Search Results (204)

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has already been described for members of the p47^phox-related protein family, individual cases have never been collected and analyzed collectively, which precluded the definition of the binding preferences and targeted discovery of further instances. Here, we apply an integrative approach that includes data collection, curation, bioinformatics analyses and state-of-the-art structure prediction methods to fill these gaps. A search of the human proteome with the sequence signatures of SH3 tandemization and follow-up structure analyses suggest that SH3 tandemization could be specific for this family. We define the optimal binding preference of tandemly arranged SH3 domains as [PAVIL]PPR[PR][^DE][^DE] and propose potential new instances of this SLiM among the family members and their binding partners. Structure predictions suggest the possibility of a novel, reverse binding mode for certain motif instances. In all, our comprehensive analysis of this unique SH3 binding mode enabled the identification of novel, interesting tandem SH3-binding motif candidates with potential therapeutic relevance. Full article

Background: Despite the emergence of new treatment modalities, including targeted therapies that are of benefit to patients whose tumours carry specific mutations, the prognosis for most patients with cholangiocarcinoma remains poor. Novel therapeutic approaches that can benefit the majority of patients whose tumour cells do not carry targetable mutations are urgently needed. Results: To identify mutation-agnostic treatment approaches, we screened a library of well-tolerated off-patent drugs against cholangiocarcinoma cells and normal biliary epithelial cells. The screen identified Niclosamide as a drug that reduces the viability of multiple cholangiocarcinoma cell lines but has a lesser effect on normal primary biliary epithelial cells. Moreover, Niclosamide treatment reduces the growth of cholangiocarcinoma tumour cells as tumour spheroids in vitro and reduces the growth of cholangiocarcinoma cells as tumours in a xenograft mouse model of this disease. Through a proteasome-dependent mechanism, Niclosamide treatment reduces the expression of the Proline-Rich Homeodomain (PRH) protein, a transcription factor which acts as an oncoprotein in cholangiocarcinoma cells. However, PRH knockout does not alter the sensitivity of cholangiocarcinoma cells to Niclosamide, indicating that this drug is not dependent on PRH to reduce cell viability. Interestingly, the CDK4/6 kinase inhibitor Palbociclib selectively reduces the viability of cholangiocarcinoma cell lines compared to normal biliary epithelial cells and, importantly, Palbociclib synergises with Niclosamide to reduce cholangiocarcinoma cell viability in vitro as well as to reduce tumour growth in a mouse xenograft model. Conclusion: These preclinical results suggest that the combination of Niclosamide and an inhibitor of CDK4/6 is worthy of clinical evaluation as a potential treatment for this disease. Full article

Aggregates of misfolded α-synuclein proteins are key markers of Parkinson’s disease. The protein α-synuclein (aSyn) is an intrinsically disordered protein (IDP) and therefore lacks a single stable 3D structure, instead sampling multiple conformations in solution. It is primarily located in presynaptic terminals and is thought to help regulate synaptic vesicle trafficking and neurotransmitter release. ASyn proteins have three domains: an N-terminal domain, a hydrophobic non-amyloid-β component (NAC) core implicated in aggregation, and a proline-rich C-terminal domain. Asyn proteins with truncated C-terminal domains are known to be prone to aggregation and suggest that understanding domain–domain interactions in aSyn monomers could help elucidate the role of the flanking domains in modulating protein structure. To this end, we used Gaussian accelerated molecular dynamics (GAMD) to simulate wild-type (WT), N-terminal truncated (ΔN), C-terminal truncated (ΔC), and isolated NAC domain (isoNAC) aSyn protein variants. Using clustering and contact analysis, we found that removal of the N-terminal domain led to increased contacts between NAC and C-terminal domains and the formation of inter-domain β-sheets. Removal of either flanking domain also resulted in increased compactness of every domain. We also found that the contacts between flanking domains in the WT protein result in an electrostatic potential (ESP) that may lead to favorable interactions with anionic lipid membranes. Removal of the C-terminal domain disrupts the ESP in a way that could result in over-stabilized protein–membrane interactions. These results suggest that cooperation between the flanking domains may modulate the protein’s structure in a way that helps maintain elongation and creates an ESP that may aid favorable interactions with the membrane. Full article

Sea cucumber (Apostichopus japonicus) is an important economically cultured species in the northern coastal regions of China. Its body wall is rich in collagen, which directly determines product quality and market value. However, with the expansion of aquaculture scale, issues such as insufficient collagen deposition have led to inconsistent quality among cultured individuals. Therefore, there is an urgent need to improve growth performance and body wall quality through nutritional regulation. As functional nutrients, amino acids play key roles in collagen synthesis, yet relevant research on A. japonicus remains limited. This study was conducted to investigate the effects of dietary proline on the growth performance, body wall collagen deposition and organoleptic quality of sea cucumber (initial body weight: 30.20 ± 2.02 g). Three kinds of feed with equal levels of nitrogen and other lipids, and supplemented with different concentrations of proline (0%, 1.5%, 3%) in the basal diet, were named P0, P1.5, and P3, and the experiment was conducted for 60 days. The results showed that supplementation with 3% proline significantly increased final body weight and weight gain rate (p < 0.05), reaching 66.39 g and 115.30%, respectively. Collagen content in the body wall increased by approximately 18.5% compared to the control group. Histological analysis of the body wall showed that the collagen fibers in the P1.5 and P3 groups were thicker, with an increased proportion of type I collagen. Texture profile analysis indicated that hardness, cohesiveness, and chewiness were significantly improved in the P3 group (p < 0.05). In summary, supplementation with 1.5% and 3% proline effectively enhanced growth, collagen deposition, and body wall quality. Compared to the P0 group, the relative expression levels of collagen type I alpha 2 chain (COL1A1), Sma- and Mad-related protein 1(SMAD1), and sp-smad2/3 (SMAD2/3) in the body wall tissue were significantly upregulated in both the P1.5 and P3 groups (p < 0.05). Full article

Grapevine cultivars (Vitis vinifera L.) generally exhibit relatively high tolerance to drought stress. In contrast, the drought tolerance of other Vitis species and their hybrids used as rootstocks differs considerably. In order to attain a better understanding of the molecular basis of drought tolerance in grapevine, we conducted a comparative transcriptomic analysis of roots of drought-stressed Cabernet Sauvignon (CS, Vitis vinifera L.) and rootstock of Kober 5BB (V. berlandieri × V. riparia) using the Affymetrix Vitis Genome Array Version 2.0. We identified 1279 (745 upregulated and 534 downregulated) and 1925 (807 upregulated and 118 downregulated) differentially expressed genes in 5BB and CS. Numerous genes that are putatively involved in aquaporins, proline-rich protein, reactive oxygen species, osmoprotection, and lipid transfer were differentially expressed in response to drought stress in both genotypes. When gene ontology analyses were examined, it was observed that CS and 5BB genotypes were associated with the highest number of similar genes in both the molecular function (protein binding, catalytic activity, and DNA binding) and the biological process (metabolic process and translation) categories. The identification of different regulated genes between 5BB and CS roots is expected to help advance our understanding of molecular mechanisms operating during drought stress in grapevine roots. Full article

The large, white paired bract is a unique trait, as well as the most intriguing feature of the dove tree (Davidia involucrata). However, the mechanisms underlying bract development remain unclear. Our previous comparative transcriptome analysis concerning Davidia bracts at different developmental stages has identified a number of bract-specific genes. Among these, the genes encoding PRPs (proline-rich proteins) show dramatic expression variation, indicating the participation of this gene family in bract development. In this study, we screened the whole Davidia genome and identified twelve Davidia PRP (DiPRP) genes, showing obvious expression variation during bract development, with some upregulated up to 100-fold at the fast-developing stage. These PRP genes are evenly distributed on seven Davidia chromosomes. The cis-element composition of the promoter regions of the DiPRPs demonstrates that these genes might be controlled by phytohormones (especially ABA, GA, and MeJA), light, and the circadian clock, which is consistent with the environmental cues during Davidia bract development. Synteny analysis indicated that the PRP genes from the Davidia genome have higher collinearity with naturally bracted plants, such as Antirhonum majus and Bougainvillea glabra, but lower collinearity with non-bracted species. Our results suggest that high expression of certain PRP genes, specifically in bracts, might be critical for leaf metamorphosis. Full article

It has previously been reported that the RhoA/Rho-associated kinase (ROCK) pathway is involved in depolarization-induced contraction triggered by high [K⁺] stimulation in rat caudal arterial smooth muscle. Furthermore, we reported that activation of the upstream Ca²⁺-dependent proline-rich tyrosine kinase 2 (Pyk2) leads to phosphorylation of myosin targeting subunit of myosin light chain phosphatase (MYPT1) and 20 kDa myosin light chain (LC₂₀). These findings suggest that Rho guanine nucleotide exchange factors (RhoGEFs) or Rho GTPase-activating proteins (RhoGAPs) may mediate RhoA activation downstream of Pyk2, thereby contributing to depolarization-induced contraction. However, it remains unclear whether Pyk2 directly interacts with RhoGEFs or RhoGAPs. In this study, we investigated the interaction between Pyk2 and RhoGEFs or RhoGAPs during depolarization stimulation of rat caudal arterial smooth muscle. We examined the interaction between Pyk2 and RhoGEFs or RhoGAPs, which previously were identified in smooth muscle, specifically in rat caudal arterial smooth muscle, in response to 60 mM K⁺ stimulation by immunoprecipitation analysis. ArhGEF11, ArhGEF12, phosphorylated ArhGAP42 at Tyr792 (pTyr792-ArhGAP42) and phosphorylated ArhGAP42 at Tyr376 (pTyr376-ArhGAP42) co-immunoprecipitated with Pyk2. The co-immunoprecipitation of pTyr792-ArhGAP42, but not pTyr376-ArhGAP42, with Pyk2 was inhibited by a Pyk2 inhibitor, sodium salicylate. Furthermore, 60 mM K⁺ stimulation increased ArhGAP42 phosphorylation at Tyr792, which was also suppressed by sodium salicylate. These findings indicate that Pyk2-mediated phosphorylation of ArhGAP42 at Tyr792 may play a role in depolarization-induced contraction of rat caudal arterial smooth muscle. Full article

Two proline-rich antimicrobial peptides (PrAMPs), named P1 and P2, purified from hemolymph of the greater wax moth Galleria mellonella, were studied for their effects on Gram-negative (Escherichia coli) and Gram-positive (Micrococcus luteus) bacteria. Both peptides decreased the M. luteus bacterial survival rate and caused E. coli bacterial membrane permeabilization. However, in both cases, the P2 peptide was approximately three times more effective than the P1 peptide. Fluorescence microscopy imaging demonstrated binding of both FITC-labeled peptides to E. coli and M. luteus cells. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) imaging of peptide-treated bacteria revealed considerable changes in cell morphology, cell surface topography, and nanomechanical properties. The interactions of the PrAMPs with bacterial cells were also analyzed by FTIR spectroscopy. The P1 peptide action toward E. coli led to partial aggregation of proteins, whereas treatment with P2 resulted in reduced protein aggregation, reflecting differences between both G. mellonella PrAMPs antibacterial action. Moreover, both PrAMPs caused a decrease and an increase in the protein content in relation to lipids on the E. coli and M. luteus cell surface, respectively. The obtained results reflect not only differences between the G. mellonella P1 and P2 peptides but also differences in the cell surface between Gram-negative and Gram-positive bacteria. Both characterized G. mellonella PrAMPs are further representatives of proline-rich peptides with a membrane-permeabilizing antimicrobial mode of action. Full article

The utilisation of edible insects for human nutrition is a long-standing practice in many parts of the globe, and is being gradually introduced into countries without an entomophagic tradition as well. These unconventional sources of protein of animal origin have arisen as a sustainable alternative to other animal protein sources, such as meat. This review intends to present the compilation of data in the scientific literature on the chemical composition and nutritional value of the bee brood of A. mellifera species and subspecies as edible foods. For this, a comprehensive search of the scientific literature was carried out using the databases ScienceDirect, Scopus, Pub-Med, BOn, and SciELO. Appropriate keywords were used for the search to reach the research works that addressed the topics of the review. The results showed that bee brood has considerable quantities of protein, fat and carbohydrates. The most abundant amino acids are leucine and lysine (these two being essential amino acids) and aspartic acid, glutamic acid, and proline (these three being non-essential amino acids). As for the fatty acids, bee broods contain approximately equal fractions of saturated and monounsaturated fatty acids, while the polyunsaturated fatty acids are negligible. The dietary minerals present in higher quantities are potassium, phosphorus, and magnesium, and the most abundant vitamins are vitamin C and niacin; choline is also present, although it is not a true vitamin. Although bee brood from A. mellifera has potential for human consumption as a nutrient-rich food, there are still many aspects that need to be further studied in the future, such as safety and hazards linked to possible regular consumption. Full article

An investigation into the biological mechanisms initiated in wounded skin following the application of mesenchymal stem cells (MSCs) and nanoparticles (NPs) (Ag, ZnO), either alone or combined, was performed in mice, with the aim of determining the optimal approach to accelerate the healing process. This combined treatment was hypothesized to be beneficial, as it is associated with the production of molecules supporting the healing process and antimicrobial activity. The samples were collected seven days after injury. When compared with untreated wounded animals (controls), the combined (MSCs+NPs) treatment induced the expression of Sprr2b, encoding small proline-rich protein 2B, which is involved in keratinocyte differentiation, the response to tissue injury, and inflammation. Pathways associated with keratinocyte differentiation were also affected. Ag NP treatment (alone or combined) modulated DNA methylation changes in genes involved in desmosome organization. The percentage of activated regulatory macrophages at the wound site was increased by MSC-alone and Ag-alone treatments, while the production of nitric oxide, an inflammatory marker, by stimulated macrophages was decreased by both MSC/Ag-alone and MSCs+Ag treatments. Ag induced the expression of Col1, encoding collagen-1, at the injury site. The results of the MSC and NP treatment of skin wounds (alone or combined) suggest an induction of processes accelerating the proliferative phase of healing. Thus, MSC-NP interactions are a key factor affecting global mRNA expression changes in the wound. Full article

Caragana korshinskii, a protein-rich feed plant in arid regions, lacks comprehensive nutrient analysis. This study compared the chemical composition of its five parts (leaves, bark, twigs, branches, and stems) and evaluated protein quality through amino acid profiling and enzymatic digestion. Results showed that leaves and bark contained higher crude protein (16.6–18.6%) than stems (6.8%), with fiber components (NDF > 81% and ADF > 65%) contributing to structural rigidity. Aspartic acid dominated caragana proteins, while bark and twigs exhibited elevated proline levels. CNCPS analysis revealed leaves contained 53.3% intermediately degradable protein (PB₂) versus 11.6% non-protein nitrogen (PA), whereas bark and twigs had 38.8% and 45.8% PA, respectively. Despite higher PA content, bark and twigs demonstrated superior in vitro protein digestibility (73.2% and 67.4%) compared to leaves (61.2%). The findings established baseline nutritional data, highlighting part-specific variations in protein characteristics critical for optimizing caragana’s application in animal feed technology within resource-limited ecosystems. Full article

Background/Objectives: Head and neck squamous cell carcinoma (HNSCC) ranks sixth in the world in terms of incidence. Small proline-rich proteins (SPRRs) are precursors of the keratinocyte envelope and act as substrates of transglutaminase. A change in SPRR expression is characteristic in a few types of cancer. Our aim was to determine the concentration of SPRR1A and SPRR2A in tumours samples obtained from 61 patients with HNSCC (OSCC, OPSCC, LSCC, HPSCC, NCSCC, and SSCC). Also, we aimed to determine the relationship between protein concentration and other clinical and/or demographic variables. Methods: An ELISA test was used to determine the concentrations of SPRR in the tumour tissue homogenates. Results: In margin samples, we found a statistically significant association between SPRR1A levels and nodal status (N) and between SPRR1A levels in tumours and margins with G2 histological grade. When we analysed the effect of tobacco and alcohol habits, we found a statistically significant difference between the SPRR1A and SPRR2A amount in smokers and non-smokers in margin samples. Also, we found a statistically significant difference between the SPRR1A and SPRR2A levels in tumour and margin samples obtained from patients that either abstain and occasionally or regularly consume alcohol. Furthermore, we found in tumour and margin samples from patients with concomitant diseases an association between SPRR1A and SPRR2A levels. Our results showed altered concentrations of SPRR1A at margins, depending on HPV status. Conclusions: These results suggest that differences in SPRR proteins are determined by disease status and unhealthy behaviours, which, in a wider perspective, can influence carcinogenesis. Full article

Symbiotic interactions between legumes and a group of soil bacteria, known as rhizobia, lead to the formation of a specialized organs called root nodules. Inside them, atmospheric nitrogen (N₂) is fixed by bacteria and reduced to forms available to plants, catalyzed by the nitrogenase enzyme complex. The development of a symbiotic relationship between legumes and nodule bacteria is a multi-stage, precisely regulated process, characterized by a high specificity of partner selection. Nodulation involves the enhanced expression of certain plant genes, referred to as early- and late-nodulin genes. Many nodulin genes encode hydroxyproline-rich glycoproteins (HRGPs) and proline-rich proteins (PRPs) which are involved in various processes, including infection thread formation, cell signaling, and defense responses, thereby affecting nodule formation and function. Cyclophilins (CyPs) belong to a family of proteins with peptidyl-prolyl cis–trans isomerase activity. Proteins with cyclophilin domain can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, and mitochondrion. They are involved in various processes, such as protein folding, cellular signaling, mRNA maturation, and response to biotic and abiotic stress. In this review, we aim to summarize the molecular processes involved in the development of symbiosis and highlight the potential role of cyclophilins (peptidyl-prolyl cis-trans isomerases) in this process. Full article

Coccidiosis, caused by Eimeria spp., significantly reduces poultry productivity and causes major economic losses. Traditional control methods are limited by drug resistance and high production costs. Recent genomic and bioinformatic advances have enabled the identification of novel antigens, making recombinant subunit vaccines a promising next-generation strategy by eliciting robust cellular and humoral immune responses. This study investigates the E. necatrix gametocyte protein 56 (EnGAM56) as a potential candidate for recombinant subunit vaccines. The full-length E. necatrix gametocyte gam56 gene (Engam56-F) was amplified, expressed in vitro, and characterized via SDS-PAGE and Western blot. Immunofluorescence assays revealed that EnGAM56-F is specifically localized in gametocytes and unsporulated oocysts. Chickens immunized with recombinant proteins (rEnGAM56-F and rEnGAM56-T) were evaluated for immunoprotection against E. necatrix infection through lesion scores, weight gain, oocyst production, anticoccidial index (ACI), and antibody and cytokine levels. The synergistic effects were evaluated by employing various combinations of recombinant proteins, including rEtGAM22, rEtGAM56-T, and rEtGAM59. Results showed that EnGAM56-F encodes a 468-amino acid protein with distinct tyrosine-serine-rich and proline-methionine-rich regions. rEnGAM56-F was specifically recognized by both anti-6 × His tag antibodies and convalescent serum from chickens infected with E. necatrix. Both rEnGAM56-F and rEnGAM56-T provided immune protection, with rEnGAM56-T showing superior efficacy. The combination of rEnGAM (22 + 59 + 56-T) yielded the strongest immune response, followed by rEnGAM (22 + 56-T). These findings highlight the potential of EnGAM56 as a candidate for recombinant subunit anticoccidial vaccines. Full article

Sheep milk is a rich source of bioactive compounds with significant potential in functional foods and biomedical applications. It contains high levels of proteins, peptides, and fatty acids with numerous health-promoting properties for the human body. Key components such as lactoferrin, proline, orotic acid, and conjugated linoleic acid (CLA) support the prevention and treatment of chronic diseases such as diabetes, cardiovascular disease, obesity, cancer, and neurodegenerative disorders. Bioactive peptides from sheep milk regulate blood glucose levels by inhibiting enzymes such as dipeptidyl peptidase-IV (DPP-IV) and α-glucosidase, while conjugated linoleic acid improves lipid metabolism and reduces inflammation. The high-quality proteins in sheep milk are essential for tissue regeneration and maintaining muscle mass, which is particularly beneficial for the elderly and infants who are allergic to cow milk. Recently, there has been an increasing interest in hydrogel dressings enriched with bioactive substances from sheep milk, which support wound healing by supporting collagen synthesis, reducing inflammation, and having antimicrobial properties. Such hydrogels are particularly promising for the treatment of chronic wounds, burns, and diabetic ulcers, making them a valuable tool in regenerative medicine. The aim of this manuscript is to review the current reports on bioactive components of sheep milk and their potential for biomedical applications. Full article