Protein and Peptide Letters最新文献

Background and objective: Canonical Wnt (Wnt/β-catenin) signaling maintains bone homeostasis by promoting osteoblastic activities. The inhibitory factor, Dickkopf-1 (DKK1), enhances bone resorption in malignant diseases. Low-density lipoprotein-related protein (LRP) 5 is antagonized by DKK1. This study aimed to investigate the expression of DKK1 and LRP5 in renal cell carcinoma bone metastasis (RCC-BM).

Methods: RCC-BM patients with paired samples of primary and metastatic lesions were selected for the study (RCC-BM group). RCC patients without any metastasis served as the control group (RCC-only group). Immunohistochemical staining with monoclonal anti-DKK1 and polyclonal anti- LRP5 antibody was conducted on paraffin-embedded slides. The staining results were recorded using scoring according to staining intensity in the renal tissue adjacent to the tumor, primary RCC lesions, and RCC-BM lesions.

Results: DKK1 was differently expressed among normal renal tissues, primary RCC, and RCC- BM tissues (p<0.001). The DKK1 expression in primary RCC was significantly lower than that in normal renal tissues (p<0.001) without a difference between the RCC-BM and RCC-only groups. DKK1 expression in bone metastasis was significantly higher than that in primary tumors (p<0.001). For RCC-BM patients, the expression of LRP5 in the primary tumor was significantly lower than that in adjacent renal tissues (p<0.01). The tendency of lower expression was found in primary RCC from RCC-BM patients compared to RCC without metastasis (p=0.073).

Conclusion: A "rebound" pattern of DKK1 expression in bone metastasis lesions and the decreasing LRP5 expression in primary lesions of RCC-BM patients suggested that Wnt/β-catenin signaling was inhibited in RCC-BM. The overexpression of DKK1 and reduced expression of LRP5 suggest that these markers may be useful for the early prediction of RCC-BM.

Background: Molting and reproduction play vital roles in the life cycle of brachyuran crabs, and these two processes are closely interconnected. A key player in the molting cycle is cryptocyanin, which is similar to hemocyanin in sequence, size, and structure. Hemocyanin is a copper-containing oxygen-binding protein, while cryptocyanin is a copper-free protein that lacks oxygen-binding capacity.

Objective: The goal of the study was to carry out the isolation, cloning, and expression of the partial cryptocyanin gene from the Indian variety of Scylla olivacea.

Methods: The partial cryptocyanin gene was isolated from the hemocytes of the S. olivacea male and female crabs by qPCR for comparative expression analysis of the cryptocyanin gene.

Results: We successfully amplified, cloned, and expressed a 519 bp partial cDNA encoding cryptocyanin from the Indian variety of Scylla olivacea, within the pRSET-B vector.

Discussion: In this study, we conducted a comprehensive analysis of cryptocyanin expression in male and female crabs during the intermolt stage. Our findings revealed Cq values of 28.97 for males and 33.68 for females, highlighting a significantly lower abundance of cryptocyanin protein in female crabs.

Conclusion: Our study showed that crustacean cDNA can be effectively expressed in bacterial vectors, and clones were stable for up to 6 months at -80oC. Real-time data showed a significant difference in cryptocyanin levels between male and female crabs. This finding highlights the need for further research with a larger sample size for better understanding.

Background: MARVEL domain-containing 1 (MARVELD1) has been implicated in the progression of several cancers, but its role in pancreatic adenocarcinoma (PAAD) remains poorly understood.

Methods: RNA-seq data from the TCGA-PAAD and GTEx-Pancreas cohorts were analyzed to assess MARVELD1 expression. Stable MARVELD1 knockdown and overexpression were conducted in BxPC3 and PANC-1 cells. Cell viability, proliferation, migration, and invasion were evaluated using functional assays, and western blotting was employed to examine EMT-associated protein levels, including Vimentin, MMP2, MMP9, and E-cadherin. Differentially expressed genes (DEGs) between MARVELD1-high and MARVELD1-low groups were identified, and pathway enrichment analyses were performed.

Results: We observed a significant increase of MARVELD1 in PAAD patient samples, with elevated MARVELD1 levels correlating with poor clinical survival. Knockdown of MARVELD1 in PAAD cells remarkably decreased cell proliferation and colony formation, while overexpression of MARVELD1 enhanced these properties. Moreover, simulated cell invasion and migration assay further suggested that MARVELD1 might contribute to PAAD cell aggressiveness. Mechanistically, MARVELD1 promoted tumor cell migration and invasion through the activation of Vimentin, MMP2, and MMP9 protein while suppressing E-cadherin. Bioinformatics analysis revealed that MARVELD1-high samples were enriched in EMT-related pathways, including TGF-β receptor signaling, actin cytoskeleton regulation, and cell adhesion.

Conclusion: Taken together, our study highlights the roles of MARVELD1 in promoting tumor cell proliferation and invasion, suggesting its potential application as a prognostic and diagnostic biomarker for PAAD in the clinical context.

Background: Gene fusion techniques have yielded promising results in the fusion of thermostable polymerases (Taq and Pfu) with single-stranded and double-stranded DNA-binding proteins. Constructing a terminal deoxynucleotidyl transferase (TdT) fusion enzyme with DNAbinding protein domains can enhance thermostability and broaden the enzyme's application field. This makes it a promising candidate for cost-effective de novo DNA synthesis and a more effective tool for demonstrating apoptosis and detecting viral DNA/RNA.

Methods: The design of fusion proteins was based on molecular dynamics and homology modeling. Native and fusion proteins were isolated using affinity chromatography on HisTrap HP. Thermostability was assessed through differential scanning fluorimetry and dynamic light scattering. HPLC analysis was conducted to evaluate enzyme activity.

Results: According to the in silico predictions of the fusion protein structure, a homotetramer was formed. The expressed fusion proteins were successfully purified under native conditions, similar to TdT. The total yields of the studied proteins were 130 mg/L for single-stranded binding protein from E. coli (EcSSB), 5 mg/L for TdT, 9 mg/L for TdT_L1_EcSSB, and 7 mg/L for TdT_L2_EcSSB. The measured radius of TdT (3.5 nm) was found to be consistent with a monomeric structure; however, the fusion proteins were expected to form a homotetramer. Additionally, fusion with EcSSB was found to prevent aggregation, which positively affected the thermal stability of the fusion protein. Instead of elongating the substrate by adding nucleotides, the fusion enzyme removed a nucleotide, specifically TTP, from the 3'-end of the DNA strand.

Conclusion: The fusion of TdT with EcSSB resulted in increased thermal stability and a reduced ability to add nucleotides to the substrate.

Immune responses depend on the identification and prediction of peptides that bind to MHC (major histocompatibility complex) class I molecules, especially when it comes to the creation of vaccines, cancer immunotherapy, and autoimmune disorders. The ability to predict and evaluate MHC class immunoproteomics have completely transformed I epitopes in conjunction with immunoinformatics technologies. However, precisely identifying epitopes across various populations and situations is extremely difficult due to the complexity and diversity of MHC class I binding peptides. The most recent developments in immunoinformatics technology that have improved MHC class I epitope prediction are examined in this article. The sensitivity and specificity of epitope prediction have been greatly enhanced by recent developments that have concentrated on bioinformatics algorithms, artificial intelligence, and machine learning models. Potential epitopes are predicted using large-scale peptide-MHC binding data, structural characteristics, and interaction dynamics using tools like NetMHC, IEDB, and MHCflurry. Additionally, the integration of proteomic, transcriptomic, and genomic data has improved prediction accuracy in real-world scenarios by enabling more accurate identification of naturally occurring peptides. Furthermore, newer techniques like deep learning and multi-omics data integration have the potential to overcome peptide binding prediction constraints. Utilizing these technologies is expected to speed up the identification of new epitopes, improve the accuracy of immunotherapy techniques, and enable customized vaccine development. These innovative techniques, their uses, and potential future developments for improving MHC class I epitope prediction in immunoproteomics are highlighted in this study.

Background: Tissue Factor (TF) is a crucial transmembrane glycoprotein that triggers blood coagulation upon vascular or tissue injury by binding to plasma factors VII and VIIa. In recent years, the demand for TF has rapidly increased due to its pivotal role in preoperative coagulation tests. However, large-scale production of TF remains challenging despite successful recombinant expression, as incorrect post-translational modifications adversely affect TF activity.

Objective: This study aims to investigate the role of post-translational modifications, specifically N-glycosylation, in TF activity and stability. Additionally, it explores strategies to enhance TF production by reducing its degradation through genetic modulation.

Methods: We compared TF activity derived from human cells and E. coli to assess the impact of post-translational modifications. Furthermore, we examined the effect of N-glycosylation on TF function. To address TF degradation, we knocked out the HRD1 gene, a key component of the endoplasmic- reticulum-associated degradation (ERAD) pathway, and evaluated its impact on TF stability and activity.

Results: TF produced in human cells exhibited higher activity than TF expressed in E. coli, emphasizing the importance of post-translational modifications. Specifically, N-glycosylation was found to influence TF activity and stability. Additionally, we observed that knocking out the HRD1 gene effectively reduced TF degradation without compromising its activity.

Conclusion: Our findings underscore the crucial role of N-glycosylation in TF function and stability. Moreover, the modulation of the ERAD pathway through knocking out HRD1 presents a promising approach for enhancing TF production. These insights could contribute to the large-scale manufacturing of functionally active TF for clinical and research applications.

Introduction: Angora goats are a distinct breed that differs significantly from common goats and shares a similar appearance to sheep. In Angora goats, only the level of glutathione (GSH) is elevated during under-stimulated conditions, as well as after the period of hypoxic stress; however, no changes are found in 2,3-diphosphoglycerate (2,3-DPG) levels, which are commonly present in the red blood cells (RBCs) of most mammals. We chose the Angora goat for our investigation because no previous studies have been conducted on the structural and functional aspects of hemoglobin (Hb). In addition, no sequence or structural information is currently available in any database.

Methods: Angora goat Hb was isolated and purified by anion-exchange chromatography, followed by crystallization using various methods. X-ray data collection for Angora goat Hb was performed under a liquid nitrogen cryo-stream using a Bruker D8 Venture Bio Photon III 28-pixel array area detector system.

Results: Good diffracting crystals were obtained using the hanging-drop vapor-diffusion method with polyethylene glycol (PEG) 3350 as the precipitant in water, without the addition of any salt or buffer. The Angora goat Hb diffracted to a resolution of 1.85 Å, and the structure solution was obtained by the molecular replacement method, using the structure of domestic goat Hb as the starting model.

Discussion: The solved structure of Angora goat crystallized in the monoclinic space group P21, consisting of one whole biological molecule in the asymmetric unit, with unit cell dimensions of a = 52.08 Å, b = 76.70 Å, c = 74.08 Å, and β = 91.77 °. The solvent content and Matthews coefficient (Vm) for the Angora goat Hb are 49.05% and 2.41 ų/Da, respectively, and are within the normal range for protein crystals.

Conclusion: Purification, crystallization, and preliminary X-ray diffraction studies of Angora goat Hb were performed successfully. Structural refinement and biophysical characterization of Angora goat Hb are in progress in the absence and presence of GSH and 2,3-DPG.

With the emergence of the precision medicine era, targeting specific proteins has emerged as a pivotal breakthrough in tumor diagnosis and treatment. Apurinic/apyrimidinic Endonuclease 1 (APE1) is a multifunctional protein that plays a crucial role in DNA repair and cellular redox regulation. This article comprehensively explores the fundamental mechanisms of APE1 as a multifunctional enzyme in biology, with particular emphasis on its potential significance in disease diagnosis and strategies for tumor treatment. Firstly, this article meticulously analyzes the intricate biological functions of APE1 at a molecular level, establishing a solid theoretical foundation for subsequent research endeavors. In terms of diagnostic applications, the presence of APE1 can be detected in patient serum samples, biopsy tissues, and through cellular in situ testing. The precise detection methods enable changes in APE1 levels to serve as reliable biomarkers for predicting tumor occurrence, progression, and patient prognosis. Moreover, this article focuses on elucidating the potential role of APE1 in tumor treatment by exploring various inhibitors, including nucleic acid-based inhibitors and small molecule drug inhibitors categories, and revealing their unique advantages in disrupting DNA repair function and modulating oxidative-reduction activity. Finally, the article provides an outlook on future research directions for APE1 while acknowledging major technical difficulties and clinical challenges that need to be overcome despite its immense potential as a target for tumor therapy.

Introduction: Gastric cancer has emerged as one of the major diseases threatening human health. Our previous studies indicated that the anti-cancer bioactive peptide (ACBP) inhibits the initiation and progression of gastric cancer through apoptosis and cell cycle arrest, yet the mechanisms remain unclear. To elucidate the relationships between the effects of ACBP and the levels of cell differentiation, as well as the functional mechanisms of ACBP, we conducted a study using three human gastric cancer cell lines: NCI-N87, MGC-803, and another unspecified line.

Methods: We investigated the impact of ACBP on the survival and morphology of these cancer cell lines, examined apoptosis and cell cycle progression, and detected the expression of TP53, TP63, and TP73 in cancer cells, as well as the expression of Bax, PUMA, and Mcl-1 in a xenograft mouse model. ACBP inhibited the proliferation of all three cancer cell lines in a dose-dependent manner, similar to the positive control and 5-fluorouracil (5-FU). The effect of ACBP correlated with the degree of differentiation of the cancer cells; the lower the differentiation degree, the stronger the inhibitory effect.

Results: After ACBP treatment, the expression of TP53, TP63, and TP73 increased in all cell lines. In the xenograft mouse model, ACBP inhibited the growth of MGC-803 cells in vivo. The apoptotic-related genes Bax and PUMA were upregulated, while Mcl-1 was downregulated. ACBP inhibited tumor cell growth by inducing apoptosis through the TP53 signaling cascade, upregulating TP53, TP63, and TP73 and their downstream apoptosis-promoting genes Bax and PUMA while downregulating the anti-apoptotic gene Mcl-1.

Conclusion: Notably, after ACBP treatment, Mcl-1 expression was significantly reduced in the tumor tissue of the xenograft model, indicating that ACBP induced apoptosis through the TP53 signaling cascade. This project provides a scientific basis for exploring the antitumor mechanism of ACBP in gastric cancer therapy.

Introduction: Tritrpticin (TRP3) is a peptide belonging to the cathelicidin family and has a broad spectrum of antimicrobial activity. However, this class of biomolecules can be easily degraded in the body, making it necessary to use an efficient transport system. The ability to form stable nanostructures from the interaction of glycyrrhizin saponin with the pluronic polymer F127 was demonstrated, forming mixed biopolymeric micelles, highly promising as drug carriers.

Objective: The present work sought to understand the physicochemical interaction of the antimicrobial peptide TRP3 with the mixed polymeric micelle made from pluronic F127 and the saponin glycyrrhizin.

Methods: The interaction of tritrpticin with mixed nanostructured micelles was evaluated through fluorescence spectroscopy and fluorescence quenching with acrylamide. The experiments were performed at room temperature (25 ± 1°C), adopting an excitation wavelength set to 280 nm and emission between 300 and 500 nm, with a slit of 5 nm.

Results: The interaction of the cationic peptide tritrpticin with the mixed biopolymeric micelles was observed through the blue shift of the fluorescence emission to shorter wavelengths, proving the change of tryptophan to a more hydrophobic environment. Through the fluorescence suppression technique, it was possible to indicate the location of the peptide in the mixed micelles, proving tritrpticin to be partially inserted inside them.

Conclusion: It was concluded that tritrpticin interacted with mixed nanostructured micelles, forming a promising system for biotechnological applications.