Faraday Discussions最新文献

{"title":"Effect of a scramblase activator upon lipid and probe scrambling and membrane domain formation in HEK 293T cells†","authors":"Shinako Kakuda and Erwin London","doi":"10.1039/D4FD00211C","DOIUrl":"10.1039/D4FD00211C","url":null,"abstract":"<p >Lipid asymmetry, a difference between the lipid composition of the inner and outer leaflets (monolayers) of a membrane, is a characteristic of mammalian plasma membranes. In artificial lipid vesicles, asymmetry can either suppress or induce the formation of coexisting ordered and disordered lipid domains depending on lipid composition. In mammalian plasma membrane preparations, loss of asymmetry induces the formation of ordered domains. In this report, we studied the effect of a scramblase activator, the ionophore BrA23187 (BrA) plus Ca<small>²⁺</small>, upon ordered domain (lipid raft) formation in human embryonic kidney 293T cells. Addition of BrA induced a decrease in FRET between the plasma membrane outer leaflet probe TMADPH, which partly associates with ordered domains, and ODRB, which localizes largely in liquid disordered domains. This is consistent with the formation of coexisting ordered and disordered domains in the plasma membrane. In addition, upon BrA addition, the plasma membrane outer leaflet probe Pro12A exhibited a decrease in the generalized polarization (GP) suggesting a decrease in outer leaflet membrane order, perhaps due to a decrease in outer leaflet cholesterol However, there are other explanations for these observations. To test if BrA induced scrambling of fluorescent membrane probes, which would complicate interpretation of the experiments described above, we measured the effect of BrA upon extractability of outer leaflet probes with MβCD (in most cases, MβCD was more effective for extraction than BSA). These experiments showed that at most a small fraction of probes migrate to the inner leaflet upon addition of BrA. Other experiments raise the possibility that BrA binding to membranes may directly influence ordered domain formation and properties or alter fluorescence by direct interactions with TMADPH, and thus not reflect changes in domain formation.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 26-44"},"PeriodicalIF":3.1,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Asymmetric membrane properties through a protein lens†","authors":"Joseph H. Lorent, Angela Cabrera-Jojoa, Kandice R. Levental, Ilya Levental and Edward Lyman","doi":"10.1039/D4FD00199K","DOIUrl":"10.1039/D4FD00199K","url":null,"abstract":"<p >Plasma membranes are asymmetric, with each monolayer presenting specific lipid compositions and biophysical properties. Transmembrane domains (TMDs) of single-pass transmembrane proteins (spTMPs) have adapted their physico-chemical properties to these asymmetric constraints. In this study, we analysed the structural features of such TMDs across the tree of life to obtain information about their interaction with asymmetric membrane bilayers and predict species-specific membrane properties. We observed that TMDs in the plasma membranes of all eukaryotic species possess asymmetries in lipid accessible surface area (ASA), hydrophobicity, aromaticity and charge. Bacteria deviate from this trend, with strong differences between bacterial clades. Notably, TMDs in the Golgi and the endoplasmic reticulum of eukaryotic species display inverted profiles for accessible surface area, hydrophobicity and aromaticity compared to their plasma-membrane counterparts. To determine how well TMD profiles reflect average membrane properties, we performed molecular dynamics simulations of a spTMP in an asymmetric lipid bilayer whose composition approximates the human plasma membrane. The simulated spTMP was chosen to represent the average TMD properties of the human proteome. We compared the electron density profiles of the simulated asymmetric membrane to the average TMD profiles derived from the human proteome and observed that phospholipid acyl-chain density overlapped very well with TMD hydrophobicity, and phosphate group density with TMD charge. The profiles of phospholipid unsaturation in the acyl chains overlapped well with the average location of TMD phenylalanines in the cytoplasmic leaflet, while there was additional accumulation of large hydrophobic and aromatic residues in the membrane midplane, which had low acyl-chain density. This study reveals the complementarity of membrane and TMD properties in asymmetric membranes, suggesting that the properties of TMDs can be used to make predictions about the properties of their solvating membranes.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 597-613"},"PeriodicalIF":3.1,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The influence of higher order geometric terms on the asymmetry and dynamics of membranes†","authors":"Jan Magnus Sischka, Ingo Nitschke and Axel Voigt","doi":"10.1039/D4FD00202D","DOIUrl":"10.1039/D4FD00202D","url":null,"abstract":"<p >We consider membranes as fluid deformable surfaces and allow for higher order geometric terms in the bending energy related to the Gaussian curvature squared and the mean curvature minus the spontaneous curvature to the fourth power. The evolution equations are derived and numerically solved using surface finite elements. The two higher order geometric terms have different effects. While the Gaussian curvature squared term has a tendency to stabilize tubes and enhance the evolution towards equilibrium shapes, thereby facilitating rapid shape changes, the mean curvature minus the spontaneous curvature to the fourth power destabilizes tubes and leads to qualitatively different equilibrium shapes but also enhances the evolution. This is demonstrated in axisymmetric settings and fully three-dimensional simulations. We therefore postulate that not only surface viscosity but also higher order geometric terms in the bending energy contribute to rapid shape changes which are relevant for morphological changes of cells.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 454-474"},"PeriodicalIF":3.1,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00202d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fabrication and characterization of phosphoinositide containing asymmetric vesicles in physiological salt","authors":"Trevor A. Paratore, Alonzo H. Ross and Arne Gericke","doi":"10.1039/D4FD00191E","DOIUrl":"10.1039/D4FD00191E","url":null,"abstract":"<p >Phosphoinositide (PIPs) lipids mediate a broad range of physiological functions by attracting proteins at specific time points to distinct cellular sites. Many of these processes are associated with the local accumulation of PIPs and PIP/protein signaling platform formation. Studies aimed at determining the physicochemical underpinnings of PIP domain formation have been limited to model systems that exhibited the same lipid composition in both bilayer leaflets. However, biological membranes are asymmetric, and it is desirable to develop an experimental approach that allows for the fabrication of lipid model systems with a non-symmetric lipid bilayer, <em>i.e.</em>, a membrane mimic that exhibits a PIP containing lipid mixture in one leaflet and a different lipid composition in the opposing leaflet. We adapted the previously introduced hemifusion method for the fabrication of asymmetric Giant Unilamellar Vesicles (aGUVs) for the fabrication of aGUVs with phosphatidylinositol-(4,5)-bisphosphate (PI(4,5)P<small>₂</small>) in a physiological ionic strength buffer solution. The general method involved the bivalent cation-initiated fusion of a symmetric GUV (sGUV) with solid-supported lipid bilayers, which leads to the exchange of the outer leaflet of the sGUV. We find that initiating the hemifusion with 6 mM Ca<small>²⁺</small> leads to a low yield and quality of the aGUVs. We attribute this to macroscopic Ca<small>²⁺</small>/PI(4,5)P<small>₂</small> domain formation of the solid support lipid bilayer (SLB), which leads to the interaction of the sGUVs with regions enriched in PI(4,5)P<small>₂</small> (domain) and other areas that are void of the PIP lipid. Using 6 mM Mg<small>²⁺</small> as the initiator instead led to an improvement in terms of yield and aGUV quality. The best results were obtained when using 1 mM Mg<small>²⁺</small>. We are introducing several data analysis approaches that allow for the identification of aGUVs that exhibit high quality in terms of the outer leaflet exchange and composition of the two aGUV leaflets.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 149-167"},"PeriodicalIF":3.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00191e?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Near-infrared responsive three-component supramolecular hydrogels of peptide, agarose and upconversion nanoparticles†","authors":"Ivo Rosenbusch, Dominik Mählmann and Bart Jan Ravoo","doi":"10.1039/D4FD00203B","DOIUrl":"10.1039/D4FD00203B","url":null,"abstract":"<p >Self-assembled, low molecular weight hydrogels are of particular interest for the development of responsive materials because they exhibit tunable viscoelasticity, high water content, and shear-thinning behavior, which make them suitable for various applications as biomimetic materials. Moreover, such hydrogels are quite easy to prepare. Here, a three-component gel is prepared by adding the peptide AAP-FGDS to an agarose polymer network. The photoresponsive peptide hydrogel exhibits excellent reversible properties. The photoisomerization of the peptide is enabled by lanthanide-doped upconversion nanoparticles (UCNP) added as a third component in the gel. UCNP can convert excitation in the near infrared (NIR) range into emission of higher energy through the process of upconversion. Irradiation with an NIR laser dissolves the self-assembled three-dimensional network structure of the peptide, resulting in a softer hydrogel. The three-component supramolecular gel can potentially be used for <em>in vivo</em> applications considering the fact that (unlike harmful UV light) NIR light can penetrate deeply into tissue.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 377-388"},"PeriodicalIF":3.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00203b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144109142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Membrane potential fluctuations and water asymmetry on plasma cell and model lipid membranes: origins, implications and properties","authors":"Zhi Li, Iwona Swiderska, Lena Dalifoski, Seonwoo Lee, Nelson Alonso Correa-Rojas, David Roesel, Maksim Eremchev, Mischa Flor, Orly B. Tarun, Arianna Marchioro and Sylvie Roke","doi":"10.1039/D4FD00197D","DOIUrl":"10.1039/D4FD00197D","url":null,"abstract":"<p >Membrane potential fluctuations have previously been detected using second harmonic (SH) water imaging on neuronal cells and model lipid bilayer membranes. We report that such fluctuations are also visible when membrane potential-sensitive fluorophores are used as contrast agents, and fluctuations are imaged on both free-standing lipid membranes (FLMs) and on the plasma membranes of neuroblastoma cells. We show that upon K<small>⁺</small> depolarization, non-uniform recovery responses occur across cells and within single cells. We discuss the origins and implications of such fluctuations, and investigate the molecular-level details of membrane potential distributions on FLMs and compare it to those on giant unilamellar vesicles (GUVs). SH water imaging shows that the hydrated part of lipid membranes is most likely composed of regions having a diffuse double layer, and other regions having an additional condensed double layer, with a high concentration of ions/ionic groups. In terms of transmembrane potential distributions, FLMs and GUVs show similar signatures, as expected from electrostatics. Comparing passive ion transport, FLMs and GUVs of identical composition behave differently, with GUVs being more permeable for proton transport (∼20×). This is likely caused by differences in the hydrophobic cores of the membranes, which create different energetic barriers for the proton transport.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 342-365"},"PeriodicalIF":3.1,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00197d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lipid–GPCR interactions in an asymmetric plasma membrane model†","authors":"Jingjing Ji and Edward Lyman","doi":"10.1039/D4FD00210E","DOIUrl":"10.1039/D4FD00210E","url":null,"abstract":"<p >We report simulations and analysis of the A<small>_2A</small> adenosine receptor in its fully active state, in two different membrane environments. The first is a model in which the lipids are distributed asymmetrically according to recent lipidomics, simulations, and biophysical measurements, which together establish the distribution of lipids and cholesterol between the two leaflets. The second is the symmetrized version, which captures the membrane state following loss of lipid asymmetry. By comparing lipid–protein interactions between these two cases we show that solvation by phosphatidyl serine (PS) is insensitive to the loss of asymmetry—an abundance of positively charged sidechains around the cytoplasmic side of the receptor enriches solvation by PS in both membrane states. Cholesterol interactions are sensitive to the loss of asymmetry, with the abundance of cholesterol in the exoplasmic leaflet driving long-lived cholesterol interactions in the asymmetric state. However, one cholesterol interaction site on helix 6 is observed in both cases, and was also observed in earlier work with different membrane models, supporting its identification as a <em>bona fide</em> cholesterol binding site.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"259 ","pages":" 545-558"},"PeriodicalIF":3.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12061045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the structure of protein-based hydrogels by overcoming cryo-SEM sample preparation challenges†","authors":"Dimitra Katrantzi, Stuart Micklethwaite, Nicole Hondow, Andy Brown and Lorna Dougan","doi":"10.1039/D4FD00204K","DOIUrl":"10.1039/D4FD00204K","url":null,"abstract":"<p >Protein-based hydrogels have gained significant attention for their potential use in applications such as drug delivery and tissue engineering. Their internal structure is complex, spans across multiple length scales and affects their functionality, yet is not well understood because of folded proteins’ sensitivity to physical and chemical perturbations and the high water content of hydrogels. Cryo-scanning electron microscopy (cryo-SEM) has the potential to reveal such hierarchical structure when hydrated hydrogels are prepared with appropriate cryofixation. We show for photochemically cross-linked, folded globular bovine serum albumin (BSA) protein hydrogels that preparation artefacts are reduced by <em>in situ</em> gelation, high pressure freezing (HPF), plasma focused ion beam (pFIB) milling, sublimation, and low dose secondary electron imaging. Cryo-SEM of folded BSA protein hydrogels prepared in this way reveals a heterogeneous network with nanoscale porosity (∼60 nm pores) surrounded by high secondary electron emission regions (∼30 nm diameter) interconnected by narrower, lower emission regions (∼20 nm length). This heterogeneous network structure is consistent with small angle scattering studies of folded protein hydrogels, with fractal-like clusters connected by intercluster regions. We further test the potential of cryo-SEM to detect the impact of protein unfolding on hydrogel network formation and reveal nanoscale differences in cluster sizes consistent with those derived from scattering data. Importantly, cryo-SEM directly images pores for sizing in both systems, with initial results on BSA suggesting protein unfolding induces an increase of ∼10 nm in pore sizes. Our findings on cryo-SEM sample preparation challenges and solutions provide new opportunities to link hydrogel structure to function.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 55-81"},"PeriodicalIF":3.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00204k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automated descriptors for high-throughput screening of peptide self-assembly†","authors":"Raj Kumar Rajaram Baskaran, Alexander van Teijlingen and Tell Tuttle","doi":"10.1039/D4FD00201F","DOIUrl":"10.1039/D4FD00201F","url":null,"abstract":"<p >We present five automated descriptors: Aggregate Detection Index (ADI); Sheet Formation Index (SFI); Vesicle Formation Index (VFI); Tube Formation Index (TFI); and Fibre Formation Index (FFI), that have been designed for analysing peptide self-assembly in molecular dynamics simulations. These descriptors, implemented as Python modules, enhance analytical precision and enable the development of screening methods tailored to specific structural targets rather than general aggregation. Initially tested on the FF dipeptide, the descriptors were validated using a comprehensive dipeptide dataset. This approach facilitates the identification of promising self-assembling moieties with nanoscale properties directly linked to macroscale functions, such as hydrogel formation.</p>","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"260 ","pages":" 252-268"},"PeriodicalIF":3.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/fd/d4fd00201f?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scanning electrochemical probe microscopy: general discussion","authors":"Paolo Actis, Lane A. Baker, Giada Caniglia, Zhifeng Ding, Andrew G. Ewing, Kaiyu X. Fu, Lachlan F. Gaudin, J. Justin Gooding, Jingshu Hui, Dechen Jiang, Frédéric Kanoufi, John J. Kasianowicz, Moonjoo Kim, Christine Kranz, Christian Kuttner, Yunchao Li, Liang Liu, Si-Min Lu, Wenjun Luo, Kim McKelvey, Andrew R. Mount, Hang Ren, Yuanhua Shao, Mei Shen, Yasufumi Takahashi, Juan Tang, Dengchao Wang, Liang Wang, Wei Wang, Yunong Wang, Ruo-Chen Xie, Yuelin Xie, Yi-Lun Ying, Guohui Zhang, Lingjie Zhang, Ziwen Zhao and Yige Zhou","doi":"10.1039/D4FD90069C","DOIUrl":"10.1039/D4FD90069C","url":null,"abstract":"","PeriodicalId":49075,"journal":{"name":"Faraday Discussions","volume":"257 ","pages":" 277-302"},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}