Journal of Biomolecular Structure & Dynamics最新文献

{"title":"Mutation-driven structural and functional changes in ACE2 and their potential implications for Alzheimer's disease.","authors":"Thamir M Eid, Mohammad E Alsulimane, Afnan Shakoori, Faisal Alandejani, Hayat M Albishi, Mazin Syed, Hisham N Altayb","doi":"10.1080/07391102.2026.2711111","DOIUrl":"https://doi.org/10.1080/07391102.2026.2711111","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by complex molecular mechanisms extending beyond amyloid-β aggregation and tau pathology. Increasing evidence implicates dysregulation of the renin-angiotensin system in AD, with angiotensin-converting enzyme 2 (ACE2) playing a critical regulatory role. However, the structural and functional consequences of ACE2 genetic polymorphisms in Alzheimer's disease remain insufficiently explored. In this study, a comprehensive in silico framework was employed to investigate the impact of ACE2 missense variants on protein stability, dynamics, and interaction with angiotensin II. Missense single nucleotide polymorphisms (SNPs) were retrieved from the dbSNP and gnomAD databases and annotated using the Ensembl Variant Effect Predictor. A multi-tiered screening strategy integrating SIFT, PANTHER, PhD-SNP, SNPs&GO, FoldX, DynaMut2, and mCSM was applied. Based on consensus predictions, four high-risk variants (F308S, L186S, Y654S, and L570S) were selected for structural analysis. Molecular dynamics simulations revealed that all selected variants induced varying degrees of structural destabilization compared to wild-type ACE2 protein. Mutant proteins exhibited increased backbone deviation, enhanced residue-level flexibility, reduced compactness, elevated solvent exposure, weakened intramolecular interactions, broader conformational sampling, and reduced energetic stability. The L570S showing the most pronounced effects, increased structural fluctuations, reduced complex stability and progressively weaker binding free energies. Protein-peptide docking demonstrated reduced interaction scores for angiotensin II across all mutant variants. Overall, this study provides mechanistic insights into how ACE2 polymorphisms may disrupt protein stability and impair angiotensin II recognition, offering a computational basis for understanding their potential contribution to Alzheimer's disease susceptibility and supporting future experimental validation.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-22"},"PeriodicalIF":2.5,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148818522","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":"Shock wave-exposed α-D-glucose: structural, optical and antibacterial studies towards understanding biological implications.","authors":"M Sandhiya, Ikhyun Kim, Raju Suresh Kumar, S A Martin Britto Dhas","doi":"10.1080/07391102.2026.2708782","DOIUrl":"https://doi.org/10.1080/07391102.2026.2708782","url":null,"abstract":"<p><p>In the present study, the effects of acoustic shock waves on α-D-glucose were investigated. The shock waves were generated using a semi-automated Reddy tube with a Mach number of 1.5, a pressure of 0.59 MPa and a transient temperature of approximately 520 K. The response of the shock-treated samples provided valuable insights, demonstrating that α-D-glucose can serve as an excellent model system for both fundamental and applied research. Powder X-ray diffraction (PXRD) analysis revealed that the control sample of α-D-glucose exhibited an orthorhombic crystal structure with the space group P2₁2₁2₁. This structure remained stable even after exposure to up to 500 shock pulses. However, a significant enhancement was observed in the diffraction peak corresponding to the (211) crystalline plane, particularly after 400 and 500 shock pulses, indicating an increase in crystallinity. Similarly, Raman spectroscopy showed noticeable intensity fluctuations in the spectral intensity for samples exposed to 400 and 500 shock pulses, suggesting modifications in the vibrational behaviour of the molecular structure. UV- DRS results revealed that the optical band gap decreased from 4.45 eV for the control sample to 4.25 eV after 500 shock pulses, indicating tuneability of the optical properties. FE-SEM images further revealed significant changes in particle size in the shock-treated samples. In addition, the antibacterial activity of both control and shock-treated samples was evaluated against Bacillus subtilis and Escherichia coli. Moreover, the results demonstrate that the solid-state properties of α-D-glucose can be significantly modified under acoustic shock-treatment conditions. Such harsh environments are believed to have played an important role in the chemical evolution of organic molecules before the emergence of life on Earth.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-18"},"PeriodicalIF":2.5,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148818611","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":"Design, synthesis, and preliminary antiproliferative evaluation of azetidine-functionalized pyrrolo[2,3-d]pyrimidines with integrated computational studies.","authors":"Deepika B V, Kiran N Gaikwad, Sourabh Malabade, Sukanya Pote, Chaluvaraju K C, Parixit Bhandurge, Vaishnavi Agalgave, Ravindra Gaikwad","doi":"10.1080/07391102.2026.2717573","DOIUrl":"https://doi.org/10.1080/07391102.2026.2717573","url":null,"abstract":"<p><p>Azetidine-functionalized pyrrolo[2,3-d]pyrimidines were designed to examine the comparative influence of methyl-, propyl-, and butylsulfonyl substitution among final synthesized analogues on antiproliferative activity and structure-based behavior. Following in silico ADME filtering and docking-based prioritization, selected analogues were synthesized and characterized. Among the evaluated compounds, BCD17 showed the most favorable predicted docking profile toward 17β-hydroxysteroid dehydrogenase type 1 (3HB5), with a docking score of -9.130 kcal/mol and Glide energy of -69.236 kcal/mol. Molecular dynamics simulation and MM-GBSA analysis further supported the stable predicted interaction profile of BCD17, with a mean binding free energy of -109.49 ± 7.52 kcal/mol. DFT analysis indicated a balanced electronic profile compatible with its predicted structure-based performance. <i>In vitro</i> MTT evaluation confirmed antiproliferative activity in MCF-7 cells, with IC₅₀ values of 0.76, 0.75, and 1.83 µM for BCD1, BCD9, and BCD17, respectively. Although BCD1 and BCD9 showed slightly lower IC₅₀ values, BCD17 was prioritized based on its integrated computational stability, apoptosis-related response, and preliminary selectivity profile. MCF-7 cell-cycle and Annexin V/PI apoptosis analyses further supported the antiproliferative and pro-apoptotic effect of BCD17, although direct 17β-HSD1 target engagement was not experimentally confirmed. In MCF-10A cells, BCD9 and BCD17 showed comparatively lower toxicity than 5-FU. Overall, BCD17 emerged as a promising integrated lead candidate for further optimization and biological validation.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.5,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148793459","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 insights into the inhibitory potential of cyclotides Psyle B and Psyle C against key surface proteins of avian influenza H5N1.","authors":"Sidra Altaf, Kainat Sarwar, Rao Zahid Abbas, Mostafa A Abdel-Maksoud, Salman Alrokayan, Bushra Hafeez Kiani","doi":"10.1080/07391102.2026.2717568","DOIUrl":"https://doi.org/10.1080/07391102.2026.2717568","url":null,"abstract":"<p><p><i>Avian influenza viruses</i> (AIVs) are RNA viruses endemic to wild birds, with highly pathogenic strains such as H5N1 causing major outbreaks. Hemagglutinin (HA) and neuraminidase (NA) proteins are key mediators of viral entry and spread. Cyclotides, plant-derived peptides with stable structures and potent bioactivity, have emerged as novel antiviral candidates. This study explored cyclotide-based drug design against H5N1 using computational approaches. HA and NA protein sequences were retrieved from NCBI and their physicochemical properties analyzed using ProtParam. Cyclotides from CyBase were modeled and refined in PyMOL, followed by molecular docking via ClusPro. Binding energies were further assessed with molecular mechanics generalized born surface area, while toxicity was predicted using ToxinPred. Molecular dynamics simulations supported the stability analyses. Results revealed that Psyle B and Psyle C exhibited strong interactions with HA and NA. Psyle B achieved a docking score of -1001.3 kcal/mol, and Psyle C -1031.6 kcal/mol, both predicted as non-toxic. These findings highlight Psyle B and Psyle C as promising antiviral leads. Nonetheless, <i>in vitro</i> and <i>in vivo</i> validation remains essential to confirm their therapeutic potential.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-20"},"PeriodicalIF":2.5,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148793471","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":"Elucidating the mechanism of ADAM10/PD-L1 interaction in pancreatic adenocarcinoma cell lines using cellular and computational analyses.","authors":"Ahmed M E Abdalla, Yu Miao, Yasir A Taha, Mohnad Abdalla, Wafa Ali Eltayb, Sami Fatehi Abdalla, Ning Meng, Chenxi Ouyang","doi":"10.1080/07391102.2026.2719939","DOIUrl":"https://doi.org/10.1080/07391102.2026.2719939","url":null,"abstract":"<p><p>Targeting the immune checkpoint programmed cell death-ligand 1 (PD-L1) faces diverse challenges against pancreatic ductal adenocarcinoma (PDAC), the most common type of cancer-related death. Shedding of PD-L1 from the tumor cell surface by A Disintegrin And Metalloprotease 10 (ADAM10) may impede the function of antitumor immune cells. Understanding the molecular mechanisms behind this interaction is urgently needed. This study elucidates the mechanism of ADAM10/PD-L1 interaction in the pancreatic adenocarcinoma cell line, PANC-1, using cellular assays, molecular docking, and molecular dynamics (MD) simulations. Cellular assays validated that ADAM10 interacts with PD-L1 and sheds the PD-L1 from the cell surface, generating soluble PD-L1 (sPD-L1). Concurrently, the docking results identified critical residues and potential contact points, providing strong evidence for a stable and specific interaction between ADAM10 and PD-L1. The molecular dynamics (MD) simulations further confirmed the structural integrity of the ADAM10/PD-L1 complex, predicting its compactness and stability. These results elucidate how ADAM10 recognizes and interacts with PD-L1, facilitating its cleavage. Future work can leverage these findings to develop potent cancer immunotherapies that inhibit the ADAM10/PD-L1 interaction and the generation of soluble molecules.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-15"},"PeriodicalIF":2.5,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148793448","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":"Sequence-dependent genesis of similar collective states in DNA molecules under low external torque.","authors":"Liliya Fedulova, Аnna Dorohova, Irina Chernukha, Ekaterina Vasilevskaya, Mikhail Drobotenko, Stepan Dzhimak","doi":"10.1080/07391102.2026.2718997","DOIUrl":"https://doi.org/10.1080/07391102.2026.2718997","url":null,"abstract":"<p><p>Molecular biology and biophysics use mathematical modelling to understand how DNA bends and responds to weak torque. The aim of this work is to test the influence of short nucleotide mutations on DNA flexibility using the <i>APOE</i> and <i>COL4A1</i> genes as examples. In this study, we used an angular mechanical DNA model to investigate the dynamics of collective conformational changes in the <i>APOE</i> and <i>COL4A1</i> genes under external torque. It was found that even weak torsional stress leads to the formation of regions with similar collective states and bends. The calculations revealed a clear dependence of the formation of these states on both the magnitude of the external stress and the nucleotide sequence. The zones of bends and conformational transitions are located in different regions of the sequence for different genes, which directly confirms the dependence of DNA rigidity on its nucleotide composition. The studied genes are of key physiological importance. The <i>APOE</i> gene regulates lipid metabolism and neuronal function. Its polymorphisms determine individual risk for developing neurodegenerative and cardiovascular diseases. The <i>COL4A1</i> gene encodes a major protein of basement membranes. Its hereditary defects cause systemic vascular pathologies affecting the brain, kidneys, and organs of vision, demonstrating the critical role of the vascular basement membrane for the stability of these organs. The obtained calculation results open a path to understanding how the primary structure of DNA influences the topology of the molecule, which, in turn, could clarify the mechanisms linking topological changes in DNA to the emergence of mutational trajectories.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-14"},"PeriodicalIF":2.5,"publicationDate":"2026-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148793544","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":"Intrinsic conformational dynamics of apo HIV-2 protease reveal two dynamical stages and multiple closed flap states.","authors":"Marine Baillif, Phuong Nhung Cao, Leslie Regad","doi":"10.1080/07391102.2026.2713125","DOIUrl":"https://doi.org/10.1080/07391102.2026.2713125","url":null,"abstract":"<p><p>HIV-2 protease (PR2) is a homodimeric protein essential for viral maturation and represents a key therapeutic target. Structural studies of PR2 report a semi-open apo form and closed ligand-bound conformations. However, these static structural observations do not fully capture the intrinsic dynamics of PR2. Here, we use molecular dynamics simulations to investigate the conformational landscape sampled by the monoprotonated PR2 in the absence of ligand. The analysis of three independent trajectories reveals a reproducible two-stage dynamical behavior. An initial stage corresponds to a transition from semi-open conformations through transient opening, followed by a second phase characterized by flap closure leading to predominantly closed conformations. These results suggest that PR2 can both access open conformations and spontaneously reach closed states in the absence of ligand. Using complementary geometric descriptors, we show that PR2 closure involves a coordinated reorientation of the flap regions, in which flap B moves from a position in front of flap A to a position behind it, consistently preceding closure. During the late stage, PR2 samples multiple structurally distinct closed conformations, including extended, bent, and inward-bent states. Some of these conformations are consistent with those observed in ligand-bound systems, suggesting that they pre-exist in the apo enzyme. These results provide mechanistic insights into flap rearrangements in PR2. They are also consistent with a conformational selection mechanism in which ligand binding preferentially stabilizes conformations already sampled by the apo enzyme. This findings provide new insights into the intrinsic dynamics of apo PR2 and may assist future structure-based inhibitor design.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-27"},"PeriodicalIF":2.5,"publicationDate":"2026-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760583","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":"Conserved structural dynamics of MTHFR2 link one-carbon metabolism to metabolite-based plant immunity.","authors":"Reecha Mohapatra, Abhijit Debnath, Arya Kumar Dibyananda Naik, Rishi Kesh, Biswa Ranjan Meher, Akhilesh Mishra, Binod Bihari Sahu","doi":"10.1080/07391102.2026.2713054","DOIUrl":"10.1080/07391102.2026.2713054","url":null,"abstract":"<p><p>Methylenetetrahydrofolate reductase 2 (MTHFR2) plays a vital role in the one-carbon (1C) pathway, mediating plant immunity in <i>Arabidopsis</i> against rice blast, a role conserved across the plant kingdom. To understand the structural, conformational dynamics, evolutionary modifications and molecular activity of MTHFR2, we identified that the ^A55_V substitution in an EMS mutant of <i>Arabidopsis</i> which diminishes disease resistance against rice blast. We hypothesized about its key role in regulating the enzyme activities involved in the 1C metabolic pathway. Molecular dynamic simulations, demonstrated that the ^A55_V mutation induces structural alterations and instability at the enzyme active site, affecting its function. Ramachandran plot analysis revealed that the mutant had a slight reduction in favored conformations (94.097% vs. 94.662%). The root mean square deviation analysis exhibited 48.7% and 183% increase in structural deviation and conformational variability, respectively, in the mutant suggesting lower stability. Root mean square fluctuation analysis showed a 39.8% increase in the flexibility of residues in the NADH binding pocket, indicating impaired ligand recognition, altering the resultant product (5-CH₃-THF). Differences in global compactness (radius of gyration) and solvent exposure (solvent-accessible surface area) were minimal, yet localized instability was apparent. Evolutionary analysis revealed that MTHFR2 was highly conserved among plant species and soybean orthologs had 81% similarity, therefore exhibit nonhost resistance. <i>In vitro</i> functional assays showed that soybean extracts suppressed <i>Magnaporthe oryzae</i> conidia germination and development, implying a conserved metabolite-based defense mechanism. Collectively, our findings establish a structural and functional framework for understanding MTHFR2's conserved role and lay the groundwork for future research aiming at connecting enzyme function to metabolite-based immunity in plants.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-18"},"PeriodicalIF":2.5,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148726034","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":"R1334 stabilizes the force-bearing von Willebrand factor A1-GPIbα interface.","authors":"Yue Cheng, Zhipeng Xu","doi":"10.1080/07391102.2026.2714431","DOIUrl":"https://doi.org/10.1080/07391102.2026.2714431","url":null,"abstract":"<p><p>The VWF A1-GPIbα interaction mediates platelet tethering under flow and exhibits a force-dependent mechanical response. Previous simulations identified R1334 within a multi-residue electrostatic region of the interface, but its specific contribution to equilibrium interfacial stability and tensile resistance has been less directly examined through matched WT and R1334A comparisons. Here, replicated equilibrium and multi-rate steered molecular dynamics simulations were used to further examine how R1334A alters these previously reported interactions and the mechanical response of the complex. R1334A decreased the mean interfacial heavy-atom contact count from <math><mn>306.9</mn><mo>±</mo><mn>15.5</mn></math> to <math><mn>244.3</mn><mo>±</mo><mn>40.1</mn></math> and left only sparse residual contacts at residue 1334. Under tensile loading, the mutation lowered the maximum observed resistance by <math><mrow><mn>423</mn></mrow></math>-<math><mrow><mn>482</mn></mrow></math> pN across all tested rates. Residue-resolved analysis showed that WT R1334 repeatedly engaged GPIbα D18, H37, S39 and N61 during maintenance and tensile separation of the bound interface, whereas these coordinated interactions were largely absent after mutation. Notably, R1334A could reach sustained interfacial contact loss at greater extension despite its lower tensile resistance, showing that delayed contact loss does not necessarily indicate stronger binding but can instead arise from the persistence of weaker residual interactions. These results refine the established role of R1334 by directly linking its interactions with neighbouring GPIbα residues to equilibrium interfacial stability and tensile resistance across multiple loading rates.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-12"},"PeriodicalIF":2.5,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148712408","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":"Characterisation of hydrophobic interactions of ubiquinol with AtAOX and EsAOX isoforms by site-directed mutagenesis, molecular dynamics and docking.","authors":"Varsha Venugopalan, Rajesh Parsanathan, Dinakar Challabathula, Kavya Bakka","doi":"10.1080/07391102.2026.2708785","DOIUrl":"https://doi.org/10.1080/07391102.2026.2708785","url":null,"abstract":"<p><p>Alternative oxidase (AOX) is cyanide insensitive terminal oxidase of plant mitochondrial electron transport chain serving as important bypass from classical cytochrome pathway for reduction in generation of reactive oxygen species (ROS) and for maintenance of redox homeostasis under diverse stress conditions. While many studies have emphasised on AOX structure in premature form, the mitochondria localised mature form which is biologically relevant for substrate interaction is not much explored. In the current study, we have performed comparative structural and molecular docking analysis of mature AOX isoforms from stress-sensitive <i>Arabidopsis thaliana</i> and extremophile <i>Eutrema salsugineum</i> to elucidate molecular determinants of ubiquinol binding and stress tolerance. Homology models of AOX isoforms were constructed and validated through SWISS-MODEL, GalaxyWEB, and Ramachandran plot. Docking of activators (pyruvate, glyoxylate, oxaloacetate, 2-oxoglutarate) and substrate (ubiquinol) revealed strong hydrophobic interactions, predominantly Pi-Pi alkyl bonds, within conserved catalytic domains. Among all isoforms, AtAOX1a and EsAOX1a exhibited highest binding affinities with ubiquinol. <i>In-silico</i> site-directed mutagenesis and molecular dynamics simulations demonstrated that substitution of conserved hydrophobic residues, Val184 in AtAOX1a and Val118 in EsAOX1a, with aspartic acid (V→D) did not alter structural stability but significantly disrupted ubiquinol-binding pocket and reduced binding affinity indicating conserved valine residues as hydrophobic anchors crucial for substrate stabilisation. The study underscores hydrophobic interactions as key determinant of AOX function proposing valine as potential site for <i>in-vitro</i> mutagenesis to modulate AOX-mediated stress responses. The findings serve as foundation for future experimental studies addressing AOX mediated stress responses and exploring strategies for improving plant stress tolerance.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.5,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148684652","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}