Biophysical chemistry最新文献

{"title":"Genetically encoded lysine photocage for spatiotemporal control of TDP-43 nuclear import","authors":"Jared A. Shadish,&nbsp;Jennifer C. Lee","doi":"10.1016/j.bpc.2024.107191","DOIUrl":"10.1016/j.bpc.2024.107191","url":null,"abstract":"<div><p>Intracellular aggregation of transactive response DNA binding protein of 43 kDa (TDP-43) is a hallmark of neurodegenerative diseases such as amyotrophic lateral sclerosis. While primarily a nuclear protein, TDP-43 translocates to the cytosol during cellular stress. Consequences of cytosolic accumulation of TDP-43 is difficult to evaluate in the absence of exogenous toxins. Here, we demonstrate spatiotemporal control over the nuclear import of TDP-43 by installing a photocage (<em>ortho</em>-nitrobenzyl ester) on a single lysine residue (K84) through amber codon suppression in HEK293T cells. Translocation of this cytosolic construct is photo-triggerable in a dose-dependent manner with 355 nm light. Interestingly, both fluid- and solid-like puncta were found based on fluorescence recovery after photobleaching experiments, similar to what is expected of stress granules and intracellular aggregates, respectively. This optogenetic method is advantageous as it is minimally perturbative and broadly applicable to other studies of protein translocation between cellular compartments.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107191"},"PeriodicalIF":3.8,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0301462224000206/pdfft?md5=c8b1dbe7e719ee52f29b565085b6a3ae&pid=1-s2.0-S0301462224000206-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139633004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Free-energy landscapes of transmembrane homodimers by bias-exchange adaptively biased molecular dynamics","authors":"Shingo Ito ,&nbsp;Yuji Sugita","doi":"10.1016/j.bpc.2024.107190","DOIUrl":"10.1016/j.bpc.2024.107190","url":null,"abstract":"<div><p><span><span><span>Membrane proteins play essential roles in various biological functions within the cell. One of the most common functional regulations involves the dimerization of two single-pass transmembrane (TM) helices. </span>Glycophorin A (GpA) and </span>amyloid precursor protein (APP) form TM </span>homodimers<span> in the membrane, which have been investigated both experimentally and computationally. The homodimer structures are well characterized using only four collective variables (CVs) when each TM helix is stable. The CVs are the interhelical distance, the crossing angle, and the Crick angles for two TM helices. However, conformational sampling with multi-dimensional replica-exchange umbrella sampling<span><span> (REUS) requires too many replicas to sample all the CVs for exploring the conformational landscapes. Here, we show that the bias-exchange adaptively biased molecular dynamics<span> (BE-ABMD) with the four CVs effectively explores the free-energy landscapes of the TM helix dimers of GpA, wild-type APP and its mutants in the IMM1 implicit membrane. Compared to the original ABMD, the bias-exchange algorithm in BE-ABMD can provide a more rapidly converged conformational landscape. The BE-ABMD simulations could also reveal TM packing interfaces of the membrane proteins and the dependence of the free-energy landscapes on the membrane thickness. This approach is valuable for numerous other applications, including those involving explicit solvent and a </span></span>lipid bilayer<span> in all-atom force fields or Martini coarse-grained models, and enhances our understanding of protein-protein interactions in biological membranes.</span></span></span></p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107190"},"PeriodicalIF":3.8,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139633088","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":"Islet amyloid polypeptide tagged with green fluorescent protein localises to mitochondria and forms filamentous aggregates in Caenorhabditis elegans","authors":"Mehmet Akdag,&nbsp;Vera van Schijndel,&nbsp;Tessa Sinnige","doi":"10.1016/j.bpc.2024.107180","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107180","url":null,"abstract":"<div><p>Type 2 diabetes (T2D) is the most common form of diabetes and represents a growing health concern. A characteristic feature of T2D is the aggregation of islet amyloid polypeptide (IAPP), which is thought to be associated with the death of pancreatic β-cells. Inhibiting IAPP aggregation is a promising therapeutic avenue to treat T2D, but the mechanisms of aggregation and toxicity are not yet fully understood. <em>Caenorhabditis elegans</em> is a well-characterised multicellular model organism that has been extensively used to study protein aggregation diseases. In this study, we aimed to develop a simple <em>in vivo</em> model to investigate IAPP aggregation and toxicity based on expression in the <em>C. elegans</em> body wall muscle cells. We show that IAPP tagged with green fluorescent protein (GFP) localises to mitochondria not only in muscle cells but also when expressed in the intestine, in line with previous observations in mouse and human pancreatic β-cells. The IAPP-GFP fusion protein forms solid aggregates, which have a filamentous appearance as seen by electron microscopy. However, the animals expressing IAPP-GFP in the body wall muscle cells do not display a strong motility phenotype, suggesting that the IAPP-GFP aggregates are not considerably toxic. Nevertheless, the mitochondrial localisation and aggregate formation may be useful read-outs to screen for IAPP-solubilizing compounds as a therapeutic strategy for T2D.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107180"},"PeriodicalIF":3.8,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0301462224000097/pdfft?md5=01b619bad69be902ca86d372a971abd5&pid=1-s2.0-S0301462224000097-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139493632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the synergistic effects of amoxicillin and methylene blue on unsaturated lipid structures: A study of Langmuir monolayers and giant unilamellar vesicles","authors":"Mateus D. Maximino,&nbsp;Henry S. Kavazoi,&nbsp;Victoria M. Katata,&nbsp;Priscila Alessio","doi":"10.1016/j.bpc.2024.107181","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107181","url":null,"abstract":"<div><p><span><span>The potentially toxic effects of emerging pollutant mixtures often deviate from the individual compound effects, presenting additive, synergistic, or agonistic interactions. This study delves into the complex world of emerging pollutants' mixtures, with a particular focus on their potential impact on unsaturated lipid<span><span><span> DOPC (1,2-dioleoyl-sn-glycerol-3-phosphocholine) structured as both monolayers and bilayers, which are valuable tools for mimicking cell membranes. Specifically, we examine the effects of two common types of pollutants: antibiotics (amoxicillin) and dyes (methylene blue). Utilizing </span>Langmuir monolayers, our research reveals a synergistic effect within the pollutant mixture, as evidenced by pressure-area isotherms and polarization-modulated </span>infrared reflection absorption spectroscopy. We identify the specific chemical interactions contributing to this synergistic effect. Furthermore, through contrast phase </span></span>microscopy<span> experiments on giant unilamellar vesicles (bilayer system), we find that the individual pollutants and the mixture exhibit similar molecular effects on the bilayer</span></span><strong>,</strong> revealing that the molecular size is a key factor in the bilayer-mixture of pollutant interaction. This highlights the importance of considering molecular size in the interactions with bilayer systems. In summary, our research dissects the critical factors of chemical interactions and molecular size concerning the effects of pollutants on DOPC, serving as simplified models of cell membranes. This study underscores the significance of comprehending the molecular effects of emerging pollutants on human health and the development of models for exploring their intricate interactions with cell membranes.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107181"},"PeriodicalIF":3.8,"publicationDate":"2024-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139480252","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":"Insights into the structure-activity relationship of pyrimidine-sulfonamide analogues for targeting BRAF V600E protein","authors":"Tarapong Srisongkram,&nbsp;Dheerapat Tookkane","doi":"10.1016/j.bpc.2024.107179","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107179","url":null,"abstract":"<div><p><span>B-rapidly accelerated fibrosarcoma (BRAF) V600E plays a crucial role in the progression of cutaneous melanoma. Core structures of BRAF V600E inhibitors are based on pyrimidine-sulfonamide scaffolds. Exploring the QSAR<span> of these structures can improve our understanding of BRAF V600E inhibitor drug design. This study utilized machine learning-based QSAR to elucidate chemical substructures of pyrimidine-sulfonamide analogues that correlated to the BRAF V600E inhibitory activity. The findings indicate that the support vector regression<span> (SVR) combined with 15 fingerprints achieved the highest statistical performances in terms of goodness-of-fit, robustness, and predictability. Nine key fingerprints from pyrimidine-sulfonamide analogues were identified to exert the BRAF V600E inhibitory activity. These key fingerprints were validated using network-based activity cliff landscape and molecular docking. Together, the developed algorithm can serve as a screening tool for designing BRAF V600E inhibitors. To further utilize this model, we deployed our developed algorithm at </span></span></span><span>https://qsarlabs.com/#braf</span><svg><path></path></svg>.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107179"},"PeriodicalIF":3.8,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139487034","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":"Wine tannins and their aggregation/release with lipids and proteins: Review and perspectives for neurodegenerative diseases","authors":"Erick J. Dufourc","doi":"10.1016/j.bpc.2024.107178","DOIUrl":"10.1016/j.bpc.2024.107178","url":null,"abstract":"<div><p><span>Tannins are amphiphilic molecules, often polymeric, which can be generally described as a core containing hydrophobic </span>aromatic rings<span><span> surrounded by hydroxyl groups. They have been known for millennia and are part of human culture. They are ubiquitous in nature and are best known in the context of wine and tea tasting and food cultures. However, they are also very useful for human health, as they are powerful </span>antioxidants<span><span> capable of combating the constant aggressions of everyday life. However, their mode of action is only just beginning to be understood. This review, using physicochemical concepts, attempts to summarize current knowledge and present an integrated view of the complex relationship between tannins, proteins and lipids, in the context of wine drinking while eating. There are many </span>thermodynamic equilibria<span> governing the interactions between tannins, saliva proteins, lipid droplets<span><span> in food, membranes and the taste receptors embedded in them. Taste sensations can be explained using these multiple equilibria: for example, astringency (dry mouth) can be explained by the strong binding of tannin </span>micelles<span> to the proline-rich proteins of saliva, suppressing their lubricating action on the palate. In the presence of lipid droplets in food, the equilibrium is shifted towards tannin-lipid complexes, a situation that reduces the astringency perceived when consuming a tannic wine with fatty foods, the so-called “camembert effect”. Tannins bind preferentially to taste receptors located in mouth membranes, but can also fluidify lipids in the non-keratinized mucous membranes of the mouth, which can impair the functioning of taste receptors there. Cholesterol, present in large quantities in keratinized mucous membranes, stiffens them and thus prevents tannins from disrupting the conduction of information through other taste receptors. As tannins assemble and disassemble depending on whether they are in contact with proteins, lipids or taste receptors, a perspective on their potential use in the context of neurodegenerative diseases where fibrillation is a key phenomenon will also be discussed.</span></span></span></span></span></p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107178"},"PeriodicalIF":3.8,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139566615","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":"Force-induced unzipping of DNA in the presence of solvent molecules","authors":"Neha Mathur,&nbsp;Amar Singh ,&nbsp;Navin Singh","doi":"10.1016/j.bpc.2024.107175","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107175","url":null,"abstract":"<div><p>The melting of double-stranded DNA<span><span> (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced </span>denaturation<span> of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair<span> close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.</span></span></span></p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107175"},"PeriodicalIF":3.8,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139503749","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":"How the immune mousetrap works: Structural evidence for the immunomodulatory action of a peptide from influenza NS1 protein","authors":"Yana Zabrodskaya ,&nbsp;Vladimir Tsvetkov ,&nbsp;Anna-Polina Shurygina ,&nbsp;Kirill Vasyliev ,&nbsp;Aram Shaldzhyan ,&nbsp;Andrey Gorshkov ,&nbsp;Alexander Kuklin ,&nbsp;Natalya Fedorova ,&nbsp;Vladimir Egorov","doi":"10.1016/j.bpc.2024.107176","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107176","url":null,"abstract":"<div><p><span><span><span><span>One of the critical stages of the T-cell immune response is the dimerization of the intramembrane domains of T-cell receptors (TCR). Structural similarities between the immunosuppressive domains of </span>viral proteins and the </span>transmembrane domains<span> of TCR have led several authors to hypothesize the mechanism of immune response suppression by highly pathogenic viruses: viral proteins embed themselves in the membrane and act on the intramembrane domain of the TCRalpha subunit, hindering its functional oligomerization. It has also been suggested that this mechanism is used by </span></span>influenza A virus<span><span> in NS1-mediated immunosuppression. We have shown that the peptide corresponding to the primary structure of the potential immunosuppressive domain of NS1 protein (G51) can reduce concanavalin A-induced proliferation of </span>PBMC cells, as well as </span></span><em>in vitro</em><span>, G51 can affect the oligomerization of the core peptide corresponding to the intramembrane domain of TCR, using AFM and small-angle neutron scattering.</span></p><p>The results obtained using <em>in cellulo</em> and <em>in vitro</em><span> model systems suggest the presence of functional interaction between the NS1 fragment and the intramembrane domain of the TCR alpha subunit. We have proposed a possible scheme for such interaction obtained by computer modeling.</span></p><p>This suggests the existence of another NS1-mediated mechanism of immunosuppression in influenza.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107176"},"PeriodicalIF":3.8,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139434416","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":"The growth of microbial cultures complies with the laws of thermodynamics","authors":"Alberto Schiraldi","doi":"10.1016/j.bpc.2024.107177","DOIUrl":"10.1016/j.bpc.2024.107177","url":null,"abstract":"<div><p><span>The paper is the translation of the previously proposed growth model in a thermodynamic balance of the Gibbs free energy of the system (medium + microbes), based on a simple scheme of the cell duplication. In each duplication step, the cells garner a small extra Gibbs energy from the surrounding medium that loses also some energy through an exothermic effect. It turns out that the each duplication step implies an increase of the entropy of the system, but a decrease of the entropy of the involved cells. The overall number of duplication steps therefore determines the energy balance of the whole growth process. The growth model implies a relationship that links this number with the maximum specific growth rate and the no-growth latency that precedes the growth onset, namely, two parameters that reflect the biological efficiency of the cells. For this reason, the overall number of duplication steps, determined according to this model, seems the best proxy of the fitness of the microbial culture. In a Long Term Evolution Experiment (LTEE), the increasing fitness would therefore correspond to larger growth extent and specific rate, as well as to shorter pre-growth latency. This suggests that the gain of Gibbs free energy accumulated through the LTEE several-thousand generations leads to a faster attainment of the eventual steady state of the growth and a faster increase of the entropy of the system. If applied to a continuous LTEE carried out with a </span>chemostat, this trend should reveal that the evolution of the culture (medium + cells) is an irreversible process.</p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"307 ","pages":"Article 107177"},"PeriodicalIF":3.8,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139454466","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":"The influence of zwitterionic and anionic phospholipids on protein aggregation","authors":"Abid Ali ,&nbsp;Tianyi Dou ,&nbsp;Aidan P. Holman ,&nbsp;Andrew Hung ,&nbsp;Luke Osborne ,&nbsp;Davis Pickett ,&nbsp;Axell Rodriguez ,&nbsp;Kiryl Zhaliazka ,&nbsp;Dmitry Kurouski","doi":"10.1016/j.bpc.2024.107174","DOIUrl":"https://doi.org/10.1016/j.bpc.2024.107174","url":null,"abstract":"<div><p><span><span><span>The progressive aggregation of misfolded proteins is the underlying molecular cause of numerous pathologies including Parkinson's disease and injection and transthyretin </span>amyloidosis<span>. A growing body of evidence indicates that protein deposits detected in organs and tissues of patients diagnosed with such pathologies contain fragments of lipid membranes<span>. In vitro experiments also showed that lipid<span><span> membranes could strongly change the aggregation rate of amyloidogenic proteins, as well as alter the secondary structure and toxicity of </span>oligomers and fibrils formed in their presence. In this review, the effect of large </span></span></span></span>unilamellar vesicles (LUVs) composed of zwitterionic and anionic </span>phospholipids<span> on the aggregation rate of insulin, lysozyme, transthyretin (TTR) and α- synuclein (α-syn) will be discussed. The manuscript will also critically review the most recent findings on the lipid-induced changes in the secondary structure of protein oligomers and fibrils, as well as reveal the extent to which lipids could alter the toxicity of protein aggregates formed in their presence.</span></p></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"306 ","pages":"Article 107174"},"PeriodicalIF":3.8,"publicationDate":"2024-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139419156","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}