The Protein Journal最新文献

{"title":"Editor-in-Chief’s Introduction to the Special Issue","authors":"Lawrence J. Berliner","doi":"10.1007/s10930-025-10270-z","DOIUrl":"10.1007/s10930-025-10270-z","url":null,"abstract":"","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 3","pages":"257 - 257"},"PeriodicalIF":1.4,"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":4,"RegionCategory":"生物学","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,&nbsp;Ankit Thakur,&nbsp;Mahesh Kulharia,&nbsp;Shailender Kumar Verma","doi":"10.1007/s10930-025-10266-9","DOIUrl":"10.1007/s10930-025-10266-9","url":null,"abstract":"<div><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></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 4","pages":"409 - 424"},"PeriodicalIF":1.4,"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":4,"RegionCategory":"生物学","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":"<div><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, <i>C. elegans</i> 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></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 4","pages":"399 - 408"},"PeriodicalIF":1.4,"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":4,"RegionCategory":"生物学","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,&nbsp;Varshita Srivastava,&nbsp;Satyendra Singh,&nbsp;Dhaneswar Prusty","doi":"10.1007/s10930-025-10265-w","DOIUrl":"10.1007/s10930-025-10265-w","url":null,"abstract":"<div><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 <i>Plasmodium falciparum</i> 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 <i>P. falciparum</i> 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></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 4","pages":"437 - 463"},"PeriodicalIF":1.4,"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":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research Progress on Douchi Fibrinolytic Enzyme","authors":"Mengxue Cheng,&nbsp;Panpan Wang,&nbsp;Mei Li,&nbsp;Cuiying Peng,&nbsp;Xuhui Fang,&nbsp;Zhilang Deng,&nbsp;Xiongwei Deng,&nbsp;Xiaomei Xie,&nbsp;Meizhi Weng","doi":"10.1007/s10930-025-10262-z","DOIUrl":"10.1007/s10930-025-10262-z","url":null,"abstract":"<div><p>In recent years, the morbidity and mortality owing to thrombotic diseases have increased. Fibrinolytic enzymes can dissolve thrombosis. Existing thrombolytic drugs are expensive, have short half-lives, and cause bleeding easily. Consequently, there is a need to develop safe, effective, and inexpensive thrombolytic drugs. The Douchi fibrinolytic enzyme (DFE), a serine protease that can dissolve fibrous proteins from the traditional fermented food Douchi, has been isolated recently. DFE is non-toxic and free from side effects like bleeding. In addition, it has a low molecular weight, owing to which it can be absorbed directly through the digestive tract or taken orally, thereby attracting increasing attention. In this review, first, we introduce the commonly used methods for determining DFE activity. Second, we summarize the strains of DFE-producing bacteria, optimization of the fermentation process, mutation breeding, and recombinant expression. Finally, we discuss the isolation and purification procedures, physicochemical properties, and in vitro and in vivo thrombolytic effects of DFE. Thus, we demonstrate that the extraction of DFE from Douchi, a traditional Chinese fermented food, has considerable potential for development.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 2","pages":"162 - 174"},"PeriodicalIF":1.9,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endoplasmic Reticulum Stress: Implications in Diseases","authors":"Neha Sylvia Walter,&nbsp;Varun Gorki,&nbsp;Rishi Bhardwaj,&nbsp;Pradeep Punnakkal","doi":"10.1007/s10930-025-10264-x","DOIUrl":"10.1007/s10930-025-10264-x","url":null,"abstract":"<div><p>Endoplasmic reticulum (ER) is a specialized organelle that plays a significant role in cellular function. The major functions of ER include protein synthesis and transport, folding of proteins, biosynthesis of lipids, calcium (Ca²⁺) storage, and redox balance. The loss of ER integrity results in the induction of ER stress within the cell due to the accumulation of unfolded, improperly folded proteins or changes in Ca²⁺ metabolism and redox balance of organelle. This ER stress commences the Unfolded Protein Response (UPR) that serves to counteract the ER stress <i>via</i> three sensors inositol requiring protein–1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor–6 (ATF6) that serve to establish ER homeostasis and alleviates ER stress. Severe ER dysfunction ultimately results in the induction of apoptosis. Increasing shreds of evidence suggest the implication of ER stress in the development and progression of several diseases viz. tuberculosis, malaria, Alzheimer’s disease, Parkinson’s disease, diabetes, and cancer. Activation of ER stress can be beneficial for treating some diseases while inhibiting the process can be useful in others. A deeper understanding of these pathways can provide key insights in designing novel therapeutics to treat these diseases.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 2","pages":"147 - 161"},"PeriodicalIF":1.9,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","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,&nbsp;Erdem Elibol,&nbsp;Zehra Günaydın,&nbsp;Tuna Demirci","doi":"10.1007/s10930-025-10249-w","DOIUrl":"10.1007/s10930-025-10249-w","url":null,"abstract":"<div><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></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 3","pages":"283 - 296"},"PeriodicalIF":1.4,"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":4,"RegionCategory":"生物学","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,&nbsp;Özlem Öztopuz,&nbsp;İhsan Karaboğa","doi":"10.1007/s10930-025-10263-y","DOIUrl":"10.1007/s10930-025-10263-y","url":null,"abstract":"<div><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 (<i>n</i> = 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&amp;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 (*<i>p</i> &lt; 0.05 and **<i>p</i> ≤ 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></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 3","pages":"317 - 324"},"PeriodicalIF":1.4,"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":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression of Recombinant Tissue Plasminogen Activator - Plasminogen Activator Inhibitor Complex in Mammal Cells as Quality Control Materials in Immunoassay","authors":"Yiqi Yang,&nbsp;Zhigao Zhang,&nbsp;Huanchang Luo,&nbsp;Changxu Chen,&nbsp;Tiancai Liu,&nbsp;Guanfeng Lin,&nbsp;Yingsong Wu","doi":"10.1007/s10930-025-10257-w","DOIUrl":"10.1007/s10930-025-10257-w","url":null,"abstract":"<div><p>Tissue plasminogen activator - plasminogen activator inhibitor complex (tPAIc) is a critical biomarker to assess fibrinolytic dysfunction, which is widely used in clinics. Quality control material (QCM) plays an important role in immunoassays for human tPAIc. The QCM of tPAIc are derived from human plasma with many disadvantages. Recombinant protein is a promising substitute for human plasma to work as the source of QCM. However, tPAIc is a protein complex, consisting of three parts, tPA-A, tPA-B, and PAI-1, which makes the expression more difficult. This study aimed to obtain recombinant tPAIc QCM with excellent performance for immunoassay. Three recombinant plasmids that matched each part of the protein complex were constructed and co-transfected to HEK293F cells. The optimal molar ratio of three plasmids was further explored. Each part of the proteins was secreted from cells and the target protein tPAIc was self-assembled in the supernatant. After being identified by western blot and chemiluminescent immunoassay (CLIA), calculating the concentration of tPAIc in the supernatant, tPAIc was diluted to approximately 50 ng/mL and 5 ng/mL, distributed, and lyophilized in ampoules, working as QCM in tPAIc immunoassay. The homogeneity, stability, and recovery of the QCM were further evaluated. The three plasmids were successfully constructed. The target protein complex, tPAIc, was obtained in the supernatant at about 6500 ng/mL, under the best three plasmids co-transfected molar ratio 1:1:1. The QCMs were uniform in different ampoules. They were verified to be highly stable for at least 1 year when stored at 4 ℃ and − 20 ℃. The recombinant tPAIc QCMs for immunoassay were obtained with high quality to replace plasma-derived QCMs, which provides valuable insight into more application scenarios of recombinant proteins.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 2","pages":"245 - 255"},"PeriodicalIF":1.9,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Regulation of TDP-43 Structure and Phase Transitions: A Review","authors":"Yanqing Liu,&nbsp;Jiani Xiang,&nbsp;Hang Gong,&nbsp;Tianxiong Yu,&nbsp;Meng Gao,&nbsp;Yongqi Huang","doi":"10.1007/s10930-025-10261-0","DOIUrl":"10.1007/s10930-025-10261-0","url":null,"abstract":"<div><p>The transactive response DNA binding protein 43 (TDP-43) is an RNA/DNA-binding protein that is involved in a number of cellular functions, including RNA processing and alternative splicing, RNA transport and translation, and stress granule assembly. It has attracted significant attention for being the primary component of cytoplasmic inclusions in patients with amyotrophic lateral sclerosis or frontotemporal dementia. Mounting evidence suggests that both cytoplasmic aggregation of TDP-43 and loss of nuclear TDP-43 function contribute to TDP-43 pathology. Furthermore, recent studies have demonstrated that TDP-43 is an important component of many constitutive or stress-induced biomolecular condensates. Dysregulation or liquid-to-gel transition of TDP-43 condensates can lead to alterations in TDP-43 function and the formation of TDP-43 amyloid fibrils. In this review, we summarize recent research progress on the structural characterization of TDP-43 and the TDP-43 phase transition. In particular, the roles that disease-associated genetic mutations, post-translational modifications, and extrinsic stressors play in the transitions among TDP-43 monomers, liquid condensates, solid condensates, and fibrils are discussed. Finally, we discuss the effectiveness of available regulators of TDP-43 phase separation and aggregation. Understanding the underlying mechanisms that drive the pathological transformation of TDP-43 could help develop therapeutic strategies for TDP-43 pathology.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 2","pages":"113 - 132"},"PeriodicalIF":1.9,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}