from which they preferentially crystallise. Namely, a high ratio between the entropic or enthalpic protein‐solvent interactions contribution to thermodynamic stability and the total thermodynamic stability of a given protein, indicate the protein's high propensity to crystallise in solutions of highly kosmotropic salts. Low such ratios on the other hand, indicate that chaotropic salts can be equally successful, i. e. that the protein in question is rather indifferent to the Hofmeister character of the salt. Testing various model proteins for crystallisation against screens containing salts found at different points on the Hofmeister series, as well as further bibliographic analysis, have yielded results that appear to largely corroborate this hypothesis. These conclusions may conceivably be used as a crystallisation predictive tool. [ABSTRACT FROM AUTHOR]

Spinophilin is an F-actin binding and protein phosphatase 1 (PP1) targeting protein that acts as a scaffold of PP1 to its substrates. Spinophilin knockout (Spino−/−) mice have decreased fat mass, increased lean mass, and improved glucose tolerance, with no difference in feeding behaviors. Although spinophilin is enriched in neurons, its roles in nonneuronal tissues, such as β cells of the pancreatic islets, are unclear. We have corroborated and expanded upon previous studies to determine that Spino−/− mice have decreased weight gain and improved glucose tolerance in two different models of obesity. We have identified multiple putative spinophilin-interacting proteins isolated from intact pancreas and observed increased interactions of spinophilin with exocrine, ribosomal, and cytoskeletal protein classes that normally act to mediate peptide hormone production, processing, and/or release in Leprdb/db and/or high-fat diet-fed (HFF) models of obesity. In addition, we have found that spinophilin interacts with proteins from similar classes in isolated islets, suggesting a role for spinophilin in the pancreatic islet. Consistent with a pancreatic β cell type-specific role for spinophilin, using our recently described conditional spinophilin knockout mice, we found that loss of spinophilin specifically in pancreatic β cells improved glucose tolerance without impacting body weight in chow-fed mice. Our data further support the role of spinophilin in mediating pathophysiological changes in body weight and whole body metabolism associated with obesity. Our data provide the first evidence that pancreatic spinophilin protein interactions are modulated by obesity and that loss of spinophilin specifically in pancreatic β cells impacts whole body glucose tolerance. NEW & NOTEWORTHY: To our knowledge, these data are the first to demonstrate that obesity impacts spinophilin protein interactions in the pancreas and identify spinophilin specifically in pancreatic β cells as a modulator of whole body glucose tolerance. [ABSTRACT FROM AUTHOR]

Peptides, composed of 2–50 amino acids, have gained attention in anti-aging treatments due to their high safety, low irritation, and cost-effective production. This study aimed to evaluate the anti-wrinkle efficacy of Tetrapeptide-68, derived from the skin structural protein Loricrin, on periorbital wrinkles in women aged 30–65 years. A 12-week, double-blind, randomized controlled trial was conducted with 25 participants who applied the Tetrapeptide-68 (100 ppm) O/W formulation around the eyes. Skin physiological parameters were assessed at baseline, 4, 8, and 12 weeks. Participants also completed efficacy and usability questionnaires. Significant improvements in wrinkle reduction were observed with Tetrapeptide-68 cream treatment, as measured by various skin roughness parameters and 3D imaging analysis. Participants reported positive changes in skin texture and moisture levels, with no adverse reactions noted. Tetrapeptide-68 cream demonstrates promising anti-wrinkle effects, highlighting its potential as an effective ingredient in anti-aging skincare formulations. Further studies are recommended to explore its long-term benefits and underlying mechanisms. [ABSTRACT FROM AUTHOR]

Background: Deep angiomyxoma (DAM) is a slow-growing benign tumor with high risk of local recurrence after surgical resection. Although DAM in a lower extremity is extremely rare, clinicians must be aware of its possible occurrence. Suspicion can be made based on clinical examination and radiological imaging but final diagnosis is confirmed on histopathological examination and immunohistochemistry. We intend to present an extremely rare case of DAM in the knee, managed successfully with marginal excision. Case Presentation: A 4-year-old male child presented with the complains of a painless, progressively increasing, soft, non-tender, and fluctuant swelling in his right knee. The plain radiograph showed a non-calcified soft-tissue swelling and MRI revealed a multi-loculated cystic lesion with multiple septations. A pre-operative diagnosis of a benign cystic lesion was made. It was managed by marginal excision of the tumor and a histological diagnosis of DAM was made. IHC staining showed positivity for SMA, CD34 and vimentin were focally positive, while desmin and calponin were negative. At 12 months of follow-up, the patient had a normal painless gait and full knee ROM, without any local recurrence. Conclusion: DAM is a rare tumor which is often misdiagnosed. In this report, we present a rare case of benign cystic lesion which turned out to be DAM on HPE of resected specimen. Marginal excision of this lesion revealed good outcomes with no recurrence until 12 months of final follow-up. With this, we conclude that surgical excision should be the gold standard in cases of DAM. [ABSTRACT FROM AUTHOR]

The mechanical resilience of the knee meniscus is provided by a group of structural proteins in the extracellular matrix. Aging can alter the quantity and molecular structure of these proteins making the meniscus more susceptible to debilitating tears. In this study, we determined the effect of aging on the quantity of structural proteins and collagen crosslinks in human lateral meniscus, and examined whether the quantity of these molecules was predictive of tensile toughness (area under the stress‐strain curve). Two age groups were tested: a young group under 40 and an older group over 65 years old. Using mass spectrometry, we quantified the abundance of proteins and collagen crosslinks in meniscal tissue that was adjacent to the dumbbell‐shaped specimens used to measure uniaxial tensile toughness parallel or perpendicular to the circumferential fiber orientation. We found that the enzymatic collagen crosslink deoxypyridinoline had a significant positive correlation with toughness, and reductions in the quantity of this crosslink with aging were associated with a loss of toughness in the ground substance and fibers. The non‐enzymatic collagen crosslink carboxymethyl‐lysine increased in quantity with aging, and these increases corresponded to reductions in ground substance toughness. For the collagenous (Types I, II, IV, VI, VIII) and non‐collagenous structural proteins (elastin, decorin, biglycan, prolargin) analyzed in this study, only the quantity of collagen VIII was predictive of toughness. This study provides valuable insights on the structure‐function relationships of the human meniscus, and how aging causes structural adaptations that weaken the tissue's mechanical integrity. [ABSTRACT FROM AUTHOR]

Simple Summary: Head and neck cancers are aggressive and challenging to treat due to the severe side effects and toxicity of current treatments. Bufalin, a natural compound from the Chinese toad, has shown promise in fighting various cancers but has not been thoroughly studied for head and neck cancers. Our research aims to explore how bufalin works against these specific cancer cells. By using different techniques, we discovered that bufalin could reduce cancer cell growth, induce cell death, and enhance the body's immune response against tumors. These findings suggest that bufalin could become a new, effective treatment option with potentially fewer side effects for patients with head and neck cancers. This research could pave the way for developing better therapies and improving outcomes for patients facing this difficult disease. Bufalin, a cardiotonic steroid derived from the Chinese toad (Bufo gargarizans), has demonstrated potent anticancer properties across various cancer types, positioning it as a promising therapeutic candidate. However, comprehensive mechanistic studies specific to head and neck cancers have been lacking. Our study aimed to bridge this gap by investigating bufalin's mechanisms of action in head and neck cancer cells. Using several methods, such as Western blotting, immunofluorescence, and flow cytometry, we observed bufalin's dose-dependent reduction in cell viability, disruption of cell membrane integrity, and inhibition of colony formation in both HPV-positive and HPV-negative cell lines. Bufalin induces apoptosis through the modulation of apoptosis-related proteins, mitochondrial function, and reactive oxygen species production. It also arrests the cell cycle at the G2/M phase and attenuates cell migration while affecting epithelial–mesenchymal transition markers and targeting pivotal signaling pathways, including Wnt/β-catenin, EGFR, and NF-κB. Additionally, bufalin exerted immunomodulatory effects by polarizing macrophages toward the M1 phenotype, bolstering antitumor immune responses. These findings underscore bufalin's potential as a multifaceted therapeutic agent against head and neck cancers, targeting essential pathways involved in proliferation, apoptosis, cell cycle regulation, metastasis, and immune modulation. Further research is warranted to validate these mechanisms and optimize bufalin's clinical application. [ABSTRACT FROM AUTHOR]

During de novo emergence, new protein coding genes emerge from previously nongenic sequences. The de novo proteins they encode are dissimilar in composition and predicted biochemical properties to conserved proteins. However, functional de novo proteins indeed exist. Both identification of functional de novo proteins and their structural characterization are experimentally laborious. To identify functional and structured de novo proteins in silico, we applied recently developed machine learning based tools and found that most de novo proteins are indeed different from conserved proteins both in their structure and sequence. However, some de novo proteins are predicted to adopt known protein folds, participate in cellular reactions, and to form biomolecular condensates. Apart from broadening our understanding of de novo protein evolution, our study also provides a large set of testable hypotheses for focused experimental studies on structure and function of de novo proteins in Drosophila. [ABSTRACT FROM AUTHOR]

The article discusses the discovery of a novel feature of group 2 innate lymphoid cells (ILC2s) called ILC2 extracellular traps (ETs) and ILC2 ETosis. The researchers found that ILC2s have the ability to engulf bacteria and produce ETs. They observed that ILC2 cells increased in volume and their nuclei became dispersed throughout the cells when exposed to Streptococcus pneumoniae bacteria. The study also explored the release of double-stranded DNA (dsDNA) by ILC2s and the protein composition of ILC2 ETs. The researchers concluded that ILC2s are capable of undergoing ETosis and generating ETs, which can trap bacteria. Further research is needed to understand the role of ILC2 ETosis and ILC2 ETs in the body. [Extracted from the article]

Simple Summary: α-keratins are the main structural proteins in the cortex of wool fibres. Variation in these proteins affects the structure and fibre characteristics of wool, making keratin genes good candidates for the development of gene markers to selectively breed for better wool. Variation was found in the keratin gene KRT85, with the presence of the A variant being associated with an increase in greasy fleece weight and clean fleece weight, and the presence of B associated with an increased wool prickle factor. This may assist in the development of gene markers to assist in sheep breeding. α-keratins are structural proteins in the cortex of wool fibres and assemble in an organized fashion into keratin intermediate filaments. Variation in these keratin proteins affects the structure and characteristics of wool fibre, making keratin genes ideal candidates for the development of gene markers that describe variations in wool traits. A region of KRT85 spanning exon 3–4 (including the entire exon 3, intron 3, exon 4 and part of intron 4) was investigated. Two banding patterns defining two variant sequences (A and B) were observed in this region, and these were characterised by the presence of two single nucleotide polymorphisms. The effect of this variation in the exon 3–4 region of KRT85 on wool traits was investigated in 463 Merino × Southdown-cross lambs. The frequencies of these two variants in these sheep were 55.6% and 44.4%, respectively. Three different genotypes were observed with frequencies of 32.6%, 46.1% and 21.3% for AA, AB and BB, respectively. The presence of A was associated with an increase in greasy fleece weight and clean fleece weight, while the presence of B was associated with an increased wool prickle factor. These findings should be replicated in a broader range of sheep breeds to determine whether the associations are robust and to clarify whether the observed effects are attributable to breed differences or to gene effects themselves. [ABSTRACT FROM AUTHOR]

Ageing populations, mass "baby-free" policies and children born to mothers at the age at which they are biologically expected to become grandmothers are growing problems in most developed societies. Therefore, any opportunity to improve the quality of infertility treatments seems important for the survival of societies. The possibility of indirectly studying the quality of developing oocytes by examining their follicular fluids (hFFs) offers new opportunities for progress in our understanding the processes of final oocyte maturation and, consequently, for predicting the quality of the resulting embryos and personalising their culture. Using mass spectrometry, we studied follicular fluids collected individually during in vitro fertilisation and compared their composition with the quality of the resulting embryos. We analysed 110 follicular fluids from 50 oocyte donors, from which we obtained 44 high-quality, 39 medium-quality, and 27 low-quality embryos. We identified 2182 proteins by Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS) using a TripleTOF 5600+ hybrid mass spectrometer, of which 484 were suitable for quantification. We were able to identify several proteins whose concentrations varied between the follicular fluids of different oocytes from the same patient and between patients. Among them, the most important appear to be immunoglobulin heavy constant alpha 1 (IgA1hc) and dickkopf-related protein 3. The first one is found at higher concentrations in hFFs from which oocytes develop into poor-quality embryos, the other one exhibits the opposite pattern. None of these have, so far, had any specific links to fertility disorders. In light of these findings, these proteins should be considered a primary target for research aimed at developing a diagnostic tool for oocyte quality control and pre-fertilisation screening. This is particularly important in cases where the fertilisation of each egg is not an option for ethical or other reasons, or in countries where it is prohibited by law. [ABSTRACT FROM AUTHOR]

Elastin, a key structural protein essential for the elasticity of the skin and elastogenic tissues, degrades with age. Replenishing elastin holds promise for anti-aging cosmetics and the supplementation of elastic activities of the cardiovascular system. We employed RiboScreenTM, a technology for identifying molecules that enhance the production of specific proteins, to target the production of tropoelastin. We make use of RiboScreenTM in two crucial steps: first, to pinpoint a target ribosomal protein (TRP), which acts as a switch to increase the production of the protein of interest (POI), and second, to identify small molecules that activate this ribosomal protein switch. Using RiboScreenTM, we identified ribosomal protein L40, henceforth eL40, as a TRP switch to boost tropoelastin production. Drug discovery identified a small-molecule hit that binds to eL40. In-cell treatment demonstrated activity of the eL40 ligand and delivered increased tropoelastin production levels in a dose-dependent manner. Thus, we demonstrate that RiboScreenTM can successfully identify a small-molecule hit capable of selectively enhancing tropoelastin production. This compound has the potential to be developed for topical or systemic applications to promote skin rejuvenation and to supplement elastic functionality within the cardiovascular system. [ABSTRACT FROM AUTHOR]

The purpose of this review is to provide a comprehensive framework for researchers, academics, and food developers regarding the techno-functional properties of the most consumed legume proteins globally, including peas, cowpeas, common beans, chickpeas, fava beans, lentils, and lupins. The review delves into the structural aspects of these proteins in detail and the techniques employed in their extraction and modification. Detailed information is provided on various techno-functional properties, such as solubility, water and oil retention capacity, emulsifying properties, foaming properties, and gelation properties of legume proteins. Practical applications in various food products are highlighted, including bakery items, pasta, snacks, dairy alternatives, sauces, meat analogues, and hybrid products. The review also explores emerging uses, such as the role of these proteins as encapsulating materials and even in 3D food printing. In addition, suggestions for future applications are presented, emphasizing their relevance in the development of innovative products and promoting the comprehensive utilization of legume proteins in the food industry. The importance of these innovations is emphasized in attracting consumers and facilitating a successful transition toward more sustainable plant-based diets. [ABSTRACT FROM AUTHOR]

The article explores the role of antinephrin antibodies in the pathogenesis of minimal change disease and focal segmental glomerulosclerosis (FSGS). Topics discussed include the function of nephrin in kidney filtration, the impact of autoantibodies on nephrin's role, and potential implications for targeting these antibodies in treatment strategies.

Eotaxin-3 is a key chemokine with a relevant role in eosinophilic esophagitis, a rare chronic immune/antigen-mediated inflammatory disorder. Eotaxin-3 is a potent activator of eosinophil emergence and migration, which may lead to allergic airway inflammation. We investigated, using bioinformatics tools, the protein structure and the possible effects of the known variations reported in public databases. Following a procedure already established, we created a 3D model of the whole protein and modeled the structure of 105 protein variants due to known point mutations. The effects of the amino acid substitution at the level of impact on protein structure, stability, and possibly function were detected by the bioinformatics procedure and described in detail. A web application was implemented to browse the results of the analysis and visualize the 3D models, with the opportunity of downloading the models and analyzing them using their own software. Among 105 amino acid substitutions investigated, the study evidenced in 44 cases at least one change in any of the investigated structural parameters. Other six variations are also relevant, although a structural effect was not detected by our analysis, because they affected amino acids highly conserved, which suggests a possible function role. All these variations should be the object of particular attention, as they may induce a loss of functionality in the protein. [ABSTRACT FROM AUTHOR]

Islet β-cell dysfunction is an underlying factor for type I diabetes (T1D) development. Insulin sensing and secretion are tightly regulated in β-cells at multiple subcellular levels. The epithelial intermediate filament (IF) protein keratin (K) 8 is the main β-cell keratin, constituting the filament network with K18. To identify the cell-autonomous functions of K8 in β-cells, mice with targeted deletion of β-cell K8 (K8flox/flox; Ins-Cre) were analyzed for islet morphology, ultrastructure, and integrity, as well as blood glucose regulation and streptozotocin (STZ)-induced diabetes development. Glucose transporter 2 (GLUT2) localization was studied in β-cells in vivo and in MIN6 cells with intact or disrupted K8/K18 filaments. Loss of β-cell K8 leads to a major reduction in K18. Islets without β-cell K8 are more fragile, and these β-cells display disjointed plasma membrane organization with less membranous E-cadherin and smaller mitochondria with diffuse cristae. Lack of β-cell K8 also leads to a reduced glucose-stimulated insulin secretion (GSIS) response in vivo, despite undisturbed systemic blood glucose regulation. K8flox/flox, Ins-Cre mice have a decreased sensitivity to STZ compared with K8 wild-type mice, which is in line with decreased membranous GLUT2 expression observed in vivo, as GLUT2 is required for STZ uptake in β-cells. In vitro, MIN6 cell plasma membrane GLUT2 is rescued in cells overexpressing K8/K18 filaments but mistargeted in cells with disrupted K8/K18 filaments. β-Cell K8 is required for islet and β-cell structural integrity, normal mitochondrial morphology, and GLUT2 plasma membrane targeting, and has implications on STZ sensitivity as well as systemic insulin responses. NEW & NOTEWORTHY: Keratin 8 is the main cytoskeletal protein in the cytoplasmic intermediate filament network in β-cells. Here for the first time, we assessed the β-cell autonomous mechanical and nonmechanical roles of keratin 8 in β-cell function. We demonstrated the importance of keratin 8 in islet and β-cell structural integrity, maintaining mitochondrial morphology and GLUT2 plasma membrane targeting. [ABSTRACT FROM AUTHOR]

Skeletal dysplasias are group of rare genetic diseases resulting from mutations in genes encoding structural proteins of the cartilage extracellular matrix (ECM), signaling molecules, transcription factors, epigenetic modifiers, and several intracellular proteins. Cell division, organelle maintenance, and intracellular transport are all orchestrated by the cytoskeleton-associated proteins, and intracellular processes affected through microtubule-associated movement are important for the function of skeletal cells. Among microtubule-associated motor proteins, kinesins in particular have been shown to play a key role in cell cycle dynamics, including chromosome segregation, mitotic spindle formation, and ciliogenesis, in addition to cargo trafficking, receptor recycling, and endocytosis. Recent studies highlight the fundamental role of kinesins in embryonic development and morphogenesis and have shown that mutations in kinesin genes lead to several skeletal dysplasias. However, many questions concerning the specific functions of kinesins and their adaptor molecules as well as specific molecular mechanisms in which the kinesin proteins are involved during skeletal development remain unanswered. Here we present a review of the skeletal dysplasias resulting from defects in kinesins and discuss the involvement of kinesin proteins in the molecular mechanisms that are active during skeletal development. [ABSTRACT FROM AUTHOR]

Context: Geometrical knots are rare structural arrangements in proteins in which the polypeptide chain ties itself into a knot, which is very intriguing due to the uncertainty of their impact on the protein properties. Presently, classical molecular dynamics is the most employed technique in the few studies found on this topic, so any information on how the presence of knots affects the reactivity and electronic properties of proteins is even scarcer. Using the electronic structure methods and quantum chemical descriptors analysis, we found that the same amino-acid residues in the knot core have statistically larger values for the unknotted protein, for both hard-hard and soft-soft interaction descriptors. In addition, we present a computationally feasible protocol, where we show it is possible to separate the contribution of the geometrical knot to the reactivity and other electronic structure properties. Methods: In order to investigate these systems, we used PRIMoRDiA, a new software developed by our research group, to explore the electronic structure of biological macromolecules. We evaluated several local quantum chemical descriptors to unveil relevant patterns potentially originating from the presence of the geometrical knot in two proteins, belonging to the ornithine transcarbamylase family. We compared several sampled structures from these two enzymes that are highly similar in both tertiary structure and function, but one of them has a knot whereas the other does not. The sampling was carried out through molecular dynamics simulations using ff14SB force field along 50 ns, and the semiempirical convergence was performed with PM7 Hamiltonian. [ABSTRACT FROM AUTHOR]

Porcine deltacoronavirus (PDCoV) is an important enteric coronavirus that has caused enormous economic losses in the pig industry worldwide. However, no commercial vaccine is currently available. Therefore, developing a safe and efficacious live-attenuated vaccine candidate is urgently needed. In this study, the PDCoV strain CH/XJYN/2016 was continuously passaged in LLC-PK cells until passage 240, and the virus growth kinetics in cell culture, pathogenicity in neonatal piglets, transcriptome differences after LLC-PK infection, changes in the functional characteristics of the spike (S) protein in the high- and low-passage strains, genetic variation of the virus genome, resistance to pepsin and acid, and protective effects of this strain when used as a live-attenuated vaccine were examined. The results of animal experiments demonstrated that the virulent PDCoV strain CH/XJYN/2016 was completely attenuated and not pathogenic in piglets following serial cell passage. Genome sequence analysis showed that amino acid mutations in nonstructural proteins were mainly concentrated in Nsp3, structural protein mutations were mainly concentrated in the S protein, and the N, M, and E genes were conserved. Transcriptome comparison revealed that compared with negative control cells, P10-infected LLC-PK cells had the most differentially expressed genes (DEGs), while P0 and P240 had the least number of DEGs. Analysis of trypsin dependence and related structural differences revealed that the P10 S protein interacted more strongly with trypsin and that the P120 S protein interacted more strongly with the APN receptor. Moreover, the infectivity of P240 was not affected by pepsin but was significantly decreased after exposure to low pH. Furthermore, the P240-based live-attenuated vaccine provided complete protection to piglets against the challenge of virulent PDCoV. In conclusion, we showed that a PDCoV strain was completely attenuated through serial passaging in vitro. These results provide insights into the potential molecular mechanisms of PDCoV attenuation and the development of a promising live-attenuated PDCoV vaccine. IMPORTANCE Porcine deltacoronavirus (PDCoV) is one of the most important enteropathogenic pathogens that cause diarrhea in pigs of various ages, especially in suckling piglets, and causes enormous economic losses in the global commercial pork industry. There are currently no effective measures to prevent and control PDCoV. As reported in previous porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus studies, inactivated vaccines usually elicit less robust protective immune responses than live-attenuated vaccines in native sows. Therefore, identifying potential attenuation mechanisms, gene evolution, pathogenicity differences during PDCoV passaging, and immunogenicity as live-attenuated vaccines is important for elucidating the mechanism of attenuation and developing safe and effective vaccines for virulent PDCoV strains. In this study, we demonstrated that the virulence of the PDCoV strain CH/XJYN/2016 was completely attenuated following serial cell passaging in vitro, and changes in the biological characteristics and protection efficacy of the strain were evaluated. Our results help elucidate the mechanism of PDCoV attenuation and support the development of appropriate designs for the study of live PDCoV vaccines. [ABSTRACT FROM AUTHOR]

African swine fever virus (ASFV) is the causative agent of a contagious disease affecting wild and domestic swine. The function of B169L protein, as a potential integral structural membrane protein, remains to be experimentally characterized. Using state-of-the-art bioinformatics tools, we confirm here earlier predictions indicating the presence of an integral membrane helical hairpin, and further suggest anchoring of this protein to the ER membrane, with both terminal ends facing the lumen of the organelle. Our evolutionary analysis confirmed the importance of purifying selection in the preservation of the identified domains during the evolution of B169L in nature. Also, we address the possible function of this hairpin transmembrane domain (HTMD) as a class IIA viroporin. Expression of GFP fusion proteins in the absence of a signal peptide supported B169L insertion into the ER as a Type III membrane protein and the formation of oligomers therein. Overlapping peptides that spanned the B169L HTMD were reconstituted into ER-like membranes and the adopted structures analyzed by infrared spectroscopy. Consistent with the predictions, B169L transmembrane sequences adopted α-helical conformations in lipid bilayers. Moreover, single vesicle permeability assays demonstrated the assembly of lytic pores in ER-like membranes by B169L transmembrane helices, a capacity confirmed by ion-channel activity measurements in planar bilayers. Emphasizing the relevance of these observations, pore-forming activities were not observed in the case of transmembrane helices derived from EP84R, another ASFV protein predicted to anchor to membranes through a α-helical HTMD. Overall, our results support predictions of viroporin-like function for the B169L HTMD. IMPORTANCE African swine fever (ASF), a devastating disease affecting domestic swine, is widely spread in Eurasia, producing significant economic problems in the pork industry. Approaches to prevent/cure the disease are mainly restricted to the limited information concerning the role of most of the genes encoded by the large (160–170 kba) virus genome. In this report, we present the experimental data on the functional characterization of the African swine fever virus (ASFV) gene B169L. Data presented here indicates that the B169L gene encodes for an essential membrane-associated protein with a viroporin function. [ABSTRACT FROM AUTHOR]

The interaction between viral proteins and host proteins plays a crucial role in the process of virus infecting cells. Tags such as HA, His, and Flag do not interfere with the function of fusion proteins and are commonly used to study protein-protein interactions. Adding these tags to viral proteins will address the challenge of the lack of antibodies for screening host proteins that interact with viral proteins during infection. Obtaining viruses with tagged fusion proteins is crucial. This study established a new reverse genetic system with T7 promoter and three plasmids, which efficiently rescued Newcastle disease virus (NDV) regardless of its ability to replicate in cells. Subsequently, using this system, NDV containing a HA-tagged structural protein and NDV carrying a unique tag on each structural protein were successfully rescued. These tagged viruses replicated normally and exhibited genetic stability. Based on tag antibodies, every NDV structural protein was readily detected and showed correct subcellular localization in infected cells. After infecting cells with NDV carrying HA-tagged M protein, several proteins interacting with the M protein during the infection process were screened using HA tag antibodies. The establishment of this system laid the foundation for comprehensive exploration of the interaction between NDV proteins and host proteins. [ABSTRACT FROM AUTHOR]

Herpesviruses antagonize host antiviral responses through a myriad of molecular strategies culminating in the death of the host cells. Pseudorabies virus (PRV) is a significant veterinary pathogen in pigs, causing neurological sequalae that ultimately lead to the animal's demise. PRV is known to trigger apoptotic cell death during the late stages of infection. The virion host shutdown protein (VHS) encoded by UL41 plays a crucial role in the PRV infection process. In this study, we demonstrate that UL41 inhibits PRV-induced activation of inflammatory cytokine and negatively regulates the cGAS-STING-mediated antiviral activity by targeting IRF3, thereby inhibiting the translocation and phosphorylation of IRF3. Notably, mutating the conserved amino acid sites (E192, D194, and D195) in the RNase domain of UL41 or knocking down UL41 inhibits the immune evasion of PRV, suggesting that UL41 may play a crucial role in PRV's evasion of the host immune response during infection. These results enhance our understanding of how PRV structural proteins assist the virus in evading the host immune response. [ABSTRACT FROM AUTHOR]

This project studied the use of lentil protein (LP) and quinoa protein (QP) in their native and modified states as carrier material in the encapsulation process by the ionic gelation technique of annatto seed extract. Soy protein (SP) was used as a model of carrier material and encapsulated bioactive compounds, respectively. The plant proteins were modified by enzymatic hydrolysis, N acylation, and N-cationization to improve their encapsulating properties. Additionally, the secondary structure, differential scanning calorimetry (DSC), solubility as a function of pH, isoelectric point (pI), molecular weight (MW), the content of free thiol groups (SH), the absorption capacity of water (WHC) and fat (FAC), emulsifier activity (EAI), emulsifier stability (ESI), and gelation temperature (Tg) were assessed on proteins in native and modified states. The results obtained demonstrated that in a native state, LP (80.52% and 63.82%) showed higher encapsulation efficiency than QP (73.63% and 45.77%), both for the hydrophilic dye and for the annatto extract. Structural modifications on proteins improve some functional properties, such as solubility, WHC, FAC, EAI, and ESI. However, enzymatic hydrolysis on the proteins decreased the gels' formation, the annatto extract's encapsulated efficiency, and the hydrophilic dye by the ionic gelation method. On the other hand, the modifications of N-acylation and N-cationization increased but did not generate statistically significant differences (p-value > 0.05) in the encapsulation efficiency of both the annatto extract and the hydrophilic dye compared to those obtained with native proteins. This research contributes to understanding how plant proteins (LP and QP) can be modified to enhance their encapsulating and solubility properties. The better encapsulation of bioactive compounds (like annatto extract) can improve product self-life, potentially benefiting the development of functional ingredients for the food industry. [ABSTRACT FROM AUTHOR]

The hepatitis C virus (HCV) is responsible for approximately 50 million infections worldwide. Effective drug treatments while available face access barriers, and vaccine development is hampered by viral hypervariability and immune evasion mechanisms. The CD4+ and CD8+ T-cell responses targeting HCV non-structural (NS) proteins have shown a role in the viral clearance. In this paper, we reviewed the studies exploring the relationship between HCV structural and NS proteins and their effects in contributing to the elicitation of an effective T-cell immune response. The use of different vaccine platforms, such as viral vectors and virus-like particles, underscores their versability and efficacy for vaccine development. Diverse HCV antigens demonstrated immunogenicity, eliciting a robust immune response, positioning them as promising vaccine candidates for protein/peptide-, DNA-, or RNA-based vaccines. Moreover, adjuvant selection plays a pivotal role in modulating the immune response. This review emphasizes the importance of HCV proteins and vaccination strategies in vaccine development. In particular, the NS proteins are the main focus, given their pivotal role in T-cell-mediated immunity and their sequence conservation, making them valuable vaccine targets. [ABSTRACT FROM AUTHOR]

Background: Raman spectroscopy is a well-known tool used in criminology, molecular biology, and histology. It is also applied to diagnose bone mineral disorders by taking advantage of the similarity of the structure of keratin and bone collagen. Raman spectroscopy can also be used in dermatology and diabetology. The purpose of the present review is to critically evaluate the available research about the use of Raman spectroscopy in the mentioned areas of medicine. Methodology: PubMed was searched for peer-reviewed articles on the subject of use of Raman spectroscopy in bone mineral disorders, dermatology, and diabetes mellitus. Results: Nail keratin and bone collagen are related structural proteins that require disulfide bond for structural stability. Therefore, Raman spectroscopy of keratin may have potential as a diagnostic tool for screening bone quality and distinguishing patients at risk of fracture for reasons different from low bone mineral density (BMD) in the adult women population. Raman spectroscopy can also investigate the changes in keratin's structure in nails affected by onychomycosis and distinguish between healthy and onychomycosis nail samples. It could also reduce the need for nail biopsy by distinguishing between dermatophytic and non-dermatophytic agents of onychomycosis. Additionally, Raman spectroscopy could expedite the diagnostic process in psoriasis (by assessing the secondary structure of keratin) and in diabetes mellitus (by examining the protein glycation level). Conclusions: In adult populations, Raman spectroscopy is a promising and safe method for assessing the structure of fingernails. However, data are scarce in the pediatric population; therefore, more studies are required in children. [ABSTRACT FROM AUTHOR]