Journal of Biomolecular Structure & Dynamics最新文献

{"title":"Unraveling the structural dynamics of A<i>β</i>42 monomer: insights from K16A and K16A + K28A mutations through molecular dynamics simulations.","authors":"Kui Xia, Weixing Tian, Huifang Xu, Le Wang, Xinpeng Li","doi":"10.1080/07391102.2025.2554351","DOIUrl":"https://doi.org/10.1080/07391102.2025.2554351","url":null,"abstract":"<p><p>Alzheimer's disease is a degenerative disease of the central nervous system that pre-dominantly affects the elderly population. The main reason is that amyloid beta 42 has a strong tendency to aggregate, which easily induces the damage to the central nervous system. It was shown that residues 16 and 28 play a key role in the self-assembly process. Moreover, these studies have revealed that substituting alanine for these residues can weaken the toxicity of A<i>β</i>. While numerous studies,including molecular dynamics simulations, have emphasized the significance of K16 and K28 in A<i>β</i> aggregation and toxicity, the specific impact of their combined mutation(K16A + K28A) on the structural dynamics and toxicity of A<i>β</i> remain unclear. Therefore, in this paper, molecular dynamics simulations were used to investigate the structural changes and kinetic properties of A<i>β</i>42 protein by the two mutant systems. The results show that both mutant systems inhibit the high flexibility of wild-type A<i>β</i> protein during the simulation. By observing the changes in protein structure in different systems, it is found that the K16A system was able to maintain the natural helical conformation of A<i>β</i>42 and also inhibit the generation of <i>β</i>-sheet structures. However, for the K16A + K28A system, it not only destroys the helical structure, but also produces more <i>β</i>-sheet structures. The analysis of residue contacts revealed that this phenomenon. The K16A system was able to decrease the interaction between the hp1fragment and the C-terminus in the A<i>β</i>42 monomer, whereas the two-point mutation increased this interaction.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.4,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145069782","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 PFOS-induced structural changes and aggregation in hen egg white lysozyme: spectroscopic and molecular insights.","authors":"Rushali Dudure, Ritika Joshi, Pulak Pritam, Alok Kumar Panda, Sujit Kumar Ghosh, Manojkumar Jadhao","doi":"10.1080/07391102.2025.2559353","DOIUrl":"https://doi.org/10.1080/07391102.2025.2559353","url":null,"abstract":"<p><p>The widespread manufacture and use of perfluoroalkyl substances (PFAS) has jeopardized human health & environment tremendously, thereby becoming a grave cause of concern for the thriving ecosystem. The current understanding of PFAS on protein aggregation is still in the early stage. Thus, the current study investigates how Perfluorooctanesulfonic acid (PFOS) affects the Lysozyme (HEWL), a protein that typically aggregates in acidic and high temperatures. Our study employed diverse techniques, including spectroscopy, thermal analysis, and <i>in silico</i> modeling, to gain intriguing insights about the same. Using a combination of steady-state fluorescence spectroscopy, ITC, molecular docking, molecular dynamic simulation and circular dichroism, our study reveals strong and significant PFOS and HEWL interactions characterized by hydrogen bonding, hydrophobic forces, and ionic interactions. PFOS significantly alters the secondary structure of HEWL, as evidenced by circular dichroism and synchronous fluorescence spectroscopy. Increased PFOS concentrations caused HEWL aggregation at room temperature (25 ^ºC) and under physiological conditions (pH 7.4 and 37 ^ºC), as is substantiated through different assays. Protein aggregation was found to rapidly accelerate at 37 ^ºC, providing new insights into the process. Our findings shed light on the health risks of PFOS exposure through protein aggregation, contributing to environmental toxicology progress.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-19"},"PeriodicalIF":2.4,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040233","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":"Exploring the novel protein drug target BAG33339.1 of <i>Porphyromonas gingivalis</i>: an integrative subtractive proteomics and structural dynamics study.","authors":"Ishani Paul, Alankar Roy, Soumyadeep Ray, Soumili Pyne, Mowmita Saha, Sujay Ray","doi":"10.1080/07391102.2025.2553155","DOIUrl":"https://doi.org/10.1080/07391102.2025.2553155","url":null,"abstract":"<p><p><i>Porphyromonas gingivalis</i>, a gram-negative, bacterium interacts favourably with host subgingival biofilms to cause adult tooth decay and loss. Consequently, the host is infested with an uncontrollable microbial community and a compromised immune system, ultimately leading to tissue damage and bone resorption. <i>P. gingivalis</i> has also been known to cause cardiovascular and metabolic diseases, Alzheimer's disease, depression, prostate and digestive system cancer, rheumatoid arthritis, and adverse pregnancy outcomes with high detection frequencies. Rising concerns in the recent past, highlight the inefficiency of antibiotics and antiseptics in the treatment of <i>P. gingivalis</i>-related infections. Hence, the current scenario impels the discovery of an alternative therapeutic avenue against <i>P. gingivalis</i>-infections. To elucidate the unidentified bacterial mechanisms of infection, we screened a non-homolog of the host and gut microbiome as a novel druggable target from 173 essential hypothetical proteins of <i>P.gingivalis</i> (BAG33339.1). BAG33339.1 was an inner membrane protein with a hydrophobic N-terminal transmembrane helix and a primarily reconfiguring C-terminal helical region (Y36 to E52) while the residues (downstream of Lys45) lay in the disordered region. Frustration index coupled with the mutation matrix showed the steadiness of the transmembrane helix and dynamicity of the C-terminal residues finally yielding a 'U'-shaped protein conformation. The tendency of the disordered C-terminal residues was to generate <i>P. gingivalis</i> variants. The overall conformational stability was determined by equilibrating RMSD, R_g and SASA values corroborated by increasing H-bonds and helix settling. Targeting the ligand binding pockets of BAG33339.1 would guide future endeavours to tackle <i>P. gingivalis</i> interaction with host systems.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-45"},"PeriodicalIF":2.4,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145040291","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":"<i>In silico</i> engineering of <i>Trichoderma harzianum</i> acetylesterase for enhanced thermal stability and efficiency.","authors":"Ali Abolhasanzadeh Parizi, Milad Lagzian","doi":"10.1080/07391102.2025.2553348","DOIUrl":"https://doi.org/10.1080/07391102.2025.2553348","url":null,"abstract":"<p><p>Acetylesterase, produced by <i>Trichoderma harzianum</i>, plays a crucial role in deacetylating hemicellulose during pulp production. Thermostable variants of this enzyme, although rare, can significantly enhance industrial efficiency by retaining activity at high temperatures. This research aims to design a thermostable variant of acetylesterase from <i>T. harzianum IOC-3844</i> (EC 3.1.1.6) using computational methods. A 3D model of the enzyme was created, and stabilizing mutations were identified. Among over 250 screened mutants, a double mutant (D75C, E296L) was recognized as the most promising variant. During 200 ns of molecular dynamics simulations at 37 °C and 70 °C, the model outperformed the native enzyme. At 70 °C, there was a 30.7% decrease in the mean RMSD (0.43 Å), a 9.5% reduction in the mean RMSF (0.06 Å), a 1.5% decrease in the mean Rg (0.29 Å) and a 3.4% reduction in the mean SASA (4.6 nm²). The mutant also displayed 36.5% more mean intramolecular hydrogen bonds and a 42.3% improvement in mean interaction energy (21.96 Kcal/mol). The PCA results showed that the double mutant maintains the native enzyme's structure at high temperatures. This variant exhibits enhanced thermal stability and catalytic activity, making it a promising eco-friendly alternative to harmful chemicals, such as chlorine, in paper production.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-25"},"PeriodicalIF":2.4,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145023362","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 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":"https://doi.org/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":"1-25"},"PeriodicalIF":2.4,"publicationDate":"2025-09-08","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}

{"title":"Deciphering protein-DNA interactions of <i>KISS1</i> with transcription factors through molecular docking, molecular dynamics simulations, and gene expression analysis.","authors":"Hetvi Shah, Pranav Pillai, Lipi Buch, A V Ramachandran, Parth Pandya","doi":"10.1080/07391102.2025.2553344","DOIUrl":"https://doi.org/10.1080/07391102.2025.2553344","url":null,"abstract":"<p><p>Metastasis is a key hallmark of cancer aggressiveness, particularly in triple-negative breast cancer (TNBC), which lacks effective targeted therapies. Kisspeptin-1 (KISS1), a known metastasis suppressor is emerging as a potential therapeutic modulator. This study investigates the structural and regulatory interactions between <i>KISS1</i> and key transcription factors (TFs) involved in metastasis: SP1, CDX2, FLI1, GATA2, NMYC, and HDAC2. TFs were identified <i>via</i> TFLink, modelled using SWISS-MODEL, and docked with <i>KISS1</i>-DNA using HADDOCK. CDX2 showed the strongest binding (HADDOCK score: -144.2; buried surface area: 2526.5 Ų), followed by HDAC2, GATA2, NMYC, SP1, and FLI1. Molecular dynamics simulations (150 ns) revealed stable complexes for SP1, NMYC, and CDX2 with low RMSD (2.1-2.7 Å), compact Rg (∼21.0 Å), and stable hydrogen bonding (5-9 bonds). In contrast, FLI1 and GATA2 showed greater flexibility and unstable interactions. Experimental validation in MDA-MB-231 cells treated with Kisspeptin-10 (IC₅₀: 100.21 nM) showed upregulation of SP1, NMYC, CDX2, and GATA2, and downregulation of FLI1 and HDAC2. These findings suggest KISS1 selectively modulates transcriptional activity toward anti-metastatic signaling. Overall, <i>KISS1</i> demonstrates strong potential as a transcriptional regulator and therapeutic agent against TNBC metastasis.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-17"},"PeriodicalIF":2.4,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000668","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":"Molecular insights into ZER1 recognition of N-terminal residue mutations.","authors":"Mingyao Tian, Wenbao Zhao, Xule Zhao, Shun Zhang, Yanjun Zhang, Xiafei Hao","doi":"10.1080/07391102.2025.2553346","DOIUrl":"https://doi.org/10.1080/07391102.2025.2553346","url":null,"abstract":"<p><p>N-terminal glycine (Gly/N-degron), as a degradation signal, can be recognized by specific E3 ubiquitin ligases and plays a crucial role in protein degradation and cellular homeostasis. As a substrate receptor in the Cullin 2-RING E3 ligase complex, ZER1 mediates protein degradation <i>via</i> the Gly/N-degron pathway by recognizing N-terminal glycine and other small residues. This study employed all-atom molecular dynamics (MD) simulations and binding free energy calculations to explore ZER1's recognition of the wild-type peptide GFLHVGQD (WT) and its N-terminal mutants (G1S, G1A, G1T, and G1C). The results show that van der Waals and electrostatic interactions are the primary driving forces stabilizing the ZER1-peptide complex. While N-terminal mutations moderately enhanced binding affinity, their impact on the overall structural stability of ZER1 was minimal. Per-residue energy decomposition revealed that the N-terminal residue is vital for subsequent recognition and degradation processes, whereas the second (F2) and third (L3) residues play dominant roles at the binding interface, contributing most significantly to binding free energy. Hydrogen bond analysis further highlighted the critical roles of key residues, F2 and H4, in anchoring the peptide within the ZER1 binding pocket. This study provides molecular-level insights into the Gly/N-degron pathway, emphasizing the role of the N-terminal residue and the critical contributions of adjacent residues. The findings offer a theoretical foundation for further exploration of protein degradation mechanisms and the development of therapeutic strategies targeting ZER1-mediated pathways.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-16"},"PeriodicalIF":2.4,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144992729","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 study of deleterious missense SNPs in the <i>USH1G</i> gene implicated in Usher syndrome.","authors":"Kenza El Khair, Madoussou Toure, Salaheddine Redouane, Hicham Charoute, Kenza Slaoui, Houda Benrahma, Abdelhamid Barakat","doi":"10.1080/07391102.2025.2553345","DOIUrl":"https://doi.org/10.1080/07391102.2025.2553345","url":null,"abstract":"<p><p>Usher syndrome is an inherited condition that causes hearing and visual impairments, along with vestibular dysfunction, due to mutations in various genes, including <i>USH1G</i>, which codes for the scaffold protein SANS, essential for proper sensory function. This study employed a computational approach in order to analyze the potential impact of missense SNPs in <i>USH1G</i>. We started by curating and filtering SNPs from the Ensembl database, followed by a variety of computational prediction methods, such as SIFT, PolyPhen-2, MetaLR, BayesDel_addAF, and MutationTaster, to identify the pathogenic impact of the nsSNPs. Then, we used CUPSAT, DUET, I-stable, I-Mutant, MUpro, and E-SNPs&GO to assess the stability of the altered proteins. To determine their conservation state, we used NCBI BLASTP. Out of 499 missense SNPs, only 5 (L396P, L426F, G434W, R436Q, and R446Q) were identified as most impactful and were subjected to molecular dynamics (MD) simulations (RMSD, RMSF, Rg, PCA, and FEL) to fully understand how these variations affect the dynamic behavior of our protein. Lastly, we conducted a Wilcoxon rank-sum test on RMSD values of the MD simulations. This analysis provided important insight into how the deleterious SNPs impact the protein's structural stability. This computational study provides a framework for identifying potentially deleterious mutations, understanding the pathological foundation of the pathology, and guiding future experimental research.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-18"},"PeriodicalIF":2.4,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955687","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":"Virtual screening and molecular dynamics reveal the potential biochemical impacts of microplastics on human protein targets.","authors":"Sivashanmugam Muthukumaran, Muthu Kannan, Honguntikar D Sachin, Konda Mani Saravanan","doi":"10.1080/07391102.2025.2553343","DOIUrl":"https://doi.org/10.1080/07391102.2025.2553343","url":null,"abstract":"<p><p>Microplastic pollution has emerged as a pressing worldwide health concern, having recently been identified in human blood. Nonetheless, the molecular specifics of microplastic's interactions with human biology remain poorly understood. This paper presents a comprehensive computational analysis of the structural mimicry and potential metabolic disruption caused by common microplastics compounds. Six prevalent microplastics were selected, and their three-dimensional structures were evaluated against the Human Metabolome Database using FTrees similarity analysis. Certain microplastic compounds, such as dimethyl terephthalate and 1-decene, exhibited significant structural resemblance to crucial human metabolites involved in lipid metabolism, detoxification, and neurotransmission. The virtual screening conducted with LigTMap and SeeSAR identified potential protein targets, revealing that dimethyl terephthalate demonstrated moderate binding affinity to Carbonic Anhydrase II. The structural stability of this interaction was validated using molecular dynamics simulation over 500 ns, with RMSD and RMSF analysis indicating the stabilization of the conformations. Free energy landscape analysis also suggested the creation of a partially stable complex. These data indicate that microplastics are not physiologically inert and may disrupt endogenous metabolites, hence affecting protein function and metabolic pathways. This study highlights the urgent need for a more in-depth toxicological examination of microplastic exposure, which would establish a mechanistic framework to understand their potential contribution to human health risks at the molecular level.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-13"},"PeriodicalIF":2.4,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955771","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":"Effect of osmolytes-TMAO and serine on the binding and stability of 5-fluorouracil with calf thymus DNA (CT-DNA): biophysical insight.","authors":"Madhuri Thorve, Nand Kishore","doi":"10.1080/07391102.2025.2549781","DOIUrl":"https://doi.org/10.1080/07391102.2025.2549781","url":null,"abstract":"<p><p>Osmolytes play major role in stabilization of macromolecules like proteins and nucleic acids. The major force responsible for stabilization of these macromolecules are preferential binding and preferential exclusion or hydration. Here, we have determined intermolecular interactions of 5-fluorouracil (5FU) with calf thymus DNA (CT-DNA) with addition of osmolytes trimethylamine oxide (TMAO) and serine (Ser). The thermal stability and conformational changes of CT-DNA with 0.08 mM TMAO and 0.08 mM Ser showed that they stabilize DNA. It has been observed that 0.5 M TMAO and 0.5 M Ser showed more stability as compared to high molality (2 M). TMAO and Ser interact with CT-DNA via electrostatic and hydrogen bond interactions. The binding constant values of 5FU increased with TMAO due to hydration effects, whereas in the presence of serine, it decreased due to presence of common residue at binding site of CT-DNA. ITC data showed that binding mode of 5FU with CT-DNA with addition of TMAO and Ser changes from two and three sequential mode to independent one. The presence of ethidium bromide at intercalation and osmolytes at minor groove site, reduces the binding affinity of 5FU from 103 to 101 M-1. From docking it has been observed that 5FU intercalates in between bases of CT-DNA by forming hydrogen bonds and electrostatic interactions with phosphate groups of DNA when TMAO or Ser added to it. The study of 5FU-osmolyte-DNA interaction using spectroscopic, calorimetric and docking methods is crucial for elucidating the underlying mechanisms of ligand-macromolecule binding and optimizing chemotherapy treatments at primary level.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"1-22"},"PeriodicalIF":2.4,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955699","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}