Journal of Biomolecular Structure & Dynamics最新文献

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Integrated computational protocol for sampling molecular databases towards allosteric inhibition of SARS-CoV-2 spike activation. 针对SARS-CoV-2尖峰激活变构抑制的采样分子数据库集成计算方案。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-08 DOI: 10.1080/07391102.2026.2658697
Vanda Boršová, Dávid Zajaček, Lukas Bucinsky, Marek Štekláč
{"title":"Integrated computational protocol for sampling molecular databases towards allosteric inhibition of SARS-CoV-2 spike activation.","authors":"Vanda Boršová, Dávid Zajaček, Lukas Bucinsky, Marek Štekláč","doi":"10.1080/07391102.2026.2658697","DOIUrl":"https://doi.org/10.1080/07391102.2026.2658697","url":null,"abstract":"<p><p>The opening of the receptor-binding domain of the SARS-CoV-2 spike (S) glycoprotein is a key conformational change required for viral entry. In this work, we use an integrated computational approach to evaluate how small molecules may allosterically alter this process. From an initial library of ∼ 60,000 ZINC compounds screened using physicochemical, absorption, and spatial criteria, 739 candidates were identified and clustered to select nine representatives to study their allosteric effect on the protein activation (opening). Classical molecular dynamics simulations revealed distinct differences in ligand stability, while steered (non-equilibrium) simulations quantified how each compound affected the opening motion of the receptor-binding domain. Free-energy profiles constructed from umbrella sampling, together with conformational population density maps derived from principal component analysis, showed that small ligands provide limited inhibition, medium-sized ligands produce the most consistent stabilizing effects, and two of the heaviest ligands substantially reshape the activation pathway by stabilizing closed or intermediate conformations. Overall, the presented approach provides a practical screening framework for analyzing the effect of small molecules on large conformational changes in viral fusion proteins allowing the assessment of reaction barriers in nanosecond timescale.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
DNA-targeting potential and biomedical applications of selected phenolic Schiff base metal complexes: a molecular biology-oriented supported by computational study. 选定的酚类希夫贱金属配合物的dna靶向潜力和生物医学应用:分子生物学取向支持的计算研究。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-08 DOI: 10.1080/07391102.2026.2666583
Ibrahim Omar Barnawi
{"title":"DNA-targeting potential and biomedical applications of selected phenolic Schiff base metal complexes: a molecular biology-oriented supported by computational study.","authors":"Ibrahim Omar Barnawi","doi":"10.1080/07391102.2026.2666583","DOIUrl":"https://doi.org/10.1080/07391102.2026.2666583","url":null,"abstract":"<p><p>Metal-based compounds continue to attract considerable attention as bioactive agents due to their versatile coordination behavior and ability to modulate biomolecular structure and function. In this study, a phenolic Schiff base ligand, 2-[(5-methoxy-2-hydroxy-phenylimino)methyl]-4-nitrophenol (MHNP), was utilized to synthesize a series of Ru(III), Zn(II), and VO(II) complexes. The structures of the obtained complexes were elucidated using various spectroscopic techniques, and their stability was evaluated to assess suitability for biological applications. Density functional theory (DFT) calculations were performed to provide molecular-level insight into electronic properties and preferred coordination geometries. The combined experimental and theoretical results indicate that the MHNP ligand coordinates through NOO donor atoms, forming octahedral geometry with Ru(III), tetrahedral geometry with Zn(II), and square pyramidal geometry with VO(II) complexes. DNA interaction studies were conducted to evaluate the binding affinity of the complexes toward double-stranded DNA. The results demonstrate enhanced DNA-binding upon metal coordination, with binding modes dependent on the metal center. Notably, the Ru(III) complex exhibited stronger interactions, suggesting groove-binding or intercalative behavior, while Zn(II) and VO(II) complexes showed moderate but stable binding profiles. Structure-interaction relationships highlight the significant role of metal ions in tuning biomolecular recognition. Additionally, the redox properties of Ru(III) and VO(II), along with the redox-modulating nature of Zn(II), suggest potential antioxidant activity through regulation of reactive oxygen species. Overall, these findings indicate that MHNP-based metal complexes are promising multifunctional candidates for antimicrobial, anticancer, and antioxidant applications, offering a rational basis for the development of metal-based therapeutics.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-39"},"PeriodicalIF":2.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Synergistic effects of glucose and reactive dicarbonyls on glycation process of serum albumin: a DoE-based FTIR and CD study. 葡萄糖和活性二羰基对血清白蛋白糖化过程的协同作用:一项基于doi的FTIR和CD研究。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-08 DOI: 10.1080/07391102.2026.2662404
Pavan Kumar Sathala, Arindam Senapati, Laltanpuii Chenkual, Madhuri Divate, Pawan Kumar Porwal
{"title":"Synergistic effects of glucose and reactive dicarbonyls on glycation process of serum albumin: a DoE-based FTIR and CD study.","authors":"Pavan Kumar Sathala, Arindam Senapati, Laltanpuii Chenkual, Madhuri Divate, Pawan Kumar Porwal","doi":"10.1080/07391102.2026.2662404","DOIUrl":"https://doi.org/10.1080/07391102.2026.2662404","url":null,"abstract":"<p><p>Non-enzymatic glycation of serum albumin by reducing sugars and reactive carbonyls was implicated in altered ligand transport and protein deposition in metabolic disease, representing a critical molecular link between chronic hyperglycemia and diabetic complications. Here, we employed a Box-Behnken Design (BBD) to systematically vary bovine serum albumin (BSA) concentration (40-50mg), glucose (1-5mg), methylglyoxal (0.4-2 µM), glyoxal (0.4-4 nM), and diacetyl (1-10 nM) in 46 independent experiments. Secondary-structure changes were probed by Fourier-transform infrared spectroscopy (FTIR) <i>via</i> deconvolution of the amide I/II region and by far-UV circular dichroism (CD) at 208 nm and 222 nm. Quadratic response-surface models were constructed for α-helix and β-sheet contributions, achieving R2 values of ∼0.76 (FTIR α-helix), ∼0.81 (FTIR β-sheet), ∼0.69 (CD 208 nm), and ∼0.98 (CD 222 nm). Results revealed that glycation strongly destabilized α-helices, with a-helix content decreasing by up to 27.4% (FTIR) and about 60% (CD @222nm) relative to native BSA control, particularly under combinations of glucose with methylglyoxal or diacetyl, and at intermediate to high BSA concentrations. β-sheet enrichment occurred primarily at high protein concentration and in the presence of dicarbonyl mixtures, indicative of aggregation-prone states. The parallel trends in FTIR and CD confirmed that helical loss preceded and triggered β-sheet formation. These findings provide a quantitative insight into how combinations of glycating agents, not simply glucose alone, govern albumin structural integrity <i>via</i> non-linear, concentration- and chemistry-dependent pathways. Unlike conventional single-variable (one-factor-at-a-time, OFAT) glycation studies, the present multivariate DoE framework captured non-linear and synergistic interactions among glycating agents, and advanced our mechanistic understanding of albumin misfolding under carbonyl stress.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Arbitrary template docking fails to recapitulate early amyloid fibril oligomers in neurodegenerative diseases. 任意模板对接不能概括神经退行性疾病的早期淀粉样蛋白纤维低聚物。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-06 DOI: 10.1080/07391102.2026.2668024
Jean-Numa Gillet
{"title":"Arbitrary template docking fails to recapitulate early amyloid fibril oligomers in neurodegenerative diseases.","authors":"Jean-Numa Gillet","doi":"10.1080/07391102.2026.2668024","DOIUrl":"https://doi.org/10.1080/07391102.2026.2668024","url":null,"abstract":"","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-9"},"PeriodicalIF":2.4,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
In silico development of an inflammation-triggered β-cyclodextrin carrier for a redox-active vanadium-INAP-tryptophan complex. 用于氧化还原活性钒- inap -色氨酸复合物的炎症触发β-环糊精载体的硅片开发。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-05 DOI: 10.1080/07391102.2026.2664605
Nour El Houda Bensiradj, Hadjar Lemghiti, Nabila Tidjani-Rahmouni, Hadjer Talhi, Ahmad Telfah
{"title":"In silico development of an inflammation-triggered β-cyclodextrin carrier for a redox-active vanadium-INAP-tryptophan complex.","authors":"Nour El Houda Bensiradj, Hadjar Lemghiti, Nabila Tidjani-Rahmouni, Hadjer Talhi, Ahmad Telfah","doi":"10.1080/07391102.2026.2664605","DOIUrl":"https://doi.org/10.1080/07391102.2026.2664605","url":null,"abstract":"<p><p>Inflammation-driven diseases are characterized by localized oxidative stress, acidosis, and hyperthermia-microenvironmental features that often compromise the effectiveness of conventional anti-inflammatory therapies due to poor site selectivity and uncontrolled systemic exposure. In this context, the present study provides an exclusively in silico investigation of an inflammation-responsive drug delivery concept based on β-cyclodextrin (β-CD) encapsulation of a redox-active vanadium complex, VO-INAP-tryptophan. Leveraging the supramolecular host-guest properties of β-CD, the computational model explores a system designed to remain stable under physiological conditions while undergoing selective destabilization within the pathological microenvironment of inflamed tissues. Two plausible inclusion modes of the vanadium complex within the β-CD cavity were systematically evaluated under simulated inflammatory conditions, including acidic pH, increased dielectric constant, and elevated temperature. Frontier molecular orbital analysis and global reactivity descriptors were used to examine how variations in electronic structure, thermodynamic stability, and chemical reactivity influence encapsulation strength and release propensity. The results identify a specific inclusion conformation particularly susceptible to solvent competition and electronic destabilization, indicating a favorable pathway for site-selective release. Component-resolved electronic analysis highlights the complementary roles of the vanadium center and the tryptophan ligand in modulating redox behavior and potential anti-inflammatory activity. Overall, this study provides computational insights that may inform a mechanistic framework for designing inflammation-responsive supramolecular delivery systems and suggests the potential of β-cyclodextrin architectures for optimizing the therapeutic performance of redox-active metal complexes, pending experimental validation.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-15"},"PeriodicalIF":2.4,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Bioinformatics analyses of lignin peroxidases from the smoky bracket fungi Bjerkandera adusta for endocrine disrupting chemical bioremediation. 烟熏菌木质素过氧化物酶在内分泌干扰化学生物修复中的生物信息学分析。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-01 Epub Date: 2025-05-04 DOI: 10.1080/07391102.2025.2498078
Mahfoud Bakli, Khelifa Bouacem, Raul Paşcalău, Laura Șmuleac, Bassem Jaouadi, Haitham Al-Madhagi, Husam Nassar, Abdulrahman H Alessa, Ahmad A Alsaigh
{"title":"Bioinformatics analyses of lignin peroxidases from the smoky bracket fungi <i>Bjerkandera adusta</i> for endocrine disrupting chemical bioremediation.","authors":"Mahfoud Bakli, Khelifa Bouacem, Raul Paşcalău, Laura Șmuleac, Bassem Jaouadi, Haitham Al-Madhagi, Husam Nassar, Abdulrahman H Alessa, Ahmad A Alsaigh","doi":"10.1080/07391102.2025.2498078","DOIUrl":"10.1080/07391102.2025.2498078","url":null,"abstract":"<p><p>Lignin peroxidases (LiP; EC 1.11.1.14) are important oxidative enzymes involved in lignin biodegradation, a key constituent of plant cell walls. Despite their environmental and industrial potential, fungal LiPs are difficult to express and purify. <i>Bjerkandera adusta</i> is a white-rot fungus that secretes LiPs, the three-dimensional structure of which remains unknown. In this study, two LiPs from <i>B. adusta</i> were subjected to various bioinformatics tools to determine their physio-chemical, structural, and functional properties. Their 3D structure was modeled and molecular dynamic simulations were performed to assess their binding to endocrine disrupting chemicals (EDCs). Moreover, molecular docking analysis revealed that among the model lignin compounds, the dimer guaiacyl 4-O-5 guaiacyl exhibited the lowest binding energy with the EDC ligands, estrone (E1) and bisphenol A showing the strongest binding affinity for LiP 588479560 and LiP 444058, respectively. Molecular dynamics simulations further confirmed the stability of these complexes, with bisphenol A exhibiting particularly high stability as indicated by its low RMSD (≤2 Å) and favorable RoG values, reflecting a strong fit within the enzyme's active site. Additionally, the binding free energy calculations showed the substrate dimer had the most favorable binding energy, driven primarily by Van der Waals and lipophilic interactions, suggesting its intrinsic compatibility with <i>B. adusta</i> LiPs. This in silico characterization advances the understanding of LiP structure-function relationships and bioremediation potential. <i>B. adusta</i> LiPs demonstrate promising capacity to target persistent EDCs, offering solutions for environmental pollution mitigation.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3738-3751"},"PeriodicalIF":2.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Unveiling the structural adaptation of a robust thermostable paraoxonase from Bacillus sp. strain S3wahi: insights into bioremediation application. 揭示来自芽孢杆菌菌株S3wahi的强大耐热对氧磷酶的结构适应性:生物修复应用的见解。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-01 Epub Date: 2025-09-08 DOI: 10.1080/07391102.2025.2553895
Ameera Aisyah Azman, Noor Dina Muhd Noor, Adam Thean Chor Leow, Siti Aminah Mohd Noor, Wahhida Latip, Mohd Shukuri Mohamad Ali
{"title":"Unveiling the structural adaptation of a robust thermostable paraoxonase from <i>Bacillus</i> sp. strain S3wahi: insights into bioremediation application.","authors":"Ameera Aisyah Azman, Noor Dina Muhd Noor, Adam Thean Chor Leow, Siti Aminah Mohd Noor, Wahhida Latip, Mohd Shukuri Mohamad Ali","doi":"10.1080/07391102.2025.2553895","DOIUrl":"10.1080/07391102.2025.2553895","url":null,"abstract":"<p><p>A thermostable paraoxonase (S3wahi-PON) from <i>Bacillus</i> sp. strain S3wahi was recently characterised and shown to possess stability across a broad temperature range. This study expands upon the initial biochemical characterisation of S3wahi-PON by investigating the structural determinants and conformational adaptability that contribute to its thermostability, using an integrated approach that combines biophysical techniques and molecular dynamics (MD) simulations across a temperature range of 10 °C to 90 °C. Biophysical analyses confirmed that S3wahi-PON retains broad stability between 10 °C and 60 °C, with its highest structural compactness and integrity observed at 30 °C - an unusual profile compared to most thermostable enzymes, which typically peak near their upper thermal tolerance. MD simulations revealed that S3wahi-PON maintains its globular stability <i>via</i> a synergistic interaction between α-helical content and intramolecular forces such as hydrogen bonding, salt bridges, and hydrophobic clusters. Notably, an inverse relationship between the radius of gyration (Rg) and solvent-accessible surface area (SASA) was observed at 50 °C and 60 °C, suggesting internal tightening of the structure without a corresponding increase in surface exposure, which appears to be a promising mechanism for preserving thermostability. Moreover, loop 16, encompassing Pro192 and located near the catalytic site, exhibited pronounced flexibility that was suggested to influence the enzyme's catalytic performance. These findings indicate that the thermostability of S3wahi-PON is not governed by a single dominant feature but rather by the cooperative contribution of multiple structural elements, which collectively preserve its catalytic conformation under thermal stress. Overall, S3wahi-PON emerges as a promising moderately thermostable enzyme suitable for the bioremediation of organophosphate (OP)-contaminated water systems. The insights gained from this study advance our understanding of its stability mechanisms and provide a foundation for future protein engineering strategies to enhance its applicability in diverse environmental and industrial contexts.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3922-3946"},"PeriodicalIF":2.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
In silico analysis of the γ-carbonic anhydrase EcoCAγ from Enterobacteria: assessing the role of the 72-residue N-terminal extension. 肠杆菌γ-碳酸酐酶EcoCAγ的硅分析:评估72残基n端延伸的作用。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-01 Epub Date: 2025-11-14 DOI: 10.1080/07391102.2025.2586041
Mariia Y Stoliarskaia, Oleg S Nikonov, Sophia S Borisevich
{"title":"<i>In silico</i> analysis of the γ-carbonic anhydrase EcoCAγ from <i>Enterobacteria</i>: assessing the role of the 72-residue N-terminal extension.","authors":"Mariia Y Stoliarskaia, Oleg S Nikonov, Sophia S Borisevich","doi":"10.1080/07391102.2025.2586041","DOIUrl":"10.1080/07391102.2025.2586041","url":null,"abstract":"<p><p>The γ-class carbonic anhydrase EcoCAγ, reported in <i>Escherichia coli</i> in 2022, contains a 72-residue N-terminal extension absent in the canonical YrdA isoform. A genomic analysis confirmed that the full-length EcoCAγ is conserved (95-100% identity) across multiple <i>E. coli</i> and <i>Shigella</i> strains but is not present in the laboratory strain K-12. A full-length trimeric model was generated using AlphaFold-Multimer and subjected to molecular dynamics simulations in aqueous and membrane environments. In membrane conditions, the N-terminal segment maintained an extended α-helical conformation, whereas in aqueous solution it underwent compaction and self-association. Throughout all simulations, the trimeric assembly and the geometry of the catalytic site remained preserved. No disruption of the active-site architecture was observed under either condition. These simulations provide structurally resolved observations of the environment-dependent behavior of the N-terminal region and its effect on the conformational dynamics of the EcoCAγ trimer.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4057-4071"},"PeriodicalIF":2.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145513002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Structural and dynamic characterization of MirA-like xenosiderophore transporters in Fusarium: in silico modeling and in vitro validation. 镰刀菌中mira样异种铁载体的结构和动态表征:硅模型和体外验证。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-01 Epub Date: 2026-03-30 DOI: 10.1080/07391102.2026.2651829
Ashutosh Singh, Azmi Khan, Micky Anand, Pratika Singh, Ravinsh Kumar, Abhilash K Tilak, Amrita Srivastava
{"title":"Structural and dynamic characterization of MirA-like xenosiderophore transporters in <i>Fusarium: in silico</i> modeling and <i>in vitro</i> validation.","authors":"Ashutosh Singh, Azmi Khan, Micky Anand, Pratika Singh, Ravinsh Kumar, Abhilash K Tilak, Amrita Srivastava","doi":"10.1080/07391102.2026.2651829","DOIUrl":"10.1080/07391102.2026.2651829","url":null,"abstract":"<p><p><i>Fusarium</i>, an omnipresent fungus is known for its pathogenic potential. Pathogenic fungi like all other organisms need iron and are known to produce siderophores for iron acquisition. Siderophore producers possess transporters for their own siderophore as well as for siderophores secreted by other organisms known as xenosiderophore. Although iron is an essential nutrient it can also cause oxidative stress and cell-death at high concentrations. While siderophore utilization is employed by the fungi for efficient iron acquisition, it can be exploited against them by supplying xenosiderophore exogenously in turn increasing iron uptake that might prove lethal. A xenosiderophore-iron transporter MirA has been identified earlier in <i>Aspergillus nidulans</i> for the transport of bacterial siderophore enterobactin. MirA has not yet been identified in <i>Fusarium</i> spp. Present study is a computational analysis that focuses on searching possible orthologs of MirA in <i>Fusarium</i> and predicting its structure using deep-learning-based structural prediction and validation approaches. Docking confirmed binding of predicted <i>Fusarium</i> MiRA transporters with the enterobactin-Fe complex, and the most stable complex was further analyzed by molecular dynamics simulations. RMSD, RMSF, Rg, and SASA analyses demonstrated that interaction with the enterobactin-Fe complex stabilizes the MirA structure, supporting its functional adaptation for siderophore-chelated iron binding. <i>In silico</i> findings are further supported by experimental validation that shows growth inhibitory effect of catecholate siderophore produced by <i>Escherichia coli</i> on <i>Fusarium</i> sp. through anti-fungal plate assay, dry weight estimation and morphological changes through microscopy using LPCB staining. The results suggest possible involvement of MirA in xenosiderophore-mediated biocontrol <i>via</i> siderophore-iron uptake.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4191-4209"},"PeriodicalIF":2.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147574132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Structural and antigenic variation in Hepatitis B virus oncogene, HBx. 乙型肝炎病毒致癌基因HBx的结构和抗原变异。
IF 2.4 3区 生物学
Journal of Biomolecular Structure & Dynamics Pub Date : 2026-05-01 Epub Date: 2025-06-16 DOI: 10.1080/07391102.2025.2517826
Fatima Fasih, Nusrat Jabeen, Mushtaq Hussain, Atiya Habib, Shaheen Sharafat, Zaheer Ul-Haq
{"title":"Structural and antigenic variation in Hepatitis B virus oncogene, HBx.","authors":"Fatima Fasih, Nusrat Jabeen, Mushtaq Hussain, Atiya Habib, Shaheen Sharafat, Zaheer Ul-Haq","doi":"10.1080/07391102.2025.2517826","DOIUrl":"10.1080/07391102.2025.2517826","url":null,"abstract":"<p><p>Hepatitis B Virus (HBV) is a known oncogenic virus, with over 50% of infections leading to hepatocellular carcinoma. The virus's primary oncogenic protein is identified as HBx. Over the past decade, only a limited number of studies have explored the structure of HBx using computational approaches. Depending on the method used, two significantly different topologies with notable variations in secondary structure elements have been predicted for this protein. In this study, we compare both predicted structural configurations of HBx and extend our analysis across different genotypes and strains of both human and non-human HBV. Phylogenetic analysis of HBx suggests zoonotic transmission of the virus between humans and orangutan HBV. Several critical residues essential for HBV transcription, including Cys61, Cys69, Cys137, and His139, are conserved across all mammalian HBV, including human strains. In contrast, residues such as Ser25 (involved in intranuclear localization of HBx), Pro90 (associated with UVDBB interaction), and Cys115 (linked to mitochondrial localization of HBx) are exclusive to human HBV, indicating potential sub-neofunctionalization of the HBx protein in human strains. Molecular models of HBx generated using I-TASSER and AlphaFold were non-superimposable. Structural alignment with a partially resolved HBx structure, along with molecular dynamics (MD) simulations, supports the prediction made by AlphaFold. Additionally, AlphaFold predicted HBx structure exhibits similarity to palmitoleoyl transferases, suggesting a possible evolutionary origin. This study provides valuable insights into the origin and evolutionary development of the oncogenic potential of HBx in mammalian HBV.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3763-3779"},"PeriodicalIF":2.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
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