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Peptide and Protein Tags for the Half-Life Extension of Therapeutic Agents: A Review Article 延长治疗药物半衰期的肽和蛋白标签:综述。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-12-01 DOI: 10.1007/s10930-025-10304-6
Sorour Aboutalebi, Fatemeh Najafi, Negin Yazdizadeh, Fatemeh Shafiee
{"title":"Peptide and Protein Tags for the Half-Life Extension of Therapeutic Agents: A Review Article","authors":"Sorour Aboutalebi,&nbsp;Fatemeh Najafi,&nbsp;Negin Yazdizadeh,&nbsp;Fatemeh Shafiee","doi":"10.1007/s10930-025-10304-6","DOIUrl":"10.1007/s10930-025-10304-6","url":null,"abstract":"<div><p>Although biological drugs have been considered as one of the effective and growing therapeutic approaches in the pharmaceutical industry in recent decades, the largest concern about them is the insufficient stability and rapid degradation in the bloodstream due to their structural nature. One of the effective methods for increasing the circulating half-life of peptide and protein drugs is the addition of half-life-extending tags, which prevent both the degradation of the biological drug and its glomerular filtration by various mechanisms, thereby increasing its half-life. This review focuses on peptide and protein tags used to enhance the pharmacokinetic profiles of biological drugs by increasing their half-life. It discusses various tags, including HSA (Human Serum Albumin), ABD (Albumin Binding Domain), DARPINS (Designed Ankyrin Repeat proteins), XTEN, CTP (Carboxy Terminal Peptide), ELP (Elastin Like Peptide), and others, and highlights both FDA-approved products and candidates currently in different stages of clinical development. In the meantime, special attention has been paid to albumin-binding domains and albumin-binding domain antibody (AlbudAb), which increases the half-life of biological drugs by binding to albumin, as the most abundant and stable protein in the body.</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":"45 1","pages":"39 - 54"},"PeriodicalIF":1.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650646","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}
引用次数: 0
Evaluating the Structural Stability of Recombinant Rotavirus Capsid Protein VP6 in Altered Physicochemical States Using Fluorescence and CD Spectroscopy 利用荧光和CD光谱评价重组轮状病毒衣壳蛋白VP6在改变物理化学状态下的结构稳定性。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-16 DOI: 10.1007/s10930-025-10307-3
Modibedi Lesego Gladys, Preenan Pillay
{"title":"Evaluating the Structural Stability of Recombinant Rotavirus Capsid Protein VP6 in Altered Physicochemical States Using Fluorescence and CD Spectroscopy","authors":"Modibedi Lesego Gladys,&nbsp;Preenan Pillay","doi":"10.1007/s10930-025-10307-3","DOIUrl":"10.1007/s10930-025-10307-3","url":null,"abstract":"<div><p>Rotaviruses (RV) are a major cause of severe childhood diarrhoea, particularly in developing nations, necessitating stable vaccines. Therefore, the presented preliminary study aimed to assess the impact of altered physicochemical properties on the structural stability of recombinant rotavirus capsid protein VP6 (RV-VP6). The expression system used in this study was designed by genetically engineering the RV-VP6 into <i>E. coli</i> (NiCo21(DE3))-pET28a host-vector system and purified using liquid chromatography. The purified RV-VP6 homology detection and structure prediction were conducted using LC–MS and HHpred computational analysis, which indicated a 100% probability of 1QHD_A Viral Capsid VP6 (1.95 Å), representing the crystal structure of VP6. The secondary and tertiary structural stability of RV-VP6 was evaluated in altered pH and Ca<sup>2+</sup> concentrations using far UV-CD and intrinsic tryptophan fluorescence spectroscopy, respectively. The computational analysis of the far-UV CD spectra revealed a significant increase in the composition of α-helices and β-sheets in altered pH and Ca<sup>2+</sup> environments compared to the denatured protein (<i>p</i> &lt; 0.0001). Intrinsic fluorescence analysis of RV-VP6 at pH 7 yielded an emission λmax of 339 nm, which shifted to 342 nm at pH 5. In 1 mM Ca<sup>2+</sup>, a λmax of 340 nm was observed, with an increase in intensity in 10 mM Ca<sup>2+</sup>, accompanied by a slight blue shift to 338 nm. Investigation of RV-VP6 under thermal stress yielded unfolding concomitant with aggregation, rendering the process irreversible and nullifying analysis using equilibrium thermodynamics. These findings form the preliminary basis for our future evaluation of manufacturing stable and enhanced RV-VP6 vaccines through the downstream process control of (1) pH, which alters the charge distribution on the surface of the protein, leading to conformational changes, and (2) Ca<sup>2+</sup> ions, which interact with specific amino acid residues in the protein, thereby affecting its structure and function.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"215 - 228"},"PeriodicalIF":1.4,"publicationDate":"2025-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535065","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}
引用次数: 0
Non-ionic Detergent-Assisted Refolding of Protein from Protein-SDS Complex 非离子洗涤剂辅助蛋白质- sds复合物中蛋白质的再折叠。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-12 DOI: 10.1007/s10930-025-10305-5
Teruo Akuta, Tomoto Ura, Takeshi Oikawa, Takashi Shibata, Kentaro Shiraki, Tsutomu Arakawa
{"title":"Non-ionic Detergent-Assisted Refolding of Protein from Protein-SDS Complex","authors":"Teruo Akuta,&nbsp;Tomoto Ura,&nbsp;Takeshi Oikawa,&nbsp;Takashi Shibata,&nbsp;Kentaro Shiraki,&nbsp;Tsutomu Arakawa","doi":"10.1007/s10930-025-10305-5","DOIUrl":"10.1007/s10930-025-10305-5","url":null,"abstract":"<div><p>Refolding of protein from denatured structure caused by sodium dodecyl sulfate (SDS) was examined using agarose native gel electrophoresis and circular dichroism (CD). Refolding of protein from SDS complex was induced with the addition of non-ionic and zwitterionic detergents followed by agarose native gel electrophoresis. The native gel electrophoresis was done without both SDS and non-ionic detergents in the agarose gel and running buffer. The electrophoretic mobility of bovine serum albumin (BSA) drastically increased with the addition of 1% SDS to the samples indicative of SDS-BSA complex formation. The SDS-denatured BSA returned to the native mobility by the addition of non-ionic Tween 20 and Triton X-100 and zwitterionic CHAPS as a function of detergent concentration. Refolding, at least partially, was confirmed by CD, which was done in the presence of both SDS and non-ionic detergents, a condition different from the native gel electrophoresis done in their absence. When BSA was denatured by both 1% SDS and a disulfide-reducing dithiothreitol, even 10% Tween 20 was insufficient to restore the native BSA mobility on agarose native gel electrophoresis. When BSA was denatured by 1% Sarkosyl and sodium lauroyl-glutamate, Tween 20 restored the native structure at Tween 20 concentration lower than the Tween 20 concentration used for SDS denaturation. A similar refolding by non-ionic detergents was also observed for a rabbit monoclonal IgG, but not for lysozyme. The results with lysozyme suggest strong SDS binding and difficulty in dissociating the bound SDS by non-ionic detergents due to high isoelectric point of the protein and thereby more SDS binding.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"185 - 196"},"PeriodicalIF":1.4,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145497777","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}
引用次数: 0
Challenges in Serum Albumin Measurements: A Comparative Study of the Bromocresol Green and the Capillary Zone Electrophoretic Method 血清白蛋白测定的挑战:溴甲酚绿法和毛细管区带电泳法的比较研究。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-12 DOI: 10.1007/s10930-025-10303-7
Mariem Othmani, Yessine Amri, Siwar Chelbi, Sondes Hadj Fredj, Taieb Messaoud, Rym Dabboubi
{"title":"Challenges in Serum Albumin Measurements: A Comparative Study of the Bromocresol Green and the Capillary Zone Electrophoretic Method","authors":"Mariem Othmani,&nbsp;Yessine Amri,&nbsp;Siwar Chelbi,&nbsp;Sondes Hadj Fredj,&nbsp;Taieb Messaoud,&nbsp;Rym Dabboubi","doi":"10.1007/s10930-025-10303-7","DOIUrl":"10.1007/s10930-025-10303-7","url":null,"abstract":"<div><p>Serum albumin (SA) is a key biomarker routinely used in clinical practice. Multiple analytical methods exist for its measurement, including bromocresol green (BCG) colorimetry and capillary zone electrophoresis (CZE). However, discrepancies between methods raise concerns regarding result consistency and clinical interpretation. This study aimed to compare the analytical concordance between BCG and CZE methods for SA measurement, and to assess their clinical interchangeability. A cross-sectional study conducted on 109 serum samples collected from patients undergoing serum protein electrophoresis at Bechir Hamza Children’s Hospital. SA was measured using BCG and CZE. Descriptive statistics were calculated for each method. Paired t-test and Wilcoxon signed-rank test were used to assess differences in means. Method agreement was evaluated using Passing-Bablok regression, Intraclass Correlation Coefficient (ICC), Bland–Altman plot, and a confusion matrix. BCG significantly overestimated SA compared to CZE (41.49 ± 7.30 g/L vs. 37.48 ± 6.85 g/L; p &lt; 0.001). Passing-Bablok regression revealed a regression line of y = 1.02x + 3.21, indicating a consistent positive bias. The R<sup>2</sup> value was 0.891, suggesting strong correlation. The ICC was 0.81 (95% CI 0.081–0.932), reflecting good agreement. The Bland–Altman analysis confirmed a mean difference of 4.01 g/L. Confusion matrix analysis showed perfect concordance in low albumin values but significant misclassification at higher levels, with BCG shifting many values into higher categories. While BCG and CZE methods show strong correlation, BCG consistently overestimates albumin concentrations. These findings underscore the need for method standardization and careful interpretation of results in clinical settings.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"178 - 184"},"PeriodicalIF":1.4,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145497850","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}
引用次数: 0
Arginine 11, Arginine 32, and Lysine 44 of a Staphylococcal Anti-sigma Factor are Indispensable Residues 精氨酸11、精氨酸32和赖氨酸44是葡萄球菌抗sigma因子不可缺少的残基。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-12 DOI: 10.1007/s10930-025-10300-w
Debasmita Sinha, Debabrata Sinha, Tushar Chakraborty, Subrata Sau
{"title":"Arginine 11, Arginine 32, and Lysine 44 of a Staphylococcal Anti-sigma Factor are Indispensable Residues","authors":"Debasmita Sinha,&nbsp;Debabrata Sinha,&nbsp;Tushar Chakraborty,&nbsp;Subrata Sau","doi":"10.1007/s10930-025-10300-w","DOIUrl":"10.1007/s10930-025-10300-w","url":null,"abstract":"<div><p>σ<sup>B</sup>, a <i>Staphylococcus aureus</i>-encoded alternative sigma factor, is inhibited by RsbW, an anti-sigma factor. RsbW also dimerizes in solution and phosphorylates RsbV, an RsbW antagonist. Of the predicted RsbW residues involved in its dimerization and/or binding cognate factors, the roles of Arg 11, Arg 32, and Lys 44 have been demonstrated here using various tools. The structural models of three RsbW mutants, harboring Ala at positions 11, 32, and 44, were built up, and their analyses suggested that all of the above Lys/Arg residues may be involved in the dimerization of this protein. Similar analyses indicated that Lys 44 and Arg 32 may be needed for binding σ<sup>B3</sup>, the domain 3 of σ<sup>B</sup>. The docking studies have confirmed the roles of Arg 11 and Arg 32 in the dimerization of RsbW, and revealed that its association with σ<sup>B3</sup> requires Arg 32 and Lys 44. Additionally, the simulation studies proposed that all of the above Lys/Arg may be needed for its structure maintenance. To verify the computational data, three Ala-substituted RsbW mutants were also purified, and their characterization indicates that the change of Arg 11 or Lys 44 to Ala, compared to the change of Arg 32 to Ala, impacts the structure, RsbV/ σ<sup>B3</sup> binding affinity, and phosphorylation activity of RsbW more severely. Further, the dimerization ability of RsbW was partly affected by Ala substitution at positions 11 and 32. Jointly, Arg 11, Arg 32, and Lys 44 of RsbW are crucial residues for this σ<sup>B</sup> inhibitor and kinase. Knowledge of crucial RsbW residues may be useful for designing antistaphylococcal drugs in the future.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"197 - 214"},"PeriodicalIF":1.4,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145497855","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}
引用次数: 0
Multi-scale In Silico and Biochemical Evaluation of Natural Bisbenzylisoquinoline Alkaloids as Aldose Reductase Inhibitors 天然双苄基异喹啉生物碱醛糖还原酶抑制剂的多尺度硅法及生化评价。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-08 DOI: 10.1007/s10930-025-10297-2
Emadeldin M. Kamel, Noha A. Ahmed, Sarah I. Othman, Adil Abalkhail, Faris F. Aba Alkhayl, Bassam A. Abuamarah, Saleh Maodaa, Al Mokhtar Lamsabhi
{"title":"Multi-scale In Silico and Biochemical Evaluation of Natural Bisbenzylisoquinoline Alkaloids as Aldose Reductase Inhibitors","authors":"Emadeldin M. Kamel,&nbsp;Noha A. Ahmed,&nbsp;Sarah I. Othman,&nbsp;Adil Abalkhail,&nbsp;Faris F. Aba Alkhayl,&nbsp;Bassam A. Abuamarah,&nbsp;Saleh Maodaa,&nbsp;Al Mokhtar Lamsabhi","doi":"10.1007/s10930-025-10297-2","DOIUrl":"10.1007/s10930-025-10297-2","url":null,"abstract":"<div><p>Aldose reductase (AR) is the rate-limiting enzyme of the polyol pathway and a validated target for preventing micro- and neurovascular complications of diabetes. Here, we combined multi-scale in-silico analyses with biochemical testing to evaluate five commercially available bisbenzylisoquinoline alkaloids—cepharanthine, dauricine, isotetrandrine, fangchinoline and sinomenine—as potential AR inhibitors. Density-functional optimization, structure-based docking and 500 ns molecular-dynamics simulations revealed that the macrocyclic scaffolds of cepharanthine (ΔG<sub>dock</sub> =  − 8.4 kcal mol<sup>−1</sup>) and dauricine (− 9.7 kcal mol<sup>−1</sup>) fully occupy the Phe122-Trp219-Trp111 aromatic cage and lock AR into a single, deep free-energy basin, whereas sinomenine explores a broad landscape. MM/PBSA calculations on the 150–200 ns of each trajectory ranked binding free energies as dauricine ≈ isotetrandrine ≈ cepharanthine &lt; sinomenine &lt; fangchinoline, with van-der-Waals forces dominating. ADMET profiling predicted high gastrointestinal absorption across the series but flagged a potential hERG potassium-channel liability for the four macrocycles. Enzyme-kinetic assays corroborated the computational hierarchy: cepharanthine, dauricine and isotetrandrine inhibited recombinant AR with IC<sub>50</sub> values of 4.25 ± 0.42, 5.38 ± 0.22 and 6.65 ± 0.40 µM, respectively, compared with 2.36 ± 0.32 µM for quercetin. Lineweaver–Burk and Michaelis–Menten analysis showed mixed inhibition for cepharanthine (<i>K</i><sub>i</sub> = 3.71 µM) and non-competitive inhibition for dauricine (<i>K</i><sub>i</sub> = 4.63 µM) and isotetrandrine (<i>K</i><sub>i</sub> = 6.99 µM). Fangchinoline and sinomenine were an order of magnitude weaker (IC<sub>50</sub> = 37–57 µM). Taken together, these data position cepharanthine and dauricine as mechanistically validated, hit-stage starting points for next-generation AR inhibitors, and identify isotetrandrine as an allosteric back-up scaffold. More broadly, the study illustrates a transparent, reproducible computational–experimental workflow for prioritizing structurally complex natural products against redox enzymes implicated in diabetic pathology.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"125 - 145"},"PeriodicalIF":1.4,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477102","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}
引用次数: 0
Strategic Approaches for Overcoming Peptide and Protein Drug Limitations 克服多肽和蛋白质药物限制的战略途径。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-08 DOI: 10.1007/s10930-025-10302-8
Mahsa Cheshomi, Nikta Shobeiri, Amineh Sadat Tajani, Bahman Khameneh
{"title":"Strategic Approaches for Overcoming Peptide and Protein Drug Limitations","authors":"Mahsa Cheshomi,&nbsp;Nikta Shobeiri,&nbsp;Amineh Sadat Tajani,&nbsp;Bahman Khameneh","doi":"10.1007/s10930-025-10302-8","DOIUrl":"10.1007/s10930-025-10302-8","url":null,"abstract":"<div><p>Protein and peptide drugs have become essential in treating numerous diseases due to their high specificity and therapeutic potential. However, their clinical application faces several challenges, including chemical instability, physical instability, short in vivo half-life, low oral bioavailability, and immunogenicity. These issues reduce drug efficacy and limit patient compliance. This review critically examines these limitations and presents current strategies to address them. PEGylation, the covalent or noncovalent attachment of polyethylene glycol (PEG) molecules to proteins, is highlighted for its ability to increase stability, reduce renal clearance, lower immunogenicity, and extend half-life. The review distinguishes between random and site-specific PEGylation, highlighting site-specific methods that preserve protein activity while optimizing pharmacokinetics. Additionally, the encapsulation of proteins in polymeric and lipid-based delivery systems is discussed to protect drugs from enzymatic degradation, control their release, and enhance absorption. Biobetter approaches, including site-directed mutagenesis, are also presented to improve protein stability and reduce immunogenicity. Market data and approved drug examples illustrate the impact of these strategies. Overall, the article provides a comprehensive overview of innovative pharmaceutical and biotechnological methods that enhance the clinical performance and market viability of protein therapeutics.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"8 - 21"},"PeriodicalIF":1.4,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477090","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}
引用次数: 0
GCMS and Molecular Docking Based Insights into the Antifungal Potential of Bacillus Bs-06 Against Fusarium oxysporum f. sp. lycopersici 基于GCMS和分子对接的芽孢杆菌Bs-06抗番茄尖孢镰刀菌潜力研究。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-08 DOI: 10.1007/s10930-025-10306-4
K. Vigneshwaran, K. Rajamohan, P. Balabaskar, P. Sivasakthivelan, N. H. Shankar Reddy
{"title":"GCMS and Molecular Docking Based Insights into the Antifungal Potential of Bacillus Bs-06 Against Fusarium oxysporum f. sp. lycopersici","authors":"K. Vigneshwaran,&nbsp;K. Rajamohan,&nbsp;P. Balabaskar,&nbsp;P. Sivasakthivelan,&nbsp;N. H. Shankar Reddy","doi":"10.1007/s10930-025-10306-4","DOIUrl":"10.1007/s10930-025-10306-4","url":null,"abstract":"<div><p>The utilization of <i>Bacillus</i> spp. as eco-compatible bioresources represented a promising strategy in antifungal biotechnology. In this study, <i>Bacillus subtilis</i> Bs-06, isolated from the rhizosphere of healthy tomato plants, exhibited strong antagonistic activity through the secretion of diverse bioactive metabolites. Gas chromatography–mass spectrometry (GC–MS) analysis of its culture extract identified ten major compounds, including Phenol-3,5-bis(1,1-dimethylethyl), palmitic acid, oleic acid, and octadecanoic acid, which had been widely reported for antimicrobial efficacy. To investigate their Molecular Docking targeted the key virulence proteins of <i>Fusarium oxysporum</i> f.sp. <i>lycopersici</i> Cutinase (5AJH), Avr1/SIX4 (7T6A), and Avr3/SIX1 (7T69). Docking simulations revealed strong binding affinities, with Phenol-3,5-bis(1,1-dimethylethyl) showing the highest interaction energy (− 11.53 kcal/mol) against Avr3. The ligand–protein complexes were stabilized by hydrogen bonding and hydrophobic interactions, suggesting potential inhibition of pathogen virulence functions. Normal mode analysis further demonstrated differential flexibility among protein–ligand complexes, where Avr1 exhibited the highest conformational mobility, while Cutinase displayed the greatest structural rigidity. These findings established Bs-06 as a valuable source of antifungal metabolites capable of targeting virulence determinants at the molecular level. The integration of GC–MS profiling, molecular docking, and dynamic simulations underscored the potential of <i>Bacillus</i> derived metabolites as sustainable biocontrol agents for managing Fusarium wilt in tomato.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"146 - 177"},"PeriodicalIF":1.4,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477108","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}
引用次数: 0
Metal Dependent Glycosidases of Sea Cucumber Eupentacta Fraudatrix and their Properties 海参金属依赖糖苷酶及其性质研究。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-11-02 DOI: 10.1007/s10930-025-10301-9
Svetlana E. Soboleva, Nadejda A. Maltseva, Irina A. Kostrikina, Pavel S. Dmitrenok, Georgy A. Nevinsky
{"title":"Metal Dependent Glycosidases of Sea Cucumber Eupentacta Fraudatrix and their Properties","authors":"Svetlana E. Soboleva,&nbsp;Nadejda A. Maltseva,&nbsp;Irina A. Kostrikina,&nbsp;Pavel S. Dmitrenok,&nbsp;Georgy A. Nevinsky","doi":"10.1007/s10930-025-10301-9","DOIUrl":"10.1007/s10930-025-10301-9","url":null,"abstract":"<div><p>Sea cucumbers <i> Eupentacta fraudatrix</i> can completely regenerate their organs within one month after evisceration. The regeneration process involves complex structural changes including restructuring of the intracellular matrix. The connective tissue of echinoderms consists of bundles of collagen fibrils and proteoglycans. It is assumed that animals capable of regeneration must possess a diverse set of proteases and glycosylases that modify the connective tissue. Glycosidases catalyze the hydrolysis of glycosidic bonds in carbohydrate molecules, and these enzymes have not yet been studied in the sea cucumber <i>E. fraudatrix</i>. Here four glycosidase-enriched fractions having optimal pH values at 7.0, 7.5 (two fractions), and 6.0 were revealed. Thе glycosidase of Peak 1 (pH 7.0) was moderately activated by Mn<sup>2+</sup>, Ca<sup>2+</sup>, and Zn<sup>2+</sup> but its best activators are Co<sup>2+</sup> and Ni<sup>2+</sup>, while Mg<sup>2+</sup> ions suppress glycosidase activity. Thе glycosidase of Peak 2 (pH 7.5) is activated at low concentrations of Ca<sup>2+</sup> and Mg<sup>2+</sup>; Mn<sup>2+</sup> and Co<sup>2+</sup> increase its activity at higher concentrations, while Ni<sup>2+</sup> and Zn<sup>2+</sup> are inhibitors of this enzyme. Thе glycosidase of Peak 3 (pH 7.5) has maximal activity in the presence of Ca<sup>2+</sup> and Mg<sup>2+</sup> ions but its activity is suppressed by Mn<sup>2</sup>+, Ni<sup>2+</sup>, and Zn<sup>2+</sup>. Acid glycosidase (pH 6.0) is Ca<sup>2+</sup> dependent enzyme, which activity suppresses by several metal ions to varying degrees: Zn<sup>2+</sup> &gt; Mg<sup>2+</sup> &gt; Ni<sup>2+</sup> &gt; Mn<sup>2+</sup> &gt; Co<sup>2+</sup>. These are the first glycosidases identified in the sea cucumber <i>E. fraudatrix</i> that can be utilized for future studies of their role in extracellular matrix remodeling.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"45 1","pages":"115 - 124"},"PeriodicalIF":1.4,"publicationDate":"2025-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145433654","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}
引用次数: 0
Methylglyoxal-Induced Modification of Hen Egg White Lysozyme: Detection of Advanced Glycation End Products by High Resolution Mass Spectrometry 甲基乙二醛诱导的蛋清溶菌酶修饰:高分辨率质谱法检测晚期糖基化终产物。
IF 1.4 4区 生物学
The Protein Journal Pub Date : 2025-10-22 DOI: 10.1007/s10930-025-10299-0
Sauradipta Banerjee
{"title":"Methylglyoxal-Induced Modification of Hen Egg White Lysozyme: Detection of Advanced Glycation End Products by High Resolution Mass Spectrometry","authors":"Sauradipta Banerjee","doi":"10.1007/s10930-025-10299-0","DOIUrl":"10.1007/s10930-025-10299-0","url":null,"abstract":"<div><p>Methylglyoxal is a highly reactive α-oxoaldehyde that forms advanced glycation end products (AGEs) on reaction with proteins. Here, we have studied the effect of methylglyoxal on hen egg white lysozyme (HEWL), after incubation for different time periods (7, 14 and 21 days). Modification with methylglyoxal induced a gradual lowering of tryptophan fluorescence of the protein associated with a blue shift in the wavelength of fluorescence maximum intensity, as observed from tryptophan fluorescence spectra. Secondary structural analysis by far-UV CD spectroscopy indicated a gradual increase in α-helical content of the protein following incubation with methylglyoxal for different time periods. Subsequent analysis of methylglyoxal incubated protein samples using high-resolution ESI–MS, indicated modification of HEWL and formation of AGE adducts. HEWL incubated with methylglyoxal for 7 days indicated the formation of the AGE hydroimidazolone. Several AGE adducts, namely, hydroimidazolone, argpyrimidine, tetrahydropyrimidine, carboxymethyllysine and pyrrolidone-carboxymethyllyine were identified for HEWL incubated with methylglyoxal for 14 days. Thus, the extent of AGE formation was found to increase with increasing period of incubation with the α-oxoaldehyde as revealed by mass spectral analysis. As indicated in further studies, methylglyoxal modification was found to afford considerable resistance to the protein against stress induced aggregation. Considering the high reactivity of the α-dicarbonyl compound, the current study appears worthwhile in terms of detection of methylglyoxal-derived AGE adducts as well as understanding AGE induced protein modifications with clinical implications in treating AGE related disorders.</p></div>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"44 6","pages":"717 - 728"},"PeriodicalIF":1.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145350751","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}
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