Protein and Peptide Letters最新文献

Introduction: Pleckstrin homology and RhoGEF domain-containing G7 (PLEKHG7) is a largely uncharacterized gene whose role in diffuse large B-cell lymphoma (DLBCL) remains unexplored. Thus, we aimed to profile PLEKHG7 expression, assess its prognostic value, and explore therapeutic implications.

Methods: RNA-seq data from TCGA-DLBCL (n=48) and GTEx normal tissues were analyzed via UCSC XENA. Differential expression was tested using the Wilcoxon rank-sum test and FDR correction. Prognostic significance was evaluated by Kaplan-Meier and multivariate Cox regression (nomogram). Gene set enrichment analysis (GSEA) mapped PLEKHG7-associated pathways. Drug sensitivity correlations were extracted from RNAactDrug. qRT-PCR validated expression in DLBCL cell lines (OCI-Ly3, SU-DHL-4) versus normal B lymphocytes (GM12878).

Results: PLEKHG7 was markedly up-regulated in DLBCL tissues (P < 0.001) and cell lines versus normal controls (AUC = 0.739). High PLEKHG7 expression predicted inferior overall survival (HR = 8.88; 95% CI: 1.09-72.27; P = 0.041) and remained an independent prognostic factor (HR = 10.109; P = 0.033). GSEA linked PLEKHG7 to ribosome, oxidative phosphorylation, proteasome, cytokine-cytokine receptor interaction, spliceosome, and ECM-receptor pathways. Elevated PLEKHG7 negatively correlated with sensitivity to idelalisib, omipalisib, belinostat, methotrexate, and dacinostat.

Discussion: The study's limitations include reliance on bioinformatics data and the lack of functional validation. Further research is needed to elucidate the molecular mechanisms underlying PLEKHG7's role in DLBCL and validate its clinical utility.

Conclusion: PLEKHG7 is significantly overexpressed in DLBCL and independently predicts poor prognosis. Its association with key oncogenic pathways and drug resistance underscores its potential as both a prognostic biomarker and a therapeutic target, warranting further functional validation.

Objective: This study aimed to identify novel proteins involved in retinoic acid (RA)-induced embryonic cleft palate development.

Methods: The palate tissues of the control and RA-treated E14.5 were dissected and subjected to iTRAQ-based proteomic analysis.

Results: Differential expression analysis identified 196 significantly upregulated and 149 downregulated considerably proteins in RA-induced palate tissues. Comprehensive Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed the significant involvement of cytoplasmic translation, ribosome biogenesis, glycolysis/gluconeogenesis, and glutathione metabolism pathways in cleft palate pathogenesis triggered by RA. In particular, ribosome-related pathways were highly enriched, while glycolysis was disrupted. Protein-protein interaction analysis, facilitated by the STRING database, revealed a tightly interconnected network of differentially expressed proteins. Further analysis using the cytoHubba plugin in Cytoscape identified ten hub proteins, including Eif4a1, Gapdh, Eno1, Imp3, Rps20, Rps27a, Eef2, Hsp90ab1, Rpl19, and Rps16, indicating their potential roles in RA-induced cleft palate development, and thus positioning them as potential biomarkers for cleft palate.

Conclusion: These findings provide valuable insights into the proteomic changes associated with RA-induced cleft palate and shed light on key pathways and proteins that can contribute significantly to the pathogenesis of this congenital condition.

Alzheimer's disease (AD) treatments currently available have ineffective results. Previously employed Acetylcholine esterase inhibitors and memantine, an NMDA receptor antagonist, target a single target structure that plays a complex role in the multifactorial progression of disease. Memantine moderates the toxic effects of excessive glutamate activity by blocking NMDA receptors, which decreases neurotoxicity in AD, while acetylcholine esterase inhibitors function by blocking cholinergic receptors (muscarinic and nicotinic), preventing the breakdown of acetylcholine, thereby enhancing cholinergic transmission, thus improving cognitive functions in mild to moderate stages of AD. Every drug class targets a distinct facet of the intricate pathophysiology of AD, indicating the diverse strategy required to counteract the advancement of this neurodegenerative disorder. Thus, patients are currently not getting much benefit from current drugs. A closer look at the course of AD revealed several potential target structures for future drug discovery. AD drug development strategies focus on developing new target structures in addition to well-established ones for combination treatment regimens, ideally with a single drug that can target two different target structures. Because of their roles in AD progression pathways like pathologic tau protein phosphorylations as well as amyloid β toxicity, protein kinases have been identified as potential targets. This review will give a quick rundown of the first inhibitors of single protein kinases, such as glycogen synthase kinase (gsk3) β, along with cyclin-dependent kinase 5. We will also look into novel inhibitors that target recently identified protein kinases in Alzheimer's disease, such as dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A). Additionally, multitargeting inhibitors, which target multiple protein kinases as well as those thought to be involved in other processes related to AD will be discussed. This kind of multitargeting offers prospective hope for improved patient outcomes down the road since it is the most effective way to impede multifactorial disease development.

Background: The role of Zona pellucida glycoprotein 3 (ZP3) is unclear in pancreatic adenocarcinoma (PAAD).

Objective: This study aimed to explore the role of ZP3 in PAAD.

Methods: A comparative analysis of ZP3 gene expression was performed to discern differences between various types of cancer and PAAD, leveraging data sourced from The Cancer Genome Atlas (TCGA). This study aimed to assess the role of ZP3 as a potential diagnostic marker for PAAD. The relationship between ZP3 levels and clinical characteristics, as well as patient outcomes, was scrutinized. Additionally, genomic enrichment analysis was carried out to uncover the underlying regulatory mechanisms associated with ZP3. The study further delved into the association of ZP3 with immune system interactions, checkpoint gene expression, Tumor Mutational Burden (TMB), microsatellite instability (MSI), and tumor stemness index (mRNAsi). The aberrant expression patterns of ZP3 in PAAD cell cultures were confirmed through the application of quantitative reverse transcription PCR (qRT-PCR) techniques.

Results: ZP3 exhibited aberrant expression in both pan-cancer and PAAD. A significant correlation was observed between increased levels of ZP3 expression in PAAD patients and histologic grade (p = 0.026). Elevated ZP3 expression in PAAD was found to be significantly associated with poorer overall survival (p = 0.003), progression-free survival (p = 0.012), and disease-specific survival (p = 0.002). In PAAD, the level of ZP3 gene expression was statistically significant (p < 0.001) and recognized as a key determinant of patient prognosis. ZP3 exhibited associations with various biological pathways, including primary immunodeficiency, oxidative phosphorylation, and other pathways. ZP3 expression demonstrated correlations with immune infiltration, immune checkpoint genes, TMB, MSI, and mRNAsi in PAAD. Moreover, a pronounced negative correlation was detected between ZP3 expression levels and the therapeutic effectiveness of various medications, including selumetinib, bleomycin, FH535, docetaxel, and tanespimycin, within the context of PAAD. Elevated levels of ZP3 were consistently observed in cell line models of PAAD.

Conclusion: ZP3 has the potential to serve as a prognostic biomarker and therapeutic target for patients with PAAD.

Autophagy is a self-eating cellular process in which the cell breaks down worn-out organelles, damaged/defective proteins, and toxins. Impaired autophagy is a significant factor in the development of various metabolic disorders, along with oxidative stress, inflammation, mitochondrial and endoplasmic reticulum dysfunction. These disorders pose a significant health and economic burden on the global human population, owing to their steadily rising prevalence. Therefore, modulating the expression of proteins involved in the autophagy-related pathways can be a promising avenue for curbing the development and progression of these disorders. Humanin (HN) is a 24-amino acid mitochondrial-derived peptide. It possesses anti-oxidant, anti-inflammatory, and pro-apoptotic properties. The analogs of HN can be generated by replacing specific amino acids in the polypeptide chain, thereby functionally modifying the peptide. Among these, humanin- glycine (HNG) is the most widely studied analog in both in vivo and in vitro disease models. It is far more potent than HN, with a potency that is 1000 times greater. To the best of our knowledge, this review is the first to discuss and examine the available evidence regarding the potential involvement of HN or its analogs in regulating autophagy pathways. The review primarily highlights that HN is an autophagy inducer, which can promote cell survival in the presence of metabolic and oxidative stress, particularly the HNG analog. Future research is imperative to comprehensively evaluate the effects of HN and its analogs on autophagy. Further investigations are needed to correlate its levels with various autophagic markers in different metabolic diseases, offering the potential for groundbreaking discoveries in understanding disease mechanisms and developing novel therapeutic strategies.

Introduction: The present study aims to compare the monotherapy of diosmetin and 5- hydroxydecanoate (5-HD) against the therapeutic effect of their combination therapy in the unilaterally injected rotenone-induced neurotoxicity in the male rats. Motor deficits accompany Parkinson's Disease (PD), while Bioflavonoids like diosmetin, which are antioxidants and anti-inflammatories, protect against neurotoxins. Moreover, mitochondrial dysfunction contributes to PD. The mitochondrial ATP-sensitive potassium channel [mito(KATP)] regulates reactive species and 5-HD, meaning decreasing it may lessen mitochondrial injury. To evaluate the effect of diosmetin, alone and in combination with 5-HD, on Oxidative Stress (OS) markers, mitochondrial function, and dopaminergic preservation in the SNpc.

Methods: Male Wistar rats were divided into seven groups, including normal control, sham, rotenone-treated, and treatment groups receiving diosmetin, 5-HD, their combination, or selegiline as a standard drug. Biochemical assays were conducted to assess OS markers, mitochondrial complex- I activity, and dopaminergic neuroprotection. Behavioral tests were performed to evaluate motor deficits.

Results: Rotenone administration significantly increased OS, impaired mitochondrial complex-I activity, and reduced motor coordination. Diosmetin treatment significantly reverses the effects of rotenone. Combined treatment with diosmetin and 5-HD showed enhanced neuroprotective effects compared to individual treatments.

Discussion: This study demonstrates that both diosmetin and 5-HD monotherapies alleviate rotenone-induced behavioral impairments in the experimental rats. Additionally, the individual treatment of diosmetin and 5-HD reduces dopaminergic toxicity induced by rotenone. At the sub-- cellular level, diosmetin and 5-HD monotherapies counteract rotenone's impact on antioxidant markers, DA metabolites, and mitochondrial function in the SNpc region of the brain. Notably, combining diosmetin and 5-HD yielded superior therapeutic effects on rotenone-induced behavioral and molecular changes compared to either monotherapy alone. These findings suggest that diosmetin and 5-HD may offer a promising alternative for PD management.

Conclusion: Diosmetin exhibits potent antioxidant and neuroprotective properties against rotenone-induced PD-like pathology. The combination of diosmetin and 5-HD offers a synergistic therapeutic potential, suggesting a promising approach for managing oxidative stress and mitochondrial dysfunction in PD.

Introduction: Superoxide Dismutases (SODs) are enzymes that catalyzes the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.

Materials and methods: Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector, followed by its subcloning in an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.

Results: The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40°C and pH 8, respectively. The enzyme remains completely stable at 40°C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50°C and 60°C for 3 h. The biophysical investigation revealed stable conformation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi- Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.

Discussion: The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn²⁺ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.

Conclusion: The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, including therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.

Background: The transformation of proteins from their native conformation into highly ordered fibrillar structures due to their misfolding and aggregation under particular conditions are described as beta-sheet enriched amyloid fibrils. The accumulation of these fibrils in different body parts is the major cause of several neurological and non-neurological conditions (proteinopathies).

Objectives: To prevent these proteinopathies, inhibition of protein aggregation is considered a promising strategy. Therefore, in this study, we synthesized montmorillonite (MMT) based poly- orthophenylenediamine (PoPD) nanocomposites (NCs) and characterized their size and morphology due to their remarkable biological properties. Further, the effect of these nanocomposites on inhibition of fibril formation was assessed.

Methods: These nanocomposites were evaluated for their anti-amyloidogenic potential on two model proteins of amyloidopathies, i.e., human lysozyme and human serum albumin (HL & HSA), by using several biophysical methods, such as Thioflavin T (ThT) and 1-anilino-8-naphthalene sulfonate (ANS) fluorescence, congo red dye binding assay (CR). Secondary structural content was evaluated by Circular dichroism (CD) spectroscopy.

Results: Results demonstrated that synthesized nanocomposites significantly inhibited fibril formation in dose-dependent manner that corresponds to their ability to arrest fibrillation. It is suggested that they may adsorb proteins to protect them against aggregation when they are subjected to aggregating conditions.

Conclusion: This study offers an opportunity to understand the mechanism of inhibition of fibril formation by nanocomposites, showing that they inhibit amyloid formation and amyloid diseases. Thus, the study concludes that these nanocomposites are promising candidates as therapeutic molecules for proteinopathies and are envisaged to enrich the area of personalized medicine, augmenting the human healthcare system.

Introduction: The progression of type 2 diabetes in humans appears to be linked to the loss of insulin-producing β-cells. One of the major contributors to β-cell loss is the formation of toxic human IAPP amyloid (hIAPP, Islet Amyloid Polypeptide, amylin) in the pancreas. Inhibiting the formation of toxic hIAPP amyloid could slow, if not prevent altogether, the progression of type 2 diabetes. Many non-human organisms also express amyloidogenic IAPP variants known to kill pancreatic cells and give rise to diabetes-like symptoms. Surprisingly, some of these non-human IAPP variants function as inhibitors of hIAPP aggregation, raising the possibility of developing non-human IAPP peptides into anti-diabetic therapeutic peptides. One such inhibitory IAPP variant is seal IAPP, which has been shown to inhibit hIAPP aggregation. Seal IAPP only differs from hIAPP by three amino acids. In this study, each of the six seal/human IAPP permutations was analyzed to identify the role of each of the three amino acid positions in inhibiting hIAPP aggregation.

Aims: This study aimed to identify the minimal amino acid substitutions to yield a peptide inhibitor of human IAPP aggregation.

Objective: The goal of the study was to determine the minimal amino acid substitutions necessary to convert human IAPP into an amyloid-inhibiting peptide.

Methods: The formation of toxic hIAPP amyloid was monitored using Thioflavin T binding assays, atomic force microscopy, and MTT cell rescue studies.

Results: One seal IAPP variant retained amyloid-inhibition activity, and two variants appeared to be more amyloidogenic and toxic than wild-type human IAPP.

Conclusion: These results suggest that inhibition of hIAPP requires both the H18R and F23L substitutions of hIAPP.

Introduction/objective: Protein phosphatases act as counterparts to protein kinases and are considered crucial for the homeostatic balance of cell signalling. In contrast to kinases, which can be categorized according to their substrate specificity, phosphatases are versatile and can detect substrates with much less distinction; hence, it is challenging to identify the physiological phosphatase-substrate pair. The Oca1 of Saccharomyces cerevisiae is a putative protein tyrosine phosphatase (PTP) and is required for cell cycle arrest in response to oxidative stress. The Oca1 mutants are sensitive to mTOR inhibitors, such as caffeine and rapamycin, and are involved in the regulation of TOR function. In an earlier research work, the enzyme exhibited no in vitro phosphatase activity and it was suggested that post-translational modifications or additional factors are necessary for it to be functional.

Methods: The modeling of Oca1 was performed to gain insight into the structural aspects. The full- length enzyme, as well as the enzyme without the N-terminal extension, was cloned, expressed, and purified to homogeneity. The structure, function, and stability of the purified enzyme were assessed using circular dichroism, fluorescence, and visible spectroscopy studies.

Results: The Oca1 was expressed and purified from Escherichia coli. The enzyme has been found to be functional, stable, and exist in an extended monomeric form, with a molecular mass of about 27 kDa. The enzyme without the extended N-terminal random coil has also been functional and slightly more stable than the full-length Oca1.

Conclusion: The purified functional enzyme may be used to gain insights into the biochemical aspects and its role in bioengineering.