Biophysical chemistry最新文献

筛选
英文 中文
A detailed review of genetically encodable RFPs and far-RFPs and their applications in advanced super-resolution imaging techniques 综述了遗传可编码rfp和远编码rfp及其在先进超分辨率成像技术中的应用。
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-15 DOI: 10.1016/j.bpc.2025.107432
Jianshu Dong , Bilal Tayyab , Jiangyun Wang
{"title":"A detailed review of genetically encodable RFPs and far-RFPs and their applications in advanced super-resolution imaging techniques","authors":"Jianshu Dong ,&nbsp;Bilal Tayyab ,&nbsp;Jiangyun Wang","doi":"10.1016/j.bpc.2025.107432","DOIUrl":"10.1016/j.bpc.2025.107432","url":null,"abstract":"<div><div>The red fluorescent proteins (RFPs) and far-red fluorescent proteins (far-RFPs) that are encoded genetically can emit fluorescence within the spectral ranges of 580–680 nm when exposed to the light of appropriate wavelengths. Unlike many RFPs derived from coral species, numerous far-RFPs are optimized synthetic constructs engineered from different orange or red-emitting progenitors. Various categories have been established for the available RFPs and far-red fluorescent proteins based on their photo-chemical profile, fluorescence mechanism, and switching kinetics. Fluorescent probes (FPs) derived from these classes are extensively utilized for labelling and visualizing in vivo and in vitro specimens. Traditional optical microscopy methods generate diffraction-limited, indistinct images owing to the restricted resolution capability of light ranging from 200 to 300 nm. Since 2005, super-resolution microscopy has been a topic of great interest due to its ability to achieve imaging at spatial resolutions of less than 100 nm. The 2014 Nobel Prize in Chemistry was awarded to Eric Betzig, Stefan Hell, and William E. Moerner for their contributions to demonstrating the effectiveness of genetically encodable fluorescent proteins in visualizing biological systems through super-resolution fluorescence microscopy. This review provides a concise overview of RFPs and far-RFPs, including the involvement of surrounding residues in chromophore intactness, stability, autocatalytic maturation and switching kinetics. All the chemical pathways proposed for photoactivation, photoconversion and photoswitching mechanisms are concisely reviewed. Subsequently, a comprehensive summary was provided regarding the various types of super-resolution techniques that are commonly employed, elucidating their underlying principles of operation, as well as the potential future applications of RFPs/far-RFPs in the field of biological imaging.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107432"},"PeriodicalIF":3.3,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Interaction of native and aggregated albumin with DMPC bilayers 天然白蛋白和聚集白蛋白与DMPC双层的相互作用
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-14 DOI: 10.1016/j.bpc.2025.107431
Brigitte Magdalena Merino , Rosa Bartucci , Rita Guzzi
{"title":"Interaction of native and aggregated albumin with DMPC bilayers","authors":"Brigitte Magdalena Merino ,&nbsp;Rosa Bartucci ,&nbsp;Rita Guzzi","doi":"10.1016/j.bpc.2025.107431","DOIUrl":"10.1016/j.bpc.2025.107431","url":null,"abstract":"<div><div>The study of protein-lipid interaction offers interesting insights into the mutual alterations determined in the formation of the supramolecular complex. It gains even more interest, not only in basic research but also in biomedical and biomaterial applications, when protein aggregation and fibril formation are involved. In this study, the reciprocal influence of human serum albumin (HSA), in both the native and the thermally aggregated state, and dimyristoylphosphatidylcholine (DMPC) bilayers is investigated by combining UV–Vis scattering, attenuated total reflection Fourier transform infrared (ATR-FTIR), and spin-label electron paramagnetic resonance (EPR) spectroscopies. Temperature-dependent optical density at fixed wavelength reveals the pre- and the main phase transitions in DMPC bilayers as well as the onset of protein aggregation at T<sub>agg</sub> ≈ 70 °C. In native protein/lipid complexes, the protein adsorption on the membrane surfaces suppresses the pre-transition and downshifts the temperature of the main phase transitions of DMPC, whereas the presence of DMPC increases T<sub>agg</sub> without affecting the thermal profile. Kinetics experiments reveal that lipid bilayers reduce the thermally-induced aggregation of the protein. ATR-FTIR data indicate that albumin weakens the hydrogen bonding network at the carbonyl groups of the membrane. Conversely, lipid bilayers in any physical state do not alter the structural features of both native and aggregated HSA. In protein/lipid complexes, spin-label EPR of the lipid component reveals that the proteins reduce the packing density of the first chain segments and stabilize the fluid state, the effect being more evident for the native protein.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107431"},"PeriodicalIF":3.3,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Decoding the interaction of an imidazo-pyrimidine derivative with serum proteins: Spectroscopic, computational and structure-activity relationship analysis 解码咪唑嘧啶衍生物与血清蛋白的相互作用:光谱,计算和构效关系分析
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-13 DOI: 10.1016/j.bpc.2025.107435
Bishwayan Chakraborty , Asmit Santra , Debangana Tah , Koushik Goswami , Anupam Jana , Agnishwar Girigoswami , Debosreeta Bose
{"title":"Decoding the interaction of an imidazo-pyrimidine derivative with serum proteins: Spectroscopic, computational and structure-activity relationship analysis","authors":"Bishwayan Chakraborty ,&nbsp;Asmit Santra ,&nbsp;Debangana Tah ,&nbsp;Koushik Goswami ,&nbsp;Anupam Jana ,&nbsp;Agnishwar Girigoswami ,&nbsp;Debosreeta Bose","doi":"10.1016/j.bpc.2025.107435","DOIUrl":"10.1016/j.bpc.2025.107435","url":null,"abstract":"<div><div>In the present article, we have tried to theoretically analyze the structure-function relationship of a novel imidazo pyrimidine derivative, IPD, and decipher its interactions with two serum proteins, BSA and HSA, spectroscopically. IPD is almost non-fluorescent in a polar environment, but its fluorescence enhancement is significant in non-polar mediums like proteins. Steady-state fluorometric investigations indicate a strong binding interaction between the probe, IPD, and serum proteins, with HSA being more strongly bound to IPD. This stronger binding affinity of the IPD–HSA complex than compared to the IPD–BSA complex was corroborated through denaturation and quenching studies, too. In silico molecular docking interactions also reveal a similar stronger binding affinity in HSA than BSA. This is attributed to the probe residing in a more hydrophobic region in HSA; thus, the π and alkyl interactions are stronger in HSA than in BSA.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"322 ","pages":"Article 107435"},"PeriodicalIF":3.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143636966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Equilibrium solubility, solvent effect, solvation and thermodynamic modeling of 1, 3-dinitropyrazole in solutions of methyl alcohol /ethyl alcohol + water 1,3 -二硝基吡唑在甲醇/乙醇+水溶液中的平衡溶解度、溶剂效应、溶剂化和热力学模型
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-10 DOI: 10.1016/j.bpc.2025.107430
Adel Noubigh , Manef Abderrabba
{"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<sup>−4</sup>, 0.492 × 10<sup>−4</sup> 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}
引用次数: 0
Autoencoder-based drug-virus association prediction with reliable negative sample selection: A case study with COVID-19 基于自编码器的药物-病毒关联预测与可靠的阴性样本选择:COVID-19病例研究
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-10 DOI: 10.1016/j.bpc.2025.107434
A.S. Aruna , K.R. Remesh Babu , K. Deepthi
{"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}
引用次数: 0
Relevance of ceramide 1-phosphate domain formation in activation of cytosolic phospholipase A2 神经酰胺1-磷酸结构域形成与胞质磷脂酶A2激活的相关性
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-09 DOI: 10.1016/j.bpc.2025.107433
Tomokazu Yasuda , Daiki Ueura , Madoka Nakagomi , Shinya Hanashima , Michio Murata
{"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 A<sub>2</sub>α (cPLA<sub>2</sub>α). Previous findings revealed that modification of the specific hydrophobic moiety decreases the affinity with cPLA<sub>2</sub>α. However, the possible biological role of the temporal C1P-enriched domains formed in biomembranes for the molecular recognition of cPLA<sub>2</sub>α 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 cPLA<sub>2</sub>α 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 cPLA<sub>2</sub>α. Thus, we speculate that C1P clusters formed under certain membrane conditions are important in specific binding with cPLA<sub>2</sub>α by increasing the interaction between the C1P headgroup and basic residues of cPLA<sub>2</sub>α. 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}
引用次数: 0
Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions 揭示治疗潜力:洞察无细胞microrna -蛋白相互作用
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-03-03 DOI: 10.1016/j.bpc.2025.107421
Vishal Kumar Sahu , Subhayan Sur , Sanjana Agarwal , Harishkumar Madhyastha , Amit Ranjan , Soumya Basu
{"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}
引用次数: 0
Investigating the functional dynamics of glyceraldehyde-3-phosphate dehydrogenase upon ligand binding at the putative allosteric binding sites 在假定的变构结合位点研究配体结合时甘油醛-3-磷酸脱氢酶的功能动力学
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-02-21 DOI: 10.1016/j.bpc.2025.107420
Merve Yuce, Ozge Kurkcuoglu
{"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<sup>+</sup> 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<sup>+</sup> binding. Dynamic coupling of NAD<sup>+</sup> 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<sup>+</sup> 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}
引用次数: 0
Transmembrane clustering of short amyloid peptide fragments: A coarse grained molecular dynamics study 短淀粉样肽片段的跨膜聚类:粗粒度分子动力学研究
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-02-20 DOI: 10.1016/j.bpc.2025.107418
Aleksandra Drajkowska, Andrzej Molski
{"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}
引用次数: 0
Decoding SARS-CoV-2 variants: Mutations, viral stability, and breakthroughs in vaccines and therapies 解码 SARS-CoV-2 变体:变异、病毒稳定性以及疫苗和疗法方面的突破
IF 3.3 3区 生物学
Biophysical chemistry Pub Date : 2025-02-20 DOI: 10.1016/j.bpc.2025.107413
Zainularifeen Abduljaleel
{"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}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信