The protein journal最新文献

{"title":"Identification of Potential RNAi Targets for Cotton Mealybug (Phenacoccus solenopsis Tinsley) Management.","authors":"Sanchita Singh, Somnath Rahangdale, Shivali Pandita, Manisha Singh, Gauri Saxena, Gourav Jain, Praveen C Verma","doi":"10.1007/s10930-025-10269-6","DOIUrl":"10.1007/s10930-025-10269-6","url":null,"abstract":"<p><p>Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), commonly known as the cotton mealybug, is a highly invasive pest worldwide, particularly in tropical and subtropical regions. Despite posing a significant economic threat to various agricultural crops, a promising, environmentally friendly control strategy against this pest is lacking. Furthermore, the molecular aspects of this insect pest remain understudied. This pioneering study provides the first proteome data for four different developmental stages of the cotton mealybug. A comparative analysis of differential protein expression (DEPs) among six groups revealed the highest number of DEPs (550 up-regulated and 1118 down-regulated) when comparing the egg and first nymphal stages to the second nymphal instar (fold change ≥ 2, P < 0.05). From the generated proteomics data, potential target genes were identified for cotton mealybug management. These genes were further evaluated for RNAi-based pest control and optimization of the dsRNA delivery system in cotton mealybug. Notably, RNAi-based pest management analysis revealed that dsRNA of the Ferritin-like precursor (Psfer) gene (TRINITY_DN17055_c1_g1_i1) induced significant mortality (~ 69%), followed by dsRNA of the probable cytochrome P450 6a14-like (Psp450 6a14) gene (TRINITY_DN47081_c0_g1) and odorant-binding protein 2 precursor (Psobp) gene (TRINITY_DN11547_c0_g1). This investigation proposes a potential alternative, eco-friendly strategy for managing cotton mealybug populations and related pests. Furthermore, this study provides valuable insights into the proteome of the cotton mealybug and Hemiptera, offering avenues for proteome-based identification of RNAi targets for pest management and crop improvement.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"464-481"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics Analysis of Cancer Related CBP Mutations on Copper Ion and Drug Binding.","authors":"Shilpa Chauhan, Ankit Thakur, Mahesh Kulharia, Shailender Kumar Verma","doi":"10.1007/s10930-025-10266-9","DOIUrl":"10.1007/s10930-025-10266-9","url":null,"abstract":"<p><p>In cancer biology, copper-binding proteins (CBPs) possess a wide range of roles that impact various aspects of tumour development and progression. Modifications in CBPs in malignancy may have an enormous effect on cellular processes essential for the development and growth of cancers. We utilised bioinformatics approaches to separate down CBPs in the cancer proteome, and 32 proteins have been determined to be putative CBPs. Twelve of these proteins were associated with a likelihood of metastatic spread from primary to secondary cancer regions. Results indicated that the point mutation causes structural and functional changes in the proteins. Point mutations also alter the Cu^2+/+ binding sites and drug molecules' binding affinity for CBPs. The majority of mutations disrupt copper binding sites in CBPs, based on subsequent mutation studies focused on proteins P61769:B2MG (Beta-2-microglobulin) and P42684:ABL2 (Tyrosine kinase protein ABL2) due to their high and low expression profile respectively, in various cancer types. The copper ion binding sites and drug-binding affinity for B2MG and ABL2 highlighted in the case study represent the impact of point mutation on the proteins. This study highlighted the possible effect of mutations in CBPs, representing that the point mutations disrupt the intramolecular interactions of the proteins and simultaneously alter the other molecules' binding affinity.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"409-424"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Purification and Characterization of a New Phytolectin Extracted from Eucalyptus vicina Fruits with Immunomodulatory Effect.","authors":"Sana Boufeker, Ahlem Bahi, Imene Torche, Yacer Boudersa, Ali Shaikh-Ibrahim, Monna Taki Ellh Bousaoula, Sondos Hejazi","doi":"10.1007/s10930-025-10277-6","DOIUrl":"10.1007/s10930-025-10277-6","url":null,"abstract":"<p><p>Plant-derived lectins are getting growing interest for their potential biomedical applications, however, there are few studies on lectins from Eucalyptus vicina fruits. The aim of the current study was to isolate and characterize a new phytolectin from Eucalyptus vicina fruits (EVL) and evaluate its immunomodulatory activity. EVL was purified through ammonium sulfate precipitation (70%) followed by ion-exchange chromatography. The purified protein appeared to have a molecular weight of around 55 kDa, determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis SDS-PAGE. EVL had strong hemagglutination activity against rabbit erythrocytes and all human blood types and displayed a high affinity against fetuin. The lectin exhibited optimal activity at alkaline pH (8-10) and was remarkably thermostable for 1 h at 70 degrees. Metal ions did not alter activity to a significant degree. The immunomodulatory effects were assessed in vivo using a carbon clearance assay, and EVL injection resulted in a dose-dependent increase in phagocytic activity. Overall, our data suggests that EVL could be a valuable candidate for research and future immunomodulatory therapies.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"351-362"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144268321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fluorescence Spectroscopy Reveals Resveratrol Binding to a Hydrophobic Pocket in Leishmania amazonensis Sir2-Related Protein 1 (LaSir2RP1).","authors":"Melissa R Fessel, Ana P R Povinelli, Veronica S Fontes, Maria Isabel N Cano, Carlos H I Ramos","doi":"10.1007/s10930-025-10275-8","DOIUrl":"10.1007/s10930-025-10275-8","url":null,"abstract":"<p><p>Resveratrol, a natural phytoalexin synthesized by certain plants in response to injury, exhibits antimicrobial properties and various medically significant effects, including anticancer and antiaging activities. Although its exact mechanism of action is still under investigation, it is believed to involve its interaction with a group of protein deacetylases known as sirtuins. Sirtuins are crucial in regulating metabolism, stress responses, and processes such as lifespan extension through caloric restriction. In this study, we report the inhibitory effect of resveratrol on the growth of Leishmania amazonensis promastigotes, highlighting its potential as a microbicide. Through fluorescence spectroscopy assays and in silico analysis, we identified and characterized the interaction between resveratrol and Sir2-related protein 1 from L. amazonensis (rLaSir2RP1). Our results demonstrate a direct interaction between resveratrol and rLaSir2RP1, characterized by a binding constant of 10⁵ M^-1. This interaction involves a single binding site located near a hydrophobic pocket, which includes its solely tryptophan residue.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"387-398"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144370026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression and Purification of Human Stem Cell Factor and Its Effect on the Growth of A549 Cells.","authors":"Zhenling Ma, Xulu Han, Yiyang Zhu, Panpan Fu, Zhenzhen Li, Yongqin Zhao, Junzheng Yang, Wei Liu","doi":"10.1007/s10930-025-10273-w","DOIUrl":"10.1007/s10930-025-10273-w","url":null,"abstract":"<p><p>Stem cell factor (SCF) is a type of hematopoietic cytokine that functions in early hematopoietic stem cells. SCF, together with its cognate receptor c-kit, plays crucial roles in cell survival, proliferation, and differentiation. A dysregulated SCF/c-kit system is reportedly, associated strongly with various kinds of cancer in humans. However, the function and mechanism of SCF in non-small cell lung cancer (NSCLC) remains to be elucidated to date. In this context, the present study attempted to purify two different sizes of human SCF proteins and then investigate the effect of these exogenous SCFs in A549 cells. First, the homo sapiens Kit ligand (KITG) transcript variants a and b were amplified, and recombinant pET-30a vectors were constructed. Soluble His-SCF and His-SCF-2 were then expressed and purified using 0.1 mM isopropyl-β-D-1-tiogalactopiranoside (IPTG) at 25 °C and 0.3 mM IPTG at 25 °C, respectively. MTT assay was conducted next, which revealed that the purified proteins significantly promoted A549 cell activity and increased the phosphorylation of P65. Further, NF-κB pathway blockade was achieved through treatment with BAY11-7082, and it was observed to decrease the A549 cell activity promoted by the purified proteins. These findings provided insights into the biological role of SCF in the development of NSCLC.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"377-386"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144210615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-Yield Biosynthesis Process for Producing Insulin Lispro.","authors":"Shuchen Pei, Shusheng Liu, Jihong Luo, Junlin Chen, Hua Luo, Wen Wu, Xinan Chen","doi":"10.1007/s10930-025-10278-5","DOIUrl":"10.1007/s10930-025-10278-5","url":null,"abstract":"<p><p>Insulin lispro, a fast-acting insulin analogue, is widely used for the treatment of diabetes due to its rapid onset and high flexibility. This study established a three-step chromatography purification process, L fermentation broth can obtain 475 mg/L insulin lispro. Through a multi-step process involving fermentation, recovery of inclusion bodies, renaturation, enzymatic digestion, and chromatographic purification, a high-purity insulin lispro product was obtained. The final product achieved a purity of 99.7%. The high molecular weight protein was ≤ 0.1%, zinc content was 0.41%, host cell protein contamination was 2.31 ng/mg, and residual DNA was 1.57 ng/mg. Analytical results, including retention time, molecular weight, and peptide mapping, were consistent with theoretical expectations and matched the control. This purification process provides a streamlined and cost-effective method for large-scale production of insulin lispro, supporting further development of recombinant insulin analogs and offering high-quality active pharmaceutical ingredients for pharmaceutical formulations.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"363-376"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144370027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling Study of Effects of Tubulin Carboxy-Terminal Tails on Dynamics of Kinesin and Dynein Motors.","authors":"Ping Xie","doi":"10.1007/s10930-025-10267-8","DOIUrl":"10.1007/s10930-025-10267-8","url":null,"abstract":"<p><p>The unstructured carboxy-terminal tails (CTTs) on tubulin α- and β-subunits can affect the motility of kinesin and dynein motors on microtubules. The CTTs can also affect the microtubule deoplymerase activity of kinesin motors. However, the underlying molecular mechanism of CTTs affecting the dynamics of kinesin and dynein motors is illusive. Here, a model for the effect of CTTs on the kinesin and dynein motors is presented, where it is proposed that the CTTs can affect both the activation energy for the ATPase activity of the kinesin and dynein motors and the microtubule-binding energy. With the model, the velocity and run length of human kinesin-1, human kinesin-2, C. elegans kinesin-2 and yeast cytoplasmic dynein as well as the microtubule depolymerization rate of kinesin-13 MCAK on microtubules with the deletion of CTT on α-subunit, the deletion of CTT on β-subunit and the deletion of both CTTs relative to those on microtubules with no deletion of CTTs are studied theoretically. With 18 parameter values the totally 27 published experimental data on the dynamics of the five types of the kinesin and dynein motors are reproduced well. The predicted results are also provided.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"399-408"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144048928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delineation of Recombinant Cestode Phosphoenolpyruvate Carboxykinase Activity Co-expressed with Molecular Chaperones.","authors":"Joplin Nongkhlaw, Superior Syngkli, Miranda Moirangthem, Bidyadhar Das","doi":"10.1007/s10930-025-10279-4","DOIUrl":"10.1007/s10930-025-10279-4","url":null,"abstract":"<p><p>Phosphoenolpyruvate carboxykinase (PEPCK; EC 4.1.1.32) of cestodes is considered a possible anthelmintic target because of its differential role in their hosts. In an earlier study, the recombinant PEPCK from Raillietina echinobothrida (rePEPCK) was overexpressed as inclusion bodies and was solubilized following renaturation with chemical additives, specifically L-arginine. Molecular chaperones are alternatives to chemical additives and detergents because they preserve the stability and conformation of the proteins. Hence, in this study, the recombinant rePEPCK was subcloned into the pE-SUMO vector and co-expressed along with the molecular chaperones (e.g. pG-KJE8, pG-Tf2) in Escherichia coli BL21 (DE3) cells. The protein was purified using affinity chromatography and subsequently characterized. The overexpressed rePEPCK was found to be a monomer of ~ 75 kDa. The optimum activity of the enzyme was observed in 50 mM Tris-HCl buffer at pH 7.0. In comparison, Mn²⁺ at 4.0 mM and GDP at 0.6 mM were observed to be the ideal cofactor and nucleotide, respectively. The V_max of the purified rePEPCK was found to be ~ 0.279 U/mg protein and K_m value of ~ 35.87 μM for its substrate. The turnover number (k_cat) of rePEPCK was found to be 4.7 s^-1 with catalytic efficiency (k_cat/K_m) 1.31 × 10⁵ M^-1 s^-1. The chaperones interacted with the key amino acids of PEPCK. This investigation explored the role of the chaperones in producing biologically active rePEPCK for its characterisation and may improve the understanding of the biochemical and biophysical properties of the enzyme as an anthelmintic target.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"425-436"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling Prospective Therapeutic Potential of Conserved Hypothetical Plasmodium falciparum Proteins by Using Integrated Proteo Genomic Annotation and In-Silico Therapeutic Discovery Approach.","authors":"Mamta Panda, Varshita Srivastava, Satyendra Singh, Dhaneswar Prusty","doi":"10.1007/s10930-025-10265-w","DOIUrl":"10.1007/s10930-025-10265-w","url":null,"abstract":"<p><p>The increasing incidence of malaria and the emergence of drug-resistant strains highlight the critical need for new therapeutic targets. A recent study employing saturation mutagenesis has identified several essential, conserved genes in Plasmodium falciparum that code for proteins with unknown functions, presenting potential new avenues for therapeutic intervention. We hypothesized that these essential conserved hypothetical proteins could be functionally annotated with therapeutic relevance using an in-silico framework. However, a comprehensive framework for the functional annotation and classification of potential drug and vaccine candidates using in-silico tools has not been well established. While approaches like proteomics, subtractive genomics, and transcriptomics offer valuable insights, their isolated application limits the thorough functional annotation of proteins, and many studies do not explore therapeutic potential fully. To address these gaps, we developed the Integrated ProteoGenomic Annotation Framework (IPGAF), an in-silico protocol designed to annotate hypothetical proteins and screen them for druggability and antigenicity. Our IPGAF framework employs a two-step methodology. The first step focuses on functional annotation, integrating Pfam score-based domain analysis, orthology inference for evolutionary insights, functional linkage evaluation, subcellular localization prediction, domain architecture identification, and protein-protein interaction analysis. The second step assesses the potential of these proteins as drug targets or vaccine candidates through physicochemical and virulence evaluation, antigenicity prediction, identification of non-homologous proteins relative to the human proteome, druggability prediction, molecular docking studies, and the identification of multiple immunogenic regions (B cell, T cell, HLA) for multiepitope vaccine design. Using the IPGAF framework, we annotated 14 conserved hypothetical P. falciparum proteins from an initial set of 44. Among them, PF3D7_1208100, a merozoite protein, emerged as a promising drug and vaccine target, while PF3D7_0703900 and PF3D7_0916400 showed strong druggability potential. Our vaccine study identified the VC6 construct, incorporating epitopes from PF3D7_1223500, PF3D7_1348400, PF3D7_1470100, and PF3D7_1208100, as the most promising candidate due to its high antigenicity, non-allergenicity, and favourable physicochemical properties. Further in vitro validation could confirm the therapeutic potential of these proteins.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"437-463"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel Self-Cleaving Affinity Purification Method for Cellular Membrane-Associated Recombinant Paraoxonase-1 (rePON1) Enzyme.","authors":"Milton S Gonzalez-Serrano, Shuhan Chen, Alicia K Friedman, Will Caines, Mason Pierce, Thomas J Magliery, David W Wood","doi":"10.1007/s10930-025-10271-y","DOIUrl":"10.1007/s10930-025-10271-y","url":null,"abstract":"<p><p>Mammalian paraoxonase-1 (PON1) is a ~ 39.45 kDa calcium-dependent hydrolytic enzyme with potential therapeutic applications in chemical defense and cardiovascular disease. The N-terminus of PON1 is embedded in the cellular membrane, imparting to a hydrophobic character that leads to increased aggregation propensity and instability during purification. Although some advances have been made in bacterial expression hosts by using solubility-enhancing fusion tags and detergent solubilization strategies, these studies have shown that proteolytic tag removal is generally problematic. Thus, ineffective tag removal limits the bioanalytical characterization of the enzyme. Furthermore, the need for stabilizing detergents during purification limits the options for affinity-tag based methods. In this study, we demonstrate a novel affinity purification strategy by combining two solubility-enhancing fusion partners with the iCapTag™ self-removing affinity tag, where the entire purification process takes place in the presence of detergent. Optimization of purification conditions, including detergent and pH, resulted in the successful solubilization and stabilization of rePON1 at room temperature, allowing the tagless and native protein to be characterized. The results confirmed the expected catalytic efficiency and molecular weight of the enzyme. This method achieved over 95% host-cell protein impurities and more than 99.9% clearance of the host cell's double-stranded DNA in a single-column affinity operation. This approach combines the power of affinity chromatography and facile tag removal, thereby offering a versatile and efficient alternative to produce other recombinant membrane-associated proteins, as well as additional target proteins that require challenging buffer conditions.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":"341-350"},"PeriodicalIF":1.4,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144210616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}