The protein journal最新文献

The presence of tumor heterogeneity is a critical issue that restricts the success of targeted therapies and negatively impacts patient outcomes. Recent studies have concentrated on the development of multi-epitope peptides that exhibit considerable overexpression in cancerous tissues with the aim of activating immune cells and utilizing immune-mediated responses to effectively suppress tumor growth. In this study, genes with increased expression in colorectal cancer (CRC) were identified using GEO data and R software. Following overexpression confirmation of APCDD1, we identified epitopes from the protein that can be recognized by various MHC molecules and presented on APC cell surfaces. Subsequent to expression and purification of the multi-epitope peptide and investigation on the BALB/c mice harboring tumor xenograft, obtained results showed a significant reduction in tumor growth, mitotic cell count, angiogenesis, metastasis, and an increase in Tumor-Infiltrating Lymphocytes (TILs) in the tumor microenvironment. Overall, the finding highlight the potential of multi-epitope peptide in CRC immunotherapy, where it may address the significant challenge of tumor heterogeneity.

Bacterial alpha-amylases have diverse industrial applications in food, fermentation, and pharmaceuticals. This study focuses on the isolation and characterization of a novel alpha-amylase-producing bacterium through molecular and in silico analyses, including molecular docking to determine enzyme-substrate specificity and binding interactions. Among nine bacterial isolates, S4 demonstrated the highest amylolytic activity of 63.68 U/ml. Molecular identification revealed isolate (S4) identity as Bacillus subtilis (OM278386). Enzyme charcterization revealed that maximum enzyme activity was observed at 40 °C and pH 7.0, after 24 h. The full-length novel alpha-amylase gene from B. subtilis (S4) was amplified, sequenced, and translated into a protein sequence. A putative protein was subjected to BLASTp, phylogenetic analysis, and physicochemical characterization. A 3D model was generated and validated through homology modeling. Molecular docking was performed using six substrates: amylopectin, maltotetraose, glycogen, starch, amylose, and cyclodextrin to determine substrate specificity. The putative AmyE protein comprised 488 amino acids. Phylogenetic analysis confirmed its close association with alpha-amylases of other Bacillus species. The enzymes exhibited industrially desirable traits, including high stability, thermotolerance, and hydrophilicity. In contrast, 3D model investigation showed excellent stereochemical quality, with 95.2% of amino acids in the favored region of the Ramachandran plot. Docking studies revealed the highest affinity for amylopectin (binding energy: - 7.2 kcal/mol). Two essential amino acid residues, Asp and Glu-318, were identified as crucial for active-site substrate interactions and enzyme catalysis across various substrates. In conclusion, the analysis presents alpha-amylase from B. subtilis stain S4 as a promising candidate for diverse industrial applications, offering cost-effective alternatives for starch processing, food preservation, and other biotechnological processes.

The review summarises the basic information on non-specific factors of mammals that potentially have antimicrobial action. A comparison of previously known factors with the latest literature data is carried out. The following peptide and protein factors are considered: lysozymes, transferrins, interferons, interleukin-2, antimicrobial peptides (defensins, cathelicidins, histatins) and protective glycoproteins (mucins, lectins). These major antibacterial factors perform regulatory functions in the immune system, and some are also able to resist viral and fungal infections or oncological pathologies. The study of the internal antibacterial factors of mammals and the mechanisms of their activation is of great importance for the fight against bacterial infections, including antibiotic-resistant ones. This knowledge is necessary for the development of new approaches to the treatment of humans and farm animals.

Glycerol kinase (GK) is a key part of glycerol metabolism. It connects the metabolic pathways for lipids and carbohydrates by phosphorylating glycerol to glycerol-3-phosphate in an ATP-dependent reaction. This is essential for maintaining carbohydrate homeostasis, plasma glycerol withdrawal, and the utilization of glycerol by different tissues. Together, these processes impact glucose uptake and lipid metabolism. This review discusses the structure of GK, highlights the implications of mutations in the primary sequence, and provides insights on the roles of the various functional domains in the GK-catalyzed reaction. It also discussed the roles of GK in glycerol metabolism, energy production, and its connections with various cellular pathways and disease conditions. The proper regulation of GK activity is crucial, reflecting its critical role in various important cellular processes. Therefore, its regulation has been analyzed from the gene level to posttranslational modification and has implications for GK-linked disease. Separately, the critical role of this enzyme in some disease-causing organisms made it a promising target for inhibitor development. We here explore the current state of GK inhibitor research and discuss strategies for their development. Challenges in GK inhibitor research are identified, and approaches such as high-throughput screening, structure-based drug design, and computational modelling for discovering novel inhibitors are reviewed. Finally, the review highlights critical areas for further research, including the role of GK in synthetic biology and tumour development, among others.

SARS-CoV-2 consists of the spike (S) protein which plays an important role in mediating the entry of virus into the host and it mainly consists of two subunits which are functionally different from each other. The first subunit S1, is involved in binding to the host receptor such as ACE2, and the second subunit S2, is involved in facilitating the viral membrane fusion with that of host membrane. Despite extensive research on the S1 domain due to its immunodominance and variability, the structurally conserved S2 domain remains relatively understudied. Recognizing the potential of S2 in modulating host responses, this study focuses on its recombinant expression, purification, and functional impact. The S2 coding region was cloned into the pGEX2TK plasmid to produce protein, which is a GST fusion-based protein and thereafter, the expression was done in BL21(DE3) strain of Escherichia coli cells. To enhance yield as well as solubility, protein expression was induced at a reduced temperature of 16 °C, minimizing aggregation and degradation. The fusion protein was purified via glutathione affinity chromatography, yielding high-purity S2 suitable for downstream applications. The S2 protein upon transfection into HEK293 and WI-38 mammalian cells leads to the expression of downregulated insulin-like growth factor 1 receptor (IGF-1R), as measured with the help of protein analysis. In order to highlight the role in pathogenesis of COVID-19 through modulation of cellular receptor and for the intervention of therapeutics, S2 can likely be considered a potential target.

D-p-hydroxyphenyl glycine (D-PHPG) is a D-amino acid used as an intermediate in the synthesis of semi-synthetic antibiotics. It is synthesized from hydantoin derivatives through two sequential enzymatic reactions involving D-hydantoinase (D-hase) and D-carbamoylase (D-case). Although whole-cell biocatalysis of D-PHPG is cost-effective, its efficiency suffers from transport obstacles, intracellular degradation, and limited substrate solubility. This study utilized a bacterial surface display system to express D-hase and D-case in Escherichia coli for D-PHPG production. Enzyme production optimization was carried out in two stages. Initially, key factors influencing cell density during co-culture were identified through culture media and fermentation parameters screening using the Plackett-Burman design, followed by optimization with the D-optimal method. Next, induction parameters were fine-tuned using response surface methodology. The optimal culture medium was found to contain glycerol (12 g/L) and yeast extract (15 g/L) under optimal induction conditions (0.17 mM IPTG, OD₆₀₀ of 1.3, and 21 °C). These conditions achieved an OD₆₀₀ of 15.6, with expression levels of 20.18% for D-case and 20.82% for D-hase. Scaling up in a stirred tank bioreactor resulted in an OD₆₀₀ of 32.15, with D-hase and D-case expression levels increasing to 25.8 and 24.2%, respectively, and enzymatic activities improving by 2.83 times for D-case and 3.42 times for D-hase. The optimized co-culture approach under optimized induction conditions achieved a conversion yield of 95% and a D-PHPG production yield of 90%. The study results showed that the suggested fermentation conditions will contribute to future scale-up studies aimed at improving enzyme activities for other surface protein production.