The protein journal最新文献

{"title":"Editorial: Advancing Biotechnology in Türkiye: A Dedication to All Women.","authors":"Bilge Hilal Çadırcı, Ali Oğuz Büyükkileci, Barış Binay","doi":"10.1007/s10930-025-10268-7","DOIUrl":"https://doi.org/10.1007/s10930-025-10268-7","url":null,"abstract":"","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087170","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":"Editor-in-Chief's Introduction to the Special Issue.","authors":"Lawrence J Berliner","doi":"10.1007/s10930-025-10270-z","DOIUrl":"https://doi.org/10.1007/s10930-025-10270-z","url":null,"abstract":"","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056814","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":"https://doi.org/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":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","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":"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":"https://doi.org/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":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-26","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":"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":"https://doi.org/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":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","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":"Utilisation of Carbon Quantum Dots from Hazelnut Husk for Folic Acid (FA) Detection: An Innovative Approach.","authors":"Ali Arda Ciritcioğlu, Erdem Elibol, Zehra Günaydın, Tuna Demirci","doi":"10.1007/s10930-025-10249-w","DOIUrl":"10.1007/s10930-025-10249-w","url":null,"abstract":"<p><p>This study presents the development of a carbon quantum dot (CQD)-based fluorescence sensor for the accurate quantification of Folic Acid (FA). CQDs were synthesized from hazelnut husk using a solvothermal method and functionalized with silver ions to create an \"off-state\" fluorescence system. Upon mixing FA solutions, prepared from pure water and pharmaceutical tablets, with phosphate-buffered saline (PBS) and \"off-state\" CQDs, fluorescence emission was restored (\"on-state\") in a concentration-dependent manner when excited at 360 nm. A strong linear relationship was observed between FA concentration and fluorescence intensity, with an R² value of ≈ 0.994. The samples were categorized into low (0.0376-0.7533 µM) and high (0.7533-7.533 µM) concentration groups for improved accuracy, achieving mean percentage errors of 0.70% and 1.85%, respectively, at concentrations as low as 0.565 µM. This CQD-based sensor demonstrated rapid, cost-effective, and highly sensitive detection capabilities, making it a promising alternative for FA quantification in biomedical and nutritional applications. Furthermore, the use of sustainable raw materials, such as hazelnut husk, highlights the eco-friendly and practical advantages of this method over conventional techniques.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582388","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":"A Phosphodiesterase Type-5 (PDE-5) Inhibitor, Sildenafil, Ameliorates the NEC Induced Inflammation.","authors":"Mehmet Akif Ovalı, Özlem Öztopuz, İhsan Karaboğa","doi":"10.1007/s10930-025-10263-y","DOIUrl":"10.1007/s10930-025-10263-y","url":null,"abstract":"<p><p>The connection between intestine microbiota and lung disease is described as the gut-lung axis, these organ systems are somehow interrelated in both homeostasis and disease development. In newborns, the most important gastrointestinal complications are necrotizing enterocolitis (NEC), and the pulmonary complication both cause significant systemic morbidity. In this study, sildenafil administered at varying doses in neonatal rat model of experimental necrotizing enterocolitis and focused on both mRNA expression and histopathological alterations. 15-day-old Wistar Albino rat pups were randomly divided into six groups; Control, NEC, DMSO, Sil_1mg, Sil_5mg, Sil_10mg (n = 5). NEC induction was performed using hypoxia/asphyxia and cold stress. At the end of the experiment, lung tissues were harvested, molecular and histopathological alterations were analysed. Histopathological examination was performed with hematoxylin&eosin and masson trichrome staining in lung samples of neonatal rats and the mRNA expression levels of TNF-α, IL-6 and HSPa5 genes were analyzed. The mRNA expression levels of TNF-α, IL-6 and HSPa5 were increased in the NEC group compared to the control group and sildenafil treatment could significantly reduced the levels of the genes and inflammation (*p < 0.05 and **p ≤ 0.0001). Alveolar edema and hemorrhage findings were observed in the lung tissue of the NEC group. Interstitial edema and hemorrhage findings were reduced in the groups treated with sildenafil compared to the NEC group. The data we obtained indicate that sildenafil administering at different doses has therapeutic effect on NEC induced lung tissue inflammation both at the mRNA expression and tissue levels.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582392","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":"Inhibitor Action of Unsaturated Fatty Acids on Equine Serum Butyrylcholinesterase.","authors":"Mehmet Berk Akay, Kubra Sener, Suat Sari, Ebru Bodur","doi":"10.1007/s10930-025-10259-8","DOIUrl":"https://doi.org/10.1007/s10930-025-10259-8","url":null,"abstract":"<p><p>Butyrylcholinesterase (BChE; EC 3.1.1.8), a serine hydrolase found in various tissues, hydrolyses choline esters such as acetylcholine and succinylcholine, as well as other esters such as heroin and acetylsalicylic acid. It is considered to play a role in lipid metabolism as it belongs to the same enzyme group as lipases and its catalytic subunits are similar. In this study, the effects of unsaturated fatty acids, namely arachidonic (AA), linoleic (LA), alpha-linolenic (ALA) and oleic acid (OA), on equine serum BChE (EqBChE) were investigated. Enzyme activity was measured by the modified Ellman method. When the activity results were evaluated, the IC50 values were found 45.49, 8.465, 1556, and 56.57 μM; while the Ki values were 63.92, 11.46, 1800, and 15.24 μM for AA, ALA, LA, and OA, respectively. Analysis of the kinetic results showed that ALA was compatible with mixed inhibition and other fatty acids were compatible with non-competitive inhibition, a special type of mixed inhibition. Molecular docking predicted binding of the fatty acids to the active site, as well as to predicted allosteric sites. The results of this study provide another support to the hypothesis that cholinesterases are associated with lipid metabolism.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476520","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":"Effects of Heavy Metal Stress on Seedling Growth and Antioxidant System in Sorghum (Sorghum Bicolor (L.) Moench).","authors":"Büşra Çevık, Hakan Arslan, Deniz Ekinci","doi":"10.1007/s10930-025-10258-9","DOIUrl":"https://doi.org/10.1007/s10930-025-10258-9","url":null,"abstract":"<p><p>Factors that impede the normal growth and development of plants are termed 'stress factors' and result in yield loss. Exposure to elevated concentrations of heavy metals has been demonstrated to induce the production of reactive oxygen species (ROS), which can affect physiological and biochemical processes. The present study investigated the effects of two common heavy metals (Hg²⁺ and Cd²⁺) on specific physiological and biochemical parameters of sorghum (Sorghum bicolor (L.) Moench). The study utilized doses ranging from 3 to 15 ppm for the application of heavy metals. The study focused on the effects of these metals on the activities of enzymes (superoxide dismutase and peroxidase), chlorophyll content, fresh weight, dry weight, and proline content in sorghum plants. The study found that applying mercury at 9 ppm resulted in the highest activity of peroxidase (POX), with an observed increase of 69.57% compared to the control. Conversely, cadmium application at 12 ppm elicited the highest activity, increasing by 102.17% compared to the control. For superoxide dismutase (SOD), the peak activity was observed at 6 ppm for both applications, with an increase of 84.16% in the mercury application control group and 121.08% in the cadmium application group compared to the control group. A similar pattern was observed in the chlorophyll content, which initially increased and then decreased. Declines in fresh weight, dry weight, and proline accumulation were also documented.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476552","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":"Low-dose Bee Venom as a Potential Therapeutic Agent Against Human Chronic Myeloid Leukaemia Cells.","authors":"Hamza Halici, Harun Un, Saffet Celik, Zeynep Karakoy, Zafer Bayraktutan, Can Ozlu, Elif Cadirci, Zekai Halici, Alptug Atila, Filiz Mercantepe","doi":"10.1007/s10930-025-10251-2","DOIUrl":"https://doi.org/10.1007/s10930-025-10251-2","url":null,"abstract":"<p><p>Bee venom is secreted by a gland in the abdominal cavity of bees. The venom, especially that of honeybees, contains certain enzymes and peptides that, when administered in high doses, are effective against various diseases. Peptides such as melittin and phospholipase A₂ can target various cancer cells. In this study, we investigated the antiproliferative effects of administering low-dose bee venom in K-562 chronic myeloid leukaemia cells. Our proteomic study revealed regional variation of the content of bee venom and high levels of melittin, apamin and secapin, as well as phospholipase A₂ and hyaluronidase. In addition, eight new, previously unidentified proteins were identified. The effects of bee venom on cell viability and drug-cell interaction were investigated at 24, 48 and 72 h. According to the MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) results, the bee venom decreased K-562 cell viability dose-dependently at all time points. Cell viability decreased 48 and 72 h after bee venom administration but increased in the control group left untreated for 72 h. The inhibition percentages for the highest bee venom concentration (0.4 µM) at 24, 48 and 72 h were 55%, 80% and 92%, respectively. The cell-drug interactions indicated that the cell surfaces, which were smooth and clear before drug application, gradually deteriorated and started to shrink after the application. In conclusion, at increasing doses, bee venom was found to have a strong antiproliferative effect in K-562 chronic myeloid leukaemia cell lines.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384625","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}