Biophysical chemistry最新文献

{"title":"Equilibrium solubility, solvent effect, solvation and thermodynamic modeling of 1, 3-dinitropyrazole in solutions of methyl alcohol /ethyl alcohol + water","authors":"Adel Noubigh ,&nbsp;Manef Abderrabba","doi":"10.1016/j.bpc.2025.107430","DOIUrl":"10.1016/j.bpc.2025.107430","url":null,"abstract":"<div><div>1,3-dinitropyrazole's (DNP) solubility was studied by utilizing the gravimetric method across temperatures ranging 278.15 to 318.15 K and a pressure of 101.2 kPa. In the study, two solvent mixtures were investigated: aqueous methyl alcohol and aqueous ethyl alcohol. Based on the findings, higher temperatures favorably influenced solute dissolution in both solvent systems. To relate the solubility of DNP in two binary solvents mixture, the KAT-LSER model was used. This implies that the polarity of the solvents, as well as the cavity term and hydrogen bonding interactions were pivotal to DNP's solubility. By utilizing the Jouyban-Acree, van't Hoff-Jouyban-Acree, Apelblat-Jouyban-Acree and Ma models, the derived results were compiled. The experimental results prove that the Apelblat-Jouyban-Acree model could give the best correlation results with the experimental data, with the overall relative average deviation values (RAD) of 2.05 %, 2.51 % and the root mean-square deviation (RMSD) of 0.415 × 10⁻⁴, 0.492 × 10⁻⁴ in aqueous methyl alcohol and aqueous ethyl alcohol, respectively. Using the inverse Kirkwood–Buff integrals method, the preferential solvation parameters for the solute DNP determined. The obtained results show that DNP exhibited a preference for solvation in methyl alcohol and ethyl alcohol at all mole fractions of alcohol.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107430"},"PeriodicalIF":3.3,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143621074","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":"Autoencoder-based drug-virus association prediction with reliable negative sample selection: A case study with COVID-19","authors":"A.S. Aruna ,&nbsp;K.R. Remesh Babu ,&nbsp;K. Deepthi","doi":"10.1016/j.bpc.2025.107434","DOIUrl":"10.1016/j.bpc.2025.107434","url":null,"abstract":"<div><div>Emergence of viruses cause unprecedented challenges and thus leading to wide-ranging consequences today. The world has faced massive disruptions like COVID-19 and continues to suffer in terms of public health and world economy. Fighting with this emergence of viruses and its reemergence plays a critical role in the health care industry. Identification of novel virus-drug associations is a vital step in drug discovery. Prediction and prioritization of novel virus-drug associations through computational approaches is an alternative and best choice considering the cost and risk of biological experiments. This study proposes a method, KR-AEVDA that relies on k-nearest neighbor based reliable negative sample selection and autoencoder based feature extraction to explore promising virus-drug associations for further experimental validation. The method analyzes complex relationships among drugs and viruses by investigating similarity and association data between drugs and viruses. It generates feature vectors from the similarity data, and reliable negative samples are extracted through an effective distance-based algorithm from the unlabeled samples in the dataset. Then high level features are extracted via an autoencoder and is fed to an ensemble classifier for inferring novel associations. Experimental results on three different datasets showed that KR-AEVDA reliably attained better performance than other state-of-the-art methods. Molecular docking is carried out between the top-predicted drugs and the crystal structure of the SARS-CoV-2's main protease to further validate the predictions. Case studies for SARS-CoV-2 illustrate the effectiveness of KR-AEVDA in identifying potential virus-drug associations.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107434"},"PeriodicalIF":3.3,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143629532","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":"Relevance of ceramide 1-phosphate domain formation in activation of cytosolic phospholipase A2","authors":"Tomokazu Yasuda ,&nbsp;Daiki Ueura ,&nbsp;Madoka Nakagomi ,&nbsp;Shinya Hanashima ,&nbsp;Michio Murata","doi":"10.1016/j.bpc.2025.107433","DOIUrl":"10.1016/j.bpc.2025.107433","url":null,"abstract":"<div><div>Ceramide 1-phosphate (C1P), as a lipid mediator, specifically binds and activates cytosolic phospholipase A₂α (cPLA₂α). Previous findings revealed that modification of the specific hydrophobic moiety decreases the affinity with cPLA₂α. However, the possible biological role of the temporal C1P-enriched domains formed in biomembranes for the molecular recognition of cPLA₂α has not been fully elucidated. In this study we elucidated the properties of segregated domains formed by C1P (and its analogs) and the affinity of cPLA₂α for C1P in different co-lipid environments by fluorescence spectroscopy using <em>trans</em>-parinaric acid and surface plasmon resonance (SPR). Fluorescence measurements suggested that the formation of C1P ordered domains is strongly influenced by interfacial 3-OH and phosphate groups of C1P, such as hydrogen-bonding and electrostatic interactions, and depends on the co-lipid composition of the host bilayer. SPR indicated that C1P under the lipid environment favorable for the formation of C1P clusters has higher affinity for cPLA₂α. Thus, we speculate that C1P clusters formed under certain membrane conditions are important in specific binding with cPLA₂α by increasing the interaction between the C1P headgroup and basic residues of cPLA₂α. In conclusion, this study revealed that the local formation of lipid mediator-rich clusters in biomembranes likely has a significant effect on the interaction between the mediator and its receptor protein.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107433"},"PeriodicalIF":3.3,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143609144","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 theranostic potential: Insights into cell-free microRNA-protein interactions","authors":"Vishal Kumar Sahu ,&nbsp;Subhayan Sur ,&nbsp;Sanjana Agarwal ,&nbsp;Harishkumar Madhyastha ,&nbsp;Amit Ranjan ,&nbsp;Soumya Basu","doi":"10.1016/j.bpc.2025.107421","DOIUrl":"10.1016/j.bpc.2025.107421","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) belong to a short endogenous class of non-coding RNAs which have been well studied for their crucial role in regulating cellular homeostasis. Their role in the modulation of diverse biological pathways by interacting with cellular proteins, genes, and RNAs through cellular communication projects them as promising biomarkers and therapeutic targets. However, studying miRNA-protein interactions specific to disease in the extracellular or cell-free environments for drug discovery and biomarker establishment is challenging and resource-intensive due to their structural complexities. In this study, we present a computational approach to uncover patterns in miRNA-protein interactions in the cell-free milieu leveraging existing experimental data. We employed motif discovery tools, extracted motifs from 3D protein and miRNA structures, and conducted molecular docking analyses to identify and rank these interactions. This <em>in silico</em>-based approach reveals 204 and 2874 consensus sequences in miRNAs and proteins, respectively, within the interactome highlighting their potential roles in the cardiovascular diseases, neurological disorders, and cancers. The role of proteins like METTL3 and AGO2 and miRNAs such as hsa-miR-484 and hsa-miR-30 families, hsa-mir-126-5p has been discussed contextually. Additionally, we discovered simple sequence repeats in the consensus patterns having unexplored functional roles. Our observations provide new insights into the extracellular miRNA-protein interactions that may drive disease initiation and progression offering potential avenues for overcoming challenges like therapy relapse and drug inefficacy. The results of our analysis are available in the miRPin database (<span><span>https://www.mirna.in/miRPin</span><svg><path></path></svg></span>).</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107421"},"PeriodicalIF":3.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143550518","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 functional dynamics of glyceraldehyde-3-phosphate dehydrogenase upon ligand binding at the putative allosteric binding sites","authors":"Merve Yuce,&nbsp;Ozge Kurkcuoglu","doi":"10.1016/j.bpc.2025.107420","DOIUrl":"10.1016/j.bpc.2025.107420","url":null,"abstract":"<div><div>The glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an attractive target to combat infection-related diseases as antibiotic resistance poses a global threat. Here, we investigated the functional dynamics of methicillin-resistant <em>S. aureus</em> GAPDH (<em>Sa</em>GAPDH) in apo-form and with ligands bound at two distinct potential allosteric binding sites in its tunnel-like region. AutoDock Vina was used for flexible docking with a library of 2447 FDA-approved drugs. After the interaction analysis and chemical fragment clustering, 5 compounds mutual to both sites were selected and subjected to independent 3 × 500 ns-long molecular dynamics (MD) simulations coupled with Molecular Mechanics Generalized Born Surface Area calculations to estimate their binding free energies. The ligand-protein dynamics pointed to either an increase or a decrease in the solvent accessibility of the co-factor NAD⁺ binding site as compared to apo-dynamics without an apparent change in residue fluctuations. Furthermore, dihedral angles of the co-factor binding site residues, particularly R12 and N316 changed upon ligand binding to the tunnel-like region. Residue network models based on the MD trajectories for each system revealed potential allosteric communication pathways linking putative allosteric binding sites to the co-factor binding sites. Favorable interactions between the ligands and the previously suggested hub residues T49-R53, E204 (S-loop) and/or Y180 seemed to affect the solvent accessibility of the binding sites that can either facilitate or prevent NAD⁺ binding. Dynamic coupling of NAD⁺ binding sites through correlated residue fluctuations was consistent in all investigated systems, revealing how cooperativity between the functional sites can be maintained by <em>Sa</em>GAPDH. All findings suggested hit compounds and the putative allosteric binding sites to change the NAD⁺ binding site dynamics that should be further evaluated by in vitro studies to assess their antibacterial activities.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"320 ","pages":"Article 107420"},"PeriodicalIF":3.3,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509081","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":"Transmembrane clustering of short amyloid peptide fragments: A coarse grained molecular dynamics study","authors":"Aleksandra Drajkowska,&nbsp;Andrzej Molski","doi":"10.1016/j.bpc.2025.107418","DOIUrl":"10.1016/j.bpc.2025.107418","url":null,"abstract":"<div><div>Toxicity of amyloid peptides has been linked to peptide aggregation and interactions with lipid bilayers. In this work we use coarse-grained molecular dynamics simulations to study aggregation and transmembrane clustering of short amyloid peptide fragments, A<em>β</em>(25–35) and A<em>β</em>(29–42), in the presence of dipalmitoylphosphatidylcholine (DPPC) and palmitoylolyoilphosphatidylcholine (POPC) bilayers. First, we explored peptide aggregation starting from free monomers placed at the interface of preformed lipid membranes. At low peptide concentrations, no transmembrane clusters were formed in DPPC or POPC membranes. At high peptide concentration, the longer fragment, A<em>β</em>(29–42), showed strong peptide-peptide interactions that led to spontaneous formation of transmembrane clusters in POPC and DPPC. However, the shorter fragment, A<em>β</em>(25–35), did not form transmembrane clusters within the simulation time in either bilayer. To overcome the free-energy barriers to transmembrane clustering, we changed the simulation protocol and started simulations from random mixtures of peptides, lipids, and solvent. Using this system self-assembly approach, we found that both A<em>β</em>(25–35) and A<em>β</em>(29–42) can form stable transmembrane clusters in DPPC and POPC bilayers. Our study suggests that the cooperative effects induced by a localized increase in peptide density may be a mechanism of membrane disruption by short amyloid peptide fragments.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"320 ","pages":"Article 107418"},"PeriodicalIF":3.3,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509079","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":"Decoding SARS-CoV-2 variants: Mutations, viral stability, and breakthroughs in vaccines and therapies","authors":"Zainularifeen Abduljaleel","doi":"10.1016/j.bpc.2025.107413","DOIUrl":"10.1016/j.bpc.2025.107413","url":null,"abstract":"<div><div>This study investigates the infectivity of SARS-CoV-2 and its immune evasion mechanisms, particularly through mutations in the spike protein that enable the virus to escape host immune responses. As global vaccination efforts continue, understanding viral evolution and immune evasion strategies remains critical. This analysis focuses on fourteen key mutations (Arg346Lys, Lys417Asp, Leu452Glu, Leu452Arg, Phe456Leu, Ser477Asp, Thr478Lys, Glu484Ala, Glu484Lys, Glu484Gln, Gln493Arg, Gly496Ser, Glu498Arg, and His655Y) within the receptor-binding domain (RBD) of the spike protein. The results reveal consistent patterns of immune escape across various SARS-CoV-2 variants, with specific mutations influencing protein stability, binding affinity to the hACE2 receptor, and antibody recognition. These findings demonstrate how single-point mutations can destabilize the spike protein and reduce the efficacy of the immune response. By correlating expression levels and thermodynamic stability with immune evasion, this study provides valuable insights into the functional characteristics of the spike protein. The findings contribute to the understanding of immune escape variants and identify potential targets for enhancing vaccine efficacy and developing therapeutic approaches in response to the evolving SARS-CoV-2 landscape.</div></div><div><h3>Short summary</h3><div>The study investigates the infectivity of SARS-CoV-2 and its implications for immune evasion. It focuses on fourteen key mutations within the spike protein's Receptor-Binding Domain (S-RBD) and reveals consistent patterns associated with immune escape in various SARS-CoV-2 variants. The research highlights the influence of factors such as protein fold stability, hACE2 binding, and antibody evasion on spike protein evolution. Single-point immune escape variants alter virus stability, impacting antibody response success. The study provides valuable insights into immune escape variants and suggests avenues for enhancing vaccine efficacy. It also opens the way for novel therapeutic approaches in the context of SARS-CoV-2 variants.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"320 ","pages":"Article 107413"},"PeriodicalIF":3.3,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471708","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":"Photophysical and structural aspects of poly-L-tryptophan: π−π stacking interaction with an excited state intermolecular proton transfer probe 3-Hydroxynaphthoic acid revealed by experiments and molecular simulation","authors":"Priyanka Mukherjee ,&nbsp;Titas Kumar Mukhopadhyay ,&nbsp;Sagarika Sanyal ,&nbsp;Kaushik Kundu ,&nbsp;Rina Ghosh ,&nbsp;Sudeshna Shyam Chowdhury ,&nbsp;Sanjib Ghosh","doi":"10.1016/j.bpc.2025.107416","DOIUrl":"10.1016/j.bpc.2025.107416","url":null,"abstract":"<div><div>In biophysical studies involving proteins, the involvement of the intrinsic fluorophore Tryptophan and its energy transfer/binding interactions are already well-investigated areas. Theoretical studies have also been well corroborated with experimental findings. However, in polymeric Tryptophans (specifically homopolymers), several queries still need to be addressed – their structure, the environment of each Tryptophan and the binding preferences of the latter. This necessitated some detailed investigations on the poly-L-Tryptophan system both from experimental and theoretical standpoints. In this work, we have carried out both steady-state and time-resolved fluorescence studies along with low-temperature phosphorescence (LTP) of poly-L-tryptophan, and the nature of the emitting Tryptophan (Trp) residue in the latter has been characterized based on a comparison with the emission features of the parent monomer. The very large red-shift of the (0–0) band of phosphorescence in poly-L-Tryptophan has been explained through triplet-triplet energy transfer along with the structure of the latter which has been developed by theoretical modelling. The nature of the environment of the emitting Trp residue in poly-L-Trp has been compared with several multi-Tryptophan proteins where different Trp residues exhibit optically resolved (0–0) bands. The interaction of the excited state proton transfer (ESIPT) probe 3-hydroxynaphthoic acid (3-HNA) with poly-L-Trp has also been investigated in detail using fluorescence, LTP, and classical molecular dynamics simulations.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"320 ","pages":"Article 107416"},"PeriodicalIF":3.3,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143474788","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":"Copper(II) enhances the antibacterial activity of nitroxoline against MRSA by promoting aerobic glycolysis","authors":"Xiaoyong Huang ,&nbsp;Huiting Yang ,&nbsp;Xiaomin Ren ,&nbsp;Qianqian Li ,&nbsp;Jianzhong Wang ,&nbsp;Jia Cheng ,&nbsp;Zilong Sun","doi":"10.1016/j.bpc.2025.107419","DOIUrl":"10.1016/j.bpc.2025.107419","url":null,"abstract":"<div><div>Nitroxoline (NIT) is an FDA-approved antibiotic with numerous pharmacological properties. However, the intricate connections between its metal-chelating ability and antimicrobial efficacy remain incompletely understood. The specific interactions of NIT with different metal ions were measured via UV–vis absorption spectroscopy. Here, we found that NIT can bind to various metal ions, including Cu²⁺, Fe²⁺, Zn²⁺ and Mn²⁺. However, the antimicrobial activity of NIT against methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) was significantly enhanced by the inclusion of Cu²⁺ as determined by a minimal inhibitory concentration (MIC) assay in Mueller-Hinton broth. The enhanced antibacterial effect was not influenced by the availability of oxygen. Mechanistically, Cu²⁺ promoted bacterial proliferation, increased the bacterial transmembrane electrical potential, and increased intracellular acidification. In addition, Cu²⁺ rewired bacterial metabolism, promoting the uptake of glucose with a lower level of ATP production. Pharmacological upregulation of glycolysis by VLX600 could potentiate the susceptibility of MRSA to NIT. Moreover, Cu²⁺ also significantly increased the survival rate of acutely infected larvae. These collective results underscore that the enhanced antibacterial efficacy of NIT by Cu²⁺ intricately involves aerobic glycolysis in MRSA.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"320 ","pages":"Article 107419"},"PeriodicalIF":3.3,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143465097","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":"Systematic molecular profiling of non-native N6-substitution effects on m6A binding to the YTH domains of human RNA m6A readers in diabetes","authors":"Yuting Li ,&nbsp;Peng Tan ,&nbsp;Qianpan Liu ,&nbsp;Huaixin Sun ,&nbsp;Yue Wang ,&nbsp;Siyi Chen ,&nbsp;Weixin Kong ,&nbsp;Xiaoyi Sun ,&nbsp;Xiang Shao","doi":"10.1016/j.bpc.2025.107417","DOIUrl":"10.1016/j.bpc.2025.107417","url":null,"abstract":"<div><div>The RNA <em>N</em>⁶-adenosine methylation, resulting in <em>N</em>⁶-methyl adenosine (m6A), is one of the most important post-transcriptional modification events in the eukaryotic transcriptome, which is dynamically regulated by methyltransferases (writers), recognition proteins (readers) and demethylases (erasers). Human has five m6A readers namely YTHDC1, YTHDC2, YTHDF1, YTHDF2 and YTHDF3 that specifically recognize and bind to the methylated m6A residue of RNA through their YT521-B homology (YTH) domains, which have been involved in the pathogenesis of diabetes mellitus and its diverse complications such as diabetic nephropathy. Instead of the native <em>N</em>⁶-methylation, we herein attempted to explore the molecular effect of various non-native <em>N</em>⁶-substitutions on adenosine (A) binding behavior to YTH domains. A systematic interaction profile of 40 reported <em>N</em>⁶-substituted adenosine (x6A) mononucleotides with 5 human reader YTH domains was created computationally. Heuristic clustering of the profile divided these YTH domains and these x6A mononucleotides into two subfamilies and three classes, respectively; they represent distinct intrinsic interaction modes between the domains and mononucleotides. Statistical survey unraveled that the volume (<em>V</em>_g) and hydrophobicity (<em>H</em>_g) of <em>N</em>⁶-substituted chemical groups exhibit linear and nonlinear correlations with the binding energy (Δ<em>G</em>_ttl) of x6A mononucleotides to YTH domains, respectively; <em>N</em>⁶-substitutions with moderate size and weak polarity are favorable for the x6A binding. From the profile the <em>N</em>⁶-bromomethyl adenosine (brm6A) was identified as a potent binder of YTHDF2 YTH domain; its affinity was improved significantly by 77.2-fold from A and considerably by 19.5-fold from m6A. Structural modeling observed that the <em>N</em>⁶-bromomethyl group of brm6A is tightly packed against an aromatic cage defined by the Trp432-Trp486-Trp491 triad of YTHDF2 YTH domain. Electron-correlation analysis revealed that the bromine atom can form geometrically and energetically satisfactory halogen-π interactions with the aromatic cage, thus conferring considerable affinity and specificity to the domain–brm6A interaction.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"320 ","pages":"Article 107417"},"PeriodicalIF":3.3,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143465059","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}