Journal of Biomolecular Structure & Dynamics最新文献

{"title":"Computational characterization of a HotDog domain-containing hypothetical protein from the food vacuole of <i>Plasmodium falciparum</i> reveals potential allosteric regulation by antimalarials.","authors":"Pooja Gupta, Naveen Kumar Kaushik, Cheryl Sachdeva, Kartavya Mathur, Somnath S Pai, Biswajit Saha, Sunny Dhir, Anil Sharma","doi":"10.1080/07391102.2025.2567918","DOIUrl":"https://doi.org/10.1080/07391102.2025.2567918","url":null,"abstract":"<p><p><i>Plasmodium falciparum</i>, the causative agent of the most lethal form of human malaria, harbors numerous uncharacterized proteins whose functions remain unexplored yet may be central to its survival and pathogenicity. Among its specialized organelles, food vacuole plays pivotal role in hemoglobin-catabolism, heme-detoxification, nutrient-assimilation and pharmacodynamic-interactions, thereby representing critical therapeutic target. However, numerous food vacuole-associated proteins remain uncharacterized. In this study, multiple bioinformatics tools were employed to comprehensively characterize a hypothetical food vacuole-associated protein, PF11_0364 (designated PfHDDCP). Conserved domain analysis identified HotDog fold, hallmark of acyl-CoA thioesterases, suggesting its possible role in lipid metabolism. 3D structural model of PfHDDCP was generated using I-TASSER and evaluated with PROCHECK and ProSA. Over 90% of residues were located in favored regions of Ramachandran plot, and ProSA Z-score fell within the range typical of native protein structures, indicating good model quality. Domain analysis <i>via</i> NCBI-CDD identified two putative ligand-binding sites in PfHDDCP. Molecular docking using HDOCK and AutoDock predicted that Acetyl-CoA and Acyl Carrier Protein, canonical substrates of thioesterases, bind at Binding-Site 1, which corresponds to the predicted catalytic site. In contrast, antimalarial compounds were predicted to bind at Binding-Site 2, distinct secondary pocket, suggesting possible allosteric site that may interfere with substrate binding. Molecular dynamics simulations performed with Desmond indicated stable PfHDDCP-ligand complexes and ligand-induced conformational changes, supporting model of ligand-mediated functional modulation. Although these results offer preliminary computational insights into structure, function, and druggability of PfHDDCP, they remain predictive and require experimental validation to confirm the proposed enzymatic activity and therapeutic relevance.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-28"},"PeriodicalIF":2.4,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238690","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}

{"title":"Investigating the chemistry of newly synthesized acetamide linker based purines/pyrimidine derivatives towards DNA receptor site using <i>in silico</i> and <i>in vitro</i> studies.","authors":"Gurmeet Kaur, Vipin Kumar Mishra, Pramodkumar P Gupta, Amandeep Kaur, Mandeep Kaur, Dhandeep Singh, Manisha Bansal","doi":"10.1080/07391102.2025.2567916","DOIUrl":"https://doi.org/10.1080/07391102.2025.2567916","url":null,"abstract":"<p><p>DNA receptor site remain a crucial class of anticancer agents for many researchers. Literature revealed extensive data explaining different involving such data to control anticancer behavior. However, the structural limitations and adverse effects of existing drugs, such as doxorubicin, necessitate the development of novel agents. To address these challenges, a series of 25 linker-based purine/pyrimidine derivatives were designed and after screening through ADMET properties, compounds (4-9) were synthesized (Compounds 1-3 were taken from Literature), and well-characterized. Further, docking analysis was carried out for compounds (1-9) towards various DNA receptor sites, which were compared with doxorubicin. The most efficient compounds 1 and 5 were taken to explore DNA binding and anticancer potential. These compounds feature strategically modified linker regions to enhance stability within the DNA duplex. Computational studies, including molecular docking and MD simulations, extensively explored the structural interactions of these compounds with DNA. Compounds 1 and 5 exhibit stable interactions with linker, particularly acetamide in compound 1 is playing a key role in binding affinity and groove fitting. Notably, compound 1 maintained strong and stable interaction with both DNA strands compared to compound 5 and doxorubicin, suggesting its potential as efficient ligands. Further, FT-IR confirmed intercalation in compound 1 with carbonyl frequency reduction, while its low IC₅₀ of 42.17 µM highlighted strong anticancer potential. Overall, this study presents a structurally refined approach to DNA receptor site, offering valuable insights for designing next-generation anticancer agents with optimized therapeutic potential.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-21"},"PeriodicalIF":2.4,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232705","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}

{"title":"Computational prioritization of deleterious human myelin protein zero gene mutations reveals structural disruption and potential myelin dysfunction through dynamic simulations and stability analysis.","authors":"Hassan H Alhassan, Malvi Surti, Mitesh Patel","doi":"10.1080/07391102.2025.2564378","DOIUrl":"https://doi.org/10.1080/07391102.2025.2564378","url":null,"abstract":"<p><p>The MPZ (Myelin Protein Zero) gene, located on chromosome 1q23.3, plays a crucial role in myelin sheath formation and maintenance. Mutations in the MPZ protein are linked to demyelinating neuropathies, yet the structural and functional consequences of these mutations remain unclear. This study aims to identify and analyze the impact of nonsynonymous single nucleotide polymorphisms (nsSNPs) on the structure and function of the MPZ protein using <i>in silico</i> approaches. Seven sequence-based predictive tools (SIFT, PANTHER, SNP&GO, Fathmm, PhD-SNP, SNAP, MetaSNP) and five structure-based tools (I-Mutant, DynaMut, CupSAT, muPRO, iStable) were used to identify harmful nsSNPs. Molecular dynamics simulations using GROMACS further evaluated the structural and conformational effects of high-risk mutations. The screening process identified G123S and N131K as high-risk mutations. Molecular dynamics simulations revealed that the G123S mutation significantly destabilizes the MPZ protein by reducing conformational flexibility and inducing compaction. Increased root mean square deviations and localized flexibility in the G123S mutant suggest potential disruption of functional dynamics. In contrast, the N131K mutation, while reducing flexibility, preserved structural similarity to the wild-type MPZ protein, indicating a milder impact. These findings suggest that nsSNP-induced structural alterations in MPZ may negatively impact protein stability and function, potentially contributing to neuropathies. Further experimental validation is necessary to confirm these computational predictions.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.4,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212316","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}

{"title":"Mechanistic insights into ESBL activity of subclass A2 in Class A beta-lactamase revealing a distinct strategy towards conferring drug resistance.","authors":"Riya Karan, Anish Pyne, Saroj K Panda, Parth S Sen Gupta, Saugata Hazra","doi":"10.1080/07391102.2025.2563080","DOIUrl":"https://doi.org/10.1080/07391102.2025.2563080","url":null,"abstract":"<p><p>The twenty first century has witnessed challenges with antimicrobial resistance (AMR) emerging as a critical global threat. Among its most concerning is antibiotic resistance (ABR), highly linked to beta-lactamases. Among others, Class A beta-lactamases, present significantly with functional diversity, although ESBLs are one of the major concerns. A key defence mechanism in Gram-negative bacteria is the overexpression of ESBLs (<b>E</b>xtended <b>s</b>pectrum <b>b</b>eta-<b>l</b>actamases) which spread across the bacterial population through horizontal gene transfer causes serious nosocomial infections. Since ESBLs have developed to increase their substrate specificity and hydrolyse most cephalosporins, penicillins, and monobactams, research into them is urgently needed.However, despite attempts functional classification, based on sequence identity, fold similarity, the presence or absence of insertions, particularly in loop regions and mode of action, a universally accepted framework remains elusive. Previous studies have broadly categorized Class A beta-lactamases into subclasses A1 and A2, yet the mechanistic intricacies of subclass A2 only as ESBL demand a more nuanced, multilevel analysis, underlying their role in antibiotic resistance. To bridge this knowledge gap, we employed on a comprehensive investigation encompassing sequence, structure, molecular docking, and dynamic analyses to elucidate the mechanistic approach of antibiotic resistance profiles for these two subclasses. Our sequence and structural studies revealed differences, particularly in insertions, structural alignments, and loop regions, including the omega loop and loops near the active site. Molecular docking study demonstrated better binding of the bigger substrate in the active site cavity of A2 subclass representatives. Dynamic analyses further confirmed our findings, employing root mean square deviation (RMSD), root mean square fluctuation (RMSF), flexibility of the extended and omega loops, radius of gyration (Rg), solvent-accessible surface area (SASA), clustering, hydrogen bonding patterns, principal component analysis (PCA), and free energy landscape (FEL). This study provides insights into the molecular distinctions and resistance mechanisms of these subclasses, paving the way for advanced research in antibiotic resistance and strengthening novel therapeutic strategies.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-22"},"PeriodicalIF":2.4,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191588","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}

{"title":"Computational identification of potential tandem pseudoknots in the 5'UTR and start codon regions of human mRNAs.","authors":"Xiaolan Huang, Zhihua Du","doi":"10.1080/07391102.2025.2563688","DOIUrl":"https://doi.org/10.1080/07391102.2025.2563688","url":null,"abstract":"<p><p>Tandem pseudoknots are distinctive RNA structures with two or more pseudoknots arranged in close proximity. While known in viral and bacterial RNAs, their presence in eukaryotic systems, especially human mRNAs, remains unexplored. Using computational tools, we conducted a transcriptome-scale study to identify potential pseudoknots in human mRNAs. Analysis of positional data revealed numerous potential tandem pseudoknots, of which we present 50 representative cases found in the 5' UTR and start codon regions. These arrays contain two or three pseudoknots, typically without intervening sequences, allowing coaxial stacking of stems to form quasi-continuous helices averaging 30 base pairs. The stem regions are GC-rich, with stabilities comparable to or exceeding known functional pseudoknots. Modeling studies of three selected tandem pseudoknots demonstrated their stereochemical feasibility and revealed both common features and diversities. These potential structures are distributed across the 5' UTR and start codon regions, often spanning the entire 5' UTR and extending nearly 100 nucleotides into the coding region. Most mRNAs containing these tandem pseudoknots encode proteins with essential functions implicated in various diseases, with many serving as drug targets. These findings suggest potential prevalence of tandem pseudoknots in regulating mRNA functions. Further investigation and characterization of these structures would enhance our understanding of RNA biology and reveal new regulatory mechanisms that could be leveraged for therapeutic benefits.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.4,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145185982","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}

{"title":"Plant-based phenolic acids: exploring the interaction of digestive enzyme trypsin/DNA and antioxidant potential.","authors":"Duygu İnci Özbağcı, Sevinç İlkar Erdağı, Rahmiye Aydın","doi":"10.1080/07391102.2025.2564377","DOIUrl":"https://doi.org/10.1080/07391102.2025.2564377","url":null,"abstract":"<p><p>Plant-based phenolic acids are abundantly present in fruits, vegetables, and other plant-based sources. Their broad spectrum of biological properties has sparked substantial interest among researchers. Hence, it seems that studies are required about the effects of phenolic acids on the structure and function of biomacromolecules. This study aimed to investigate the binding interactions of two plant-derived phenolic acids, gentisic and protocatechuic acid, with calf thymus DNA (CT-DNA) and trypsin. Experimental analyses were performed using fluorescence spectroscopy, FTIR, antioxidant assays, and molecular docking techniques. Results indicated that both phenolic acids bind to CT-DNA <i>via</i> the minor groove and interact with trypsin, as confirmed by fluorescence quenching. Thermodynamic parameters in agreement with molecular docking results demonstrated that both phenolic acids could interact with trypsin spontaneously through hydrogen bonds and Van der Waals forces. The distance between phenolic acids and trypsin after interaction was calculated according to fluorescence resonance energy transfer (FRET) theory. Synchronous fluorescence, three-dimensional fluorescence, and FTIR analyses indicated that the conformation of trypsin was changed upon binding with both phenolic acids. Molecular docking supported these findings by showing stable binding modes with comparable energies, influenced by hydroxyl group positions. Furthermore, changes in the number and position of hydroxyl groups revealed that gentisic acid has higher antioxidant potential than protocatechuic acid. These findings provide structural insight into the potential enzyme-inhibitory and nucleic acid-binding properties of both phenolic acids. Additionally, this work contributes to the knowledge of interactions between trypsin/DNA and both phenolic acids under physiological conditions and radical scavenging activities.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.4,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145175599","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}

{"title":"K294E change in the rotavirus factory forming protein NSP2 stabilizes a rare C-terminal conformation.","authors":"Sarah L Nichols, Thomas Hollis, Freddie R Salsbury, Sarah M Esstman","doi":"10.1080/07391102.2025.2563689","DOIUrl":"https://doi.org/10.1080/07391102.2025.2563689","url":null,"abstract":"<p><p>Rotaviruses (RVs) induce the formation of cytoplasmic viral factories, termed viroplasms, which are the sites of early particle assembly and viral RNA synthesis. The RV octameric nonstructural protein 2 (NSP2) plays critical, albeit incompletely understood, roles during viroplasm biogenesis. Previous work by our lab demonstrated that a RV bearing a lysine-to-glutamic acid (K294E) change in the flexible C-terminus of NSP2 exhibits defects in viral replication and induces smaller, more numerous viroplasms as compared to the wildtype (WT) virus. In this study, we sought to better understand if/how this K294E amino acid change altered the structure and/or dynamics of the NSP2 protein. We first determined the X-ray crystal structures of untagged, recombinant NSP2_K294E and NSP2_WT. We found that both proteins formed highly similar octamers and crystallized in the I422 space group. To better understand the possible impacts of the K294E change on the conformations and backbone flexibility of NSP2, we performed molecular dynamics simulations. The results showed that NSP2_K294E adopted distinct C-terminal conformations relative to NSP2_WT and had subtle flexibility differences. Most notably, the data suggest that the K294E change stabilized a rare C-terminal conformation that was only infrequently sampled by NSP2_WT. This shift in conformational preference may help explain why NSP2_K294E displayed decreased capacity to mediate robust viroplasm formation during RV infection. These results provide mechanistic insights into how a single amino acid change in the NSP2 C-terminus can have large effects on structural ensemble, shedding light on features of the protein that underpin RV viroplasm formation.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-17"},"PeriodicalIF":2.4,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145149217","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}

{"title":"Unveiling KRAS G12D inhibition: from molecular dynamics to therapeutic strategies.","authors":"Bamidele Samson Omotara, Pruthvirajsinh Rajendrasinh Solanki, Amena Khatun Manica, Chinedum Favour Ajala, Idris Oladimeji Junaid, Lateef Owolabi Anifowose, Temilade Rukayat Adeniran, Favour Nwachukwu, Racheal Olatunmike Farayola, Ibrahim Tope Abdulrazaq, Mojeed Ayoola Ashiru, Abdul-Quddus Kehinde Oyedele","doi":"10.1080/07391102.2025.2563084","DOIUrl":"https://doi.org/10.1080/07391102.2025.2563084","url":null,"abstract":"<p><p>Addressing the KRAS G12D mutation, a common driver in various cancers, remains a formidable challenge in targeted therapy development. In our study, we performed an extensive molecular dynamics simulation totaling 12 μs across several protein-ligand complexes to uncover the most promising inhibitors against this mutation. Among experimental candidates, THZ835, MTRX1133 and THZ816-THZ835 stood out, exhibiting exceptional stability and binding energy within the KRAS G12D switch II pocket at an atomistic level. This robust performance established THZ835 as the pharmacophore model for our subsequent structure-based drug design. Furthermore, our virtual screening identified structurally similar compounds, notably CID_146527942 and CID_132145180, which demonstrated binding affinities comparable to THZ835. Intriguingly, our analysis suggests that the enhanced binding efficacy of CID_146527942 may be attributed to the formation of salt bridges with key residues such as Asp12 in KRAS G12D, adding a novel dimension to our understanding of stabilizing factors within the binding pocket, while THZ835's efficacy likely stems from other interactions. While THZ835 exhibited the highest binding affinity, the potential of CID_146527942 and CID_132145180 as alternative inhibitors highlights the importance of considering diverse interaction dynamics in drug efficacy. Overall, our study, leveraging a 12-μs MD simulation and detailed molecular interaction analysis, lays the groundwork for innovative therapeutic strategies targeting KRAS G12D-mutant cancers.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-24"},"PeriodicalIF":2.4,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124749","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}

{"title":"Integrating biological regulatory network analysis and structural bioinformatics to probe CABP4 transcriptional regulation in night blindness.","authors":"Sana Fatima, Zoya Amjad, Mahnoor Hashmi, Ishrat Jabeen","doi":"10.1080/07391102.2025.2562134","DOIUrl":"https://doi.org/10.1080/07391102.2025.2562134","url":null,"abstract":"<p><p>The focus of this study is to exploit the role of calcium-binding protein 4 (CABP4) and calcium Ca²⁺ levels in the regulation of the Cav1.4 channel in rod photoreceptors. Moreover, It also examines the changes in the regulation that contribute to the development of night blindness. A biological regulatory network (BRN) model was developed, to simulate CABP4 regulation under varying Ca²⁺ levels as in normal and disease conditions. Subsequently, the IQ domain of the wild-type and mutant CABP4 was analyzed through molecular docking to exploit the Cav1.4 regulation mechanism. Resultantly, MD simulations were performed to evaluate complex stability, residue fluctuations, and hydrogen bonding interactions. According to the BRN simulation, there was a dynamic response in CABP4 expression due to the variations in Ca²⁺. CABP4, Ca²⁺ modulators serve as a potent therapeutic target. Subsequently, for the identification of the most favorable binding hypothesis molecular docking and simulation studies were conducted. Both wild-type and mutant CABP4 were docked with the IQ domain. The stability of the docked complexes was assessed using MD simulations. The wild CABP4-IQ complex exhibited consistent stability (RMSD ranging from 0.4 to 0.5 nm compared to fluctuations observed in the mutant CABP4-IQ complex (RMSD ranging from 0.2 to 0.8 nm). The residues critical for the interaction between the IQ domain and CABP4 and essential for functional rod photoreceptors were analyzed. This study elucidates the role of CABP4 and Ca²⁺ in night blindness, potentially paving the way for therapeutic interventions targeting these elements.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-21"},"PeriodicalIF":2.4,"publicationDate":"2025-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145112846","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}

{"title":"Azoreductases of <i>Pseudomonas</i> sp. PNPG3: a bioinformatics and molecular simulation study for azo dye detoxification.","authors":"Sk Aftabul Alam, Pradipta Saha","doi":"10.1080/07391102.2025.2562136","DOIUrl":"https://doi.org/10.1080/07391102.2025.2562136","url":null,"abstract":"<p><p>Synthetic dyes represent a significant environmental concern due to their persistence and toxicity. These compounds are extensively used across various industries, especially textiles, and are engineered to resist degradation, making them recalcitrant in natural ecosystems. This study focused on azoreductase (Azo) enzymes as potential bioremediation agents capable of degrading diverse azo dyes. Genome analysis of <i>Pseudomonas</i> sp. strain PNPG3 identified the presence of two distinct Azo genes, which were subsequently subjected to structural modelling. The models exhibited notably high aliphatic index values which are indicative of considerable thermostability. Structural validation of both models were performed using the ERRAT, PROCHECK, and QMEAN4 tools, confirming their reliability. Among the azo dyes evaluated, solvent black 3 exhibited the highest binding affinity, with a binding energy of -10.1 kcal/mol. It formed multiple h bonds and van der Waals interactions within the active sites of Azo-1. Congo red showed a maximum binding energy of -9.4 kcal/mol with Azo-2 from strain PNPG3, forming three h bonds within its active site. The Azo2-solvent black 3 complex exhibited the highest structural stability, as indicated by consistently low RMSD values averaging approximately 0.6 nm. Additionally, the complex maintained a low and uniform RMSF profile ranging from ∼0.2 to 0.34 nm, alongside the formation of multiple h bonds and a notable reduction in SASA, further suggested a more compact conformation with limited solvent exposure. PCA analysis further confirmed this stability. Overall, the study highlights the robust azo dye-degrading potential of strain PNPG3, emphasizing its promise for large-scale dye remediation.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-17"},"PeriodicalIF":2.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091748","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}