Protein and Peptide Letters - Volume 30, Issue 6, 2023

Proteins are essential biomacromolecules in all living systems because they are the prominent ultimate executives of the genetic information stored in DNA. Thus, studying protein is one of the central tasks in biological sciences. The complexity, diversity, and dynamics of a protein's structure, function, and structure-function relationship, the inherent structural fragility and thus the requirements on handling proteins to maintain protein's structural and functional orderliness make it a rather tricky task to work with protein. The approach to understanding the functions of a protein has been progressing steadily. In this paper, we reviewed the progress on the approach to the functional study of proteins that tremendously contributed to understanding their biological significance. Emphasis was put on the advances in the age in which high-throughput DNA sequencing and bioinformatics analysis are revolutionizing biological study.

Background: Ulcerative colitis (UC) is an inflammatory intestinal disorder featured by mucosal injury. MicroRNAs (miRNAs) play a role in the pathogenesis underlying UC. Objectives: This study was conducted to investigate the role of miR-29c-3p in a dextran sodium sulfate (DSS)-induced UC mouse model and provide targets for UC treatment. Methods: The UC mouse model was established by DSS induction. The expression levels of miR- 29c-3p, lysine-specific demethylase 6B (KDM6B), zonula occludens-1 (ZO-1), Occludin, and lactate dehydrogenase A (LDHA) were detected by real-time quantitative polymerase chain reaction or Western blot assays. The mucosal injury was evaluated by disease activity index (DAI), colon length, Hematoxylin-Eosin staining, and fluorescein isothiocyanate-glucan permeability test. The binding between miR-29c-3p and KDM6B and the occupation of KDM6B or trimethylated H3 lysine 27 (H3K27me3) on the LDHA promoter were analyzed by the dual-luciferase and chromatinimmunoprecipitation assays. Results: miR-29c-3p was downregulated while KDM6B and LDHA were upregulated in DSS mice. miR-29c-3p overexpression reduced DAI and inflammatory cell infiltration while increasing colon length, intestinal permeability, and levels of ZO-1 and Occludin. miR-29c-3p inhibited KDM6B expression and increased H3K27me3 occupation on the LDHA promoter, thus inhibiting LDHA transcription. Overexpression of KDM6B or LDHA averted the protective role of miR-29c-3p upregulation in mucosal injury. Conclusion: miR-29c-3p limited KDM6B expression and increased the H3K27me3 occupation on the LDHA promoter to enhance LDHA transcription, moderating mucosal injury and delaying UC progression.

Introduction: Colorectal cancer (CRC) is hackneyed cancer and a major lethiferous cancer. Circular RNAs (CircRNAs) have been discovered to own important roles in controlling CRC progression. CircPSMC3 is known to exhibit lower expression in diversified cancers. However, the regulatory function of CircPSMC3 in CRC keeps unclear. Methods: The expression of CircPSMC3 and miR-31-5p was confirmed through RT-qPCR. The cell proliferation was measured through CCK-8 and EdU assays. The protein expression of genes was examined through a western blot. The cell invasion and migration were tested through Transwell and wound healing assays. The binding ability between CircPSMC3 and miR-31-5p was confirmed through the luciferase reporter assay. Results: CircPSMC3 exhibited lower expression in CRC tissues and cell lines. Additionally, CircPSMC3 was revealed to suppress cell proliferation in CRC. Moreover, through Transwell and wound healing assays, CircPSMC3 was discovered to repress CRC cell invasion and migration. In CRC tissues, miR-31-5p expression was up-regulated and negatively correlated with CircPSMC3 expression. Further mechanism exploration experiments disclosed that CircPSMC3 is bound with miR-31-5p to modulate the YAP/β-catenin axis in CRC. At last, through rescue assays, CircPSMC3 inhibited cell proliferation, invasion and migration through sponging miR-31-5p in CRC. Conclusion: Our work was the first time to probe the potential regulatory effects of CircPSMC3 in CRC, and these above results uncovered that CircPSMC3 inhibited CRC cell growth and migration through regulating miR-31-5p/YAP/β-catenin. This discovery hinted that CircPSMC3 may serve as a useful therapeutic candidate for CRC.

Background: The creation of brand-new, potent, and less harmful medications to treat leukemia is urgently needed. Antimicrobial peptides (AMPs) have drawn a lot of interest as potential substitutes for chemotherapy. Objective: In the present investigation, the anticancer activity of CM11, a short cationic AMP, was assessed on Jurkat and Raji leukemia cell lines and peripheral blood mononuclear cells (PBMCs). Methods: Different CM11 doses were applied to the Jurkat and Raji cell lines and PBMCs throughout a 24-hour period. The impact of the CM11 on cell viability and toxicity was assessed using an MTT assay. Flow cytometry and Real-Time PCR were used to analyze the effect of this peptide on apoptotic/necrosis pathways and assess the ratio expression of the P53 and Bcl-2 genes, respectively. Results: Despite the fact that peptide toxicity was successful in a variety of cell lines, cancer cells were more sensitive to the medication. The survival of Jurkat and Raji cell lines treated with 32 μg/ml peptide was 47% and 51%, respectively, while the survival of normal PBMC cells was about 65%. According to flow cytometry, Jurkat and Raji cells exposed to peptide had much greater levels of apoptosis than PBMCs. Peptide-treated cells were associated with increased expression of P53 the gene and decreased expression of the Bcl-2 gene. Conclusion: These results revealed that the CM11 caused more cytotoxicity to leukemia Raji and Jurkat leukemia cells compared to the normal cells by apoptosis pathway. Our findings demonstrated the potential of CM11 peptide to develop as a new antileukemic agent.

Introduction: Diabetic peripheral neuropathy (DN) is the most common complication of type 2 diabetes mellitus (T2DM). Objective: This study aimed to explore the role of fibrinogen (FIB) in T2DM neuropathy and its preliminary mechanism. Methods: Ten male Sprague-Dawley rats were divided into a normal control group (NC group) and a T2DM neuropathy model group (DN group). The DN group was given a high-energy diet and streptozotocin, while the NC group was given a normal diet and a citric acid buffer. The expression levels of related proteins were analysed. Results: Electrophysiology: Compared with the NC group, the conduction latency of the somatosensory-evoked potential and nerve conduction velocity was prolonged in the DN group, while the motor nerve action potential was decreased. As seen under a light microscope, the peripheral nerve fibres in the DN group were swollen, and the nerve fibres in the posterior funiculus of the spinal cord were loose or missing. Moreover, as seen under an electron microscope, the peripheral nerve demyelination of the DN group was severe, with microvascular blood coagulation, luminal stenosis, and collapse. Compared with the NC group, in the DN group, the expression of FIB was positively correlated with the expression of both ionised calcium-binding adaptor molecule-1 and glial fibrillary acidic protein. Compared with the NC group, in the DN group, the expression of platelet/endothelial cell adhesion molecule-1 and B-cell lymphoma 2 was negatively correlated. Conclusion: The increased concentration of FIB may be the cause of neuropathy, and its mechanism may be related to its promotion of inflammatory response, blood coagulation, and vascular stenosis.

Background: Knobs-into-holes (KiH) technology has been widely used in asymmetric bispecific antibody (bsAb) construction to promote heavy chain heterodimerization. However, despite the great improvement of heterodimer formation by this strategy, homodimers (especially the holehole homodimer) can still be generated at low levels. Consequently, hole-hole homodimer is a common byproduct associated with the production of KiH bsAbs. In addition, previous studies showed that hole-hole homodimer exists as two different isoforms. As the major difference between these two isoforms lies in the Fc region, we speculated that Protein A media, which bind IgG Fc region with high affinity, and CaptureSelect FcXP, a CH3 domain-specific affinity resin, may provide certain resolution between these two conformational isoforms. Objective: The objective of this study was to study the capability of Protein A and CaptureSelect FcXP affinity resins in differentiating hole-hole homodimer isoforms. Methods: The hole-hole homodimer was produced in CHO cells by expressing the hole half-antibody. The homodimer, along with the half-antibody was initially captured by Protein A chromatography and was then further purified by size-exclusion chromatography (SEC), which separated the homodimer from the unpaired half-antibody. The purified hole-hole homodimer was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and analytical hydrophobic interaction chromatography (HIC). The purified hole-hole homodimer was separately processed by columns packed with Protein A and CaptureSelect FcXP resins. The purified hole-hole homodimer was also analyzed by Protein A-high-performance liquid chromatography (HPLC). Results: SDS-PAGE analysis and analytical HIC study confirmed that hole-hole homodimer exists as two conformational isoforms. When the hole-hole homodimer was processed by Protein A and CaptureSelect FcXP chromatography, the elution profiles contained two peaks, indicating that both affinity resins possess the capability of differentiating hole-hole homodimer isoforms. Conclusion: Our data suggest that Protein A and CaptureSelect FcXP affinity resins both possess the capability of differentiating hole-hole homodimer isoforms and, therefore, can be used for monitoring isoform conversion under various conditions.

Introduction: Poly (ethylene terephthalate) (PET) is one of the most abundant polyester materials used in daily life and it is also one of the main culprits of environmental pollution. ICCG (F243I/D238C/S283C/Y127G) is an enzyme that performs four modifications on the leaf branch compost keratase (LCC). It shows excellent performance in the hydrolysis of PET and has a great potential in further applications. Method: Here, we used ICCG to degrade PET particles of various sizes and use the density of attack sites (Γattack) and kinetic parameters to evaluate the effect of particle size on enzyme degradation efficiency. We are surprised to observe that there is a certain relationship between Kcm and Γattack. In order to further confirm the relationship, we obtained three different enzymes (Y95K, M166S and H218S) by site-directed mutagenesis on the basis of ICCG. Result: The results confirmed that there was a negative correlation between Km and Γattack. In addition, we also found that increasing the affinity between the enzyme and the substrate does not necessarily lead to the increase of degradation rate. Conclusion: These findings show that the granulation of PET and the selection of appropriate particle size are helpful to improve its industrial application value. At the same time, additional protein engineering to increase ICCG performance is realistic, but it can’t be limited to enhance the affinity between enzyme and substrate.

Background: OS is the most frequent malignant bone tumor with a poor prognosis. TRIM21 has been reported to play a critical role in OS by regulating the expression of the TXNIP/p21 axis and inhibiting the senescence of OS cells. Aim: Investigation of the molecular mechanism of tripartite motif 21 (TRIM21) in osteosarcoma (OS) would shed light on the understanding of the pathogenesis of OS. Objective: This study aimed to explore the mechanism regulating the protein stability of TRIM21 in the process of OS senescence. Methods: Human U2 OS cells were used to establish stable cells overexpressing TRIM21 (induced by Dox) or knocking down TRIM21. The co-immunoprecipitation (co-IP) assay was used to examine the interaction between TRIM21 and HSP90. Immunofluorescence (IF) assay was used to observe colocalization in OS cells. Western blot analysis was applied to detect the protein expression, and quantitative real-time PCR (qRT-PCR) assay was used to test the mRNA expression of corresponding genes. SA-β-gal staining was used to evaluate OS senescence. Results: In this study, we verified the interaction between HSP90 and TRIM21 using a co-IP assay. Knockdown or inhibition of HSP90 with its inhibitor 17-AAG accelerated the degradation of TRIM21 by the proteasome in OS cells. CHIP E3 ligase mediated this degradation of TRIM21, with the knockdown of CHIP rescuing the downregulation of TRIM21 induced by 17-AAG. TRIM21 inhibited OS senescence and downregulated the expression of senescence marker p21, while CHIP exhibited an opposite regulatory role on p21 expression. Conclusion: Taken together, our results demonstrated that HSP90 is responsible for the stabilization of TRIM21 in OS and that the CHIP/TRIM21/p21 axis controlled by HSP90 affects the senescence of OS cells.

Introduction: Plant non-specific lipid transfer proteins (nsLTPs) play an important role in plant resistance to various stresses, and show potential applications in agriculture, industrial manufacturing, and medicine. In addition, as more and more nsLTPs are identified as allergens, nsLTPs have attracted interest due to their allergenicity. Two nsLTPs from Tartary buckwheat have been isolated and identified. There is a need to study their biochemical characteristics and allergenicity. Objective: The study aims to investigate the biochemical characteristics of two nsLTPs from Tartary buckwheat seeds and evaluate their potential allergenicity. Methods: Two nsLTPs derived from Tartary buckwheat, namely FtLTP1a and FtLTP1b, were produced by gene cloning, expression, and purification. Sequence analysis and biochemical characteristics of the proteins, including lipid binding ability, α-amylase inhibition activity, antifungal activity, and allergenic activity, were investigated. Results: High-purity recombinant FtLTP1a and FtLTP1b were obtained. FtLTP1a and FtLTP1b exhibited similar lipid binding and antifungal properties. Only FtLTP1b showed weak inhibitory activity against α-amylase. Conclusion: FtLTP1b could specifically bind IgE in the serum allergic to buckwheat and cross-react with pollen (w6). FtLTP1b is a novel allergenic member of the lipid-transfer protein 1 family found in Tartary buckwheat.