In unity, there is strength: Phase separation controls receptor tyrosine kinase signal transduction.

Lin et al. (2022) discover that FGFR2 undergoes liquid-liquid phase separation with its downstream effectors SHP2 and PLCγ1, and the formation of phase separated condensates is essential for signaling competency.

Raf promotes dimerization of the Ras G-domain with increased allosteric connections.

Ras dimerization is critical for Raf activation. Here we show that the Ras binding domain of Raf (Raf-RBD) induces robust Ras dimerization at low surface densities on supported lipid bilayers and, to a lesser extent, in solution as observed by size exclusion chromatography and confirmed by SAXS. Community network analysis based on molecular dynamics simulations shows robust allosteric connections linking the two Raf-RBD D113 residues located in the Galectin scaffold protein binding site of each Raf-RBD molecule and 85 Å apart on opposite ends of the dimer complex. Our results suggest that Raf-RBD binding and Ras dimerization are concerted events that lead to a high-affinity signaling complex at the membrane that we propose is an essential unit in the macromolecular assembly of higher order Ras/Raf/Galectin complexes important for signaling through the Ras/Raf/MEK/ERK pathway.

Stochastic geometry sensing and polarization in a lipid kinase-phosphatase competitive reaction.

Phosphorylation reactions, driven by competing kinases and phosphatases, are central elements of cellular signal transduction. We reconstituted a native eukaryotic lipid kinase-phosphatase reaction that drives the interconversion of phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-phosphate [PI(4,5)P2] on membrane surfaces. This system exhibited bistability and formed spatial composition patterns on supported membranes. In smaller confined regions of membrane, rapid diffusion ensures the system remains spatially homogeneous, but the final outcome-a predominantly PI(4)P or PI(4,5)P2 membrane composition-was governed by the size of the reaction environment. In larger confined regions, interplay between the reactions, diffusion, and confinement created a variety of differentially patterned states, including polarization. Experiments and kinetic modeling reveal how these geometric confinement effects arise from a mechanism based on stochastic fluctuations in the copy number of membrane-bound kinases and phosphatases. The underlying requirements for such behavior are unexpectedly simple and likely to occur in natural biological signaling systems.

K-Ras4B Remains Monomeric on Membranes over a Wide Range of Surface Densities and Lipid Compositions.

Ras is a membrane-anchored signaling protein that serves as a hub for many signaling pathways and also plays a prominent role in cancer. The intrinsic behavior of Ras on the membrane has captivated the biophysics community in recent years, especially the possibility that it may form dimers. In this article, we describe results from a comprehensive series of experiments using fluorescence correlation spectroscopy and single-molecule tracking to probe the possible dimerization of natively expressed and fully processed K-Ras4B in supported lipid bilayer membranes. Key to these studies is the fact that K-Ras4B has its native membrane anchor, including both the farnesylation and methylation of the terminal cysteine, enabling detailed exploration of possible effects of cholesterol and lipid composition on K-Ras4B membrane organization. The results from all conditions studied indicate that full-length K-Ras4B lacks intrinsic dimerization capability. This suggests that any lateral organization of Ras in living cell membranes likely stems from interactions with other factors.

Spatiomechanical Modulation of EphB4-Ephrin-B2 Signaling in Neural Stem Cell Differentiation.

Interactions between EphB4 receptor tyrosine kinases and their membrane-bound ephrin-B2 ligands on apposed cells play a regulatory role in neural stem cell differentiation. With both receptor and ligand constrained to move within the membranes of their respective cells, this signaling system inevitably experiences spatial confinement and mechanical forces in conjunction with receptor-ligand binding. In this study, we reconstitute the EphB4-ephrin-B2 juxtacrine signaling geometry using a supported-lipid-bilayer system presenting laterally mobile and monomeric ephrin-B2 ligands to live neural stem cells. This experimental platform successfully reconstitutes EphB4-ephrin-B2 binding, lateral clustering, downstream signaling activation, and neuronal differentiation, all in a configuration that preserves the spatiomechanical aspects of the natural juxtacrine signaling geometry. Additionally, the supported bilayer system allows control of lateral movement and clustering of the receptor-ligand complexes through patterns of physical barriers to lateral diffusion fabricated onto the underlying substrate. The results from this study reveal a distinct spatiomechanical effect on the ability of EphB4-ephrin-B2 signaling to induce neuronal differentiation. These observations parallel similar studies of the EphA2-ephrin-A1 system in a very different biological context, suggesting that such spatiomechanical regulation may be a common feature of Eph-ephrin signaling.

Four unreported types of glycans containing mannose-6-phosphate are heterogeneously attached at three sites (including newly found Asn 233) to recombinant human acid alpha-glucosidase that is the only approved treatment for Pompe disease.

Myozyme is a recombinant human acid alpha-glucosidase (rhGAA) that is currently the only drug approved for treating Pompe disease, and its low efficacy means that a high dose is required. Mannose-6-phosphate (M6P) glycosylation on rhGAA is a key factor influencing lysosomal enzyme targeting and the efficacy of enzyme replacement therapy (ERT); however, its complex structure and relatively small quantity still remain to be characterized. This study investigated M6P glycosylation on rhGAA using liquid chromatography (LC)-electrospray ionization (ESI)-high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS). The glycans released from rhGAA were labeled with procainamide to improve mass ionization efficiency and the sensitivity of MS/MS. The relative quantities (%) of 78 glycans were obtained, and 1.0% of them were glycans containing M6P (M6P glycans). These were categorized according to their structure into 4 types: 3 newly found ones, comprising high-mannose-type M6P glycans capped with N-acetylglucosamine (GlcNAc) (2 variants, 17.5%), hybrid-type M6P glycans (2 variants, 11.2%), and hybrid-type M6P glycans capped with GlcNAc (3 variants, 6.9%), as well as high-mannose-type M6P glycans (3 variants, 64.4%). HCD-MS/MS spectra identified six distinctive M6P-derived oxonium ions. The glycopeptides obtained from protease-digested rhGAA were analyzed using nano-LC-ESI-HCD-MS/MS, and the extracted-ion chromatograms of M6P-derived oxonium ions confirmed three M6P glycosylation sites comprising Asn 140, Asn 233 (newly found), and Asn 470 attached heterogeneously to nine M6P glycans (two types), eight M6P glycans (four types), and seven M6P glycans (two types), respectively. This is the first study of rhGAA to differentiate M6P glycans and identify their attachment sites, despite rhGAA already being an approved drug for Pompe disease.

Optokinetically Encoded Nanoprobe-Based Multiplexing Strategy for MicroRNA Profiling.

Multiplexed real-time analysis on multiple interacting molecules and particles is needed to obtain information on binding patterns between multiple ligands and receptors, specificity of bond formations, and interacting pairs in a complex medium, often found in chemical and biological systems, and difference in binding affinity and kinetics for different binding pairs in one solution. In particular, multiplexed profiling of microRNA (miRNA) in a reliable, quantitative manner is of great demand for the use of miRNA in cell biology, biosensing, and clinical diagnostic applications, and accurate diagnosis of cancers with miRNA is not possible without detecting multiple miRNA sequences in a highly specific manner. Here, we report a multiplexed molecular detection strategy with optokinetically (OK) coded nanoprobes (NPs) that show high photostability, distinct optical signals, and dynamic behaviors on a supported lipid bilayer (SLB) (OK-NLB assay). Metal NPs with three distinct dark-field light scattering signals [red (R), green (G), and blue (B)] and three different target miRNA half-complements were tethered to a two dimensionally fluidic SLB with mobile (M) or immobile (I) state. In situ single-particle monitoring and normalized RGB analysis of the optokinetically combinatorial assemblies among three M-NPs and three I-NPs with dark-field microscopy (DFM) allow for differentiating and quantifying 9 different miRNA targets in one sample. The OK-NP-based assay enables simultaneous detection of multiple miRNA targets in a highly quantitative, specific manner within 1 h and can be potentially used for diagnosis of different cancer types. We validated the OK-NLB assay with single-base mismatched experiments and HeLa cell-extracted total RNA samples by comparing the assay results to the quantitative reverse transcription polymerase chain reaction (qRT-PCR) results.

Graphene-Templated Supported Lipid Bilayer Nanochannels.

The use of patterned substrates to impose geometrical restriction on the lateral mobility of molecules in supported lipid membranes has found widespread utility in studies of cell membranes. Here, we template-pattern supported lipid membranes with nanopatterned graphene. We utilize focused ion beam milling to pattern graphene on its growth substrate, then transfer the patterned graphene to fresh glass substrates for subsequent supported membrane formation. We observe that graphene functions as an excellent lateral diffusion barrier for supported lipid bilayers. Additionally, the observed diffusion dynamics of lipids in nanoscale graphene channels reveal extremely low boundary effects, a common problem with other materials. We suggest this is attributable to the ultimate thinness of graphene.

Associating and Dissociating Nanodimer Analysis for Quantifying Ultrasmall Amounts of DNA.

The amplification- and enzyme-free quantification of DNA at ultralow concentrations, on the order of 10-1000 targets, is highly beneficial but extremely challenging. To address this challenge, true detection signals must be reliably discriminated from false or noise signals. Herein, we describe the development of associating and dissociating nanodimer analysis (ADNA) as a method that enables a maximum number of detection signals to be collected from true target-binding events while keeping nonspecific signals at a minimum level. In the ADNA assay for ultralow target concentrations, Au nanoprobes on a lipid micropattern were monitored and analyzed in situ, and newly defined dissociating dimers, which are eventually decoupled into monomers again, were incorporated into the detection results. Tens to thousands of DNA copies can be reliably quantified with excellent single-base-mismatch differentiation capability by this non-enzymatic, amplification-free ADNA method.

Covalent Ras Dimerization on Membrane Surfaces through Photosensitized Oxidation.

Ras, a small GTPase found primarily on the inner leaflet of the plasma membrane, is an important signaling node and an attractive target for anticancer therapies. Lateral organization of Ras on cellular membranes has long been a subject of intense research; in particular, whether it forms dimers on membranes as part of its regulatory function has been a point of great interest. Here we report Ras dimer formation on membranes by Type II photosensitization reactions, in which molecular oxygen mediates the radicalization of proteins under typical fluorescence experimental conditions. The presence of Ras dimers on membranes was detected by diffusion-based fluorescence techniques including fluorescence correlation spectroscopy and single particle tracking, and molecular weights of the stable covalently coupled species were confirmed by gel electrophoresis. Fluorescence spectroscopy implicates interprotein dityrosine as one of the dimerization motifs. The specific surface tyrosine distribution on Ras renders the protein especially sensitive to this reaction, and point mutations affecting surface tyrosines are observed to alter dimerization potential. The photosensitization reactions are reflective of physiological oxidative stress induced by reactive oxygen species, suggesting such processes may occur naturally and influence signaling pathways in cells.

Significant reduction in allergenicity of ovalbumin from chicken egg white following treatment with ascidian viscera N-acetylglucosaminidase.

Ovalbumin (OA) is the most abundant ingredient of chicken egg-white allergenic proteins. In the present study we investigated the possibility of reducing OA allergenicity by treatment with a natural protein exhibiting N-acetylglucosaminidase (NA) activity. Ascidian is cultivated as a food resource in northeast Asia. The ascidian viscera NA (AVNA) with almost no other exoglycosidases or proteolytic enzymes was isolated by applying size-exclusion chromatography to a protein precipitate of ascidian viscera. Intact OA was mixed with AVNA containing 0.2, 1.0, and 5.0 Units of NA. Anion-exchange chromatography was then used to isolate OA from AVNA-treated OA. The electrophoretic patterns and N-glycans of each isolated OA from AVNA-treated OA (iOA) were analyzed, and the terminal N-acetylglucosamines of iOA were selectively cleaved with no other degradation occurring. A competitive indirect enzyme-linked immunosorbent assay using rabbit anti-OA sera was performed to investigate the allergenicity of iOA, which was found to be significantly reduced depending on the increased NA activity compared to that of intact OA. These results indicate that OA allergenicity was reduced using a simple and mild treatment process with AVNA, and suggest that ascidian NA is an efficient natural protein for reducing the allergenicity of OA without requiring the use of harsh physical treatments or chemical conjugation.

Dark-field-based observation of single-nanoparticle dynamics on a supported lipid bilayer for in situ analysis of interacting molecules and nanoparticles.

Observation of single plasmonic nanoparticles in reconstituted biological systems allows us to obtain snapshots of dynamic processes between molecules and nanoparticles with unprecedented spatiotemporal resolution and single-molecule/single-particle-level data acquisition. This Concept is intended to introduce nanoparticle-tethered supported lipid bilayer platforms that allow for the dynamic confinement of nanoparticles on a two-dimensional fluidic surface. The dark-field-based long-term, stable, real-time observation of freely diffusing plasmonic nanoparticles on a lipid bilayer enables one to extract a broad range of information about interparticle and molecular interactions throughout the entire reaction period. Herein, we highlight important developments in this context to provide ideas on how molecular interactions can be interpreted by monitoring dynamic behaviors and optical signals of laterally mobile nanoparticles.

Massively parallel and highly quantitative single-particle analysis on interactions between nanoparticles on supported lipid bilayer.

Observation of individual single-nanoparticle reactions provides direct information and insight for many complex chemical, physical, and biological processes, but this is utterly challenging with conventional high-resolution imaging techniques on conventional platforms. Here, we developed a photostable plasmonic nanoparticle-modified supported lipid bilayer (PNP-SLB) platform that allows for massively parallel in situ analysis of the interactions between nanoparticles with single-particle resolution on a two-dimensional (2D) fluidic surface. Each particle-by-particle PNP clustering process was monitored in real time and quantified via analysis of individual particle diffusion trajectories and single-particle-level plasmonic coupling. Importantly, the PNP-SLB-based nanoparticle cluster growth kinetics result was fitted well. As an application example, we performed a DNA detection assay, and the result suggests that our approach has very promising sensitivity and dynamic range (high attomolar to high femtomolar) without optimization, as well as remarkable single-base mismatch discrimination capability. The method shown herein can be readily applied for many different types of intermolecular and interparticle interactions and provide convenient tools and new insights for studying dynamic interactions on a highly controllable and analytical platform.

Impact of surface cooling on the water harvesting efficiency of nanostructured window glass.

Humans face a severe shortage of fresh water due to economic growth, climate change, overpopulation, and overutilization. Atmospheric water harvesting (AWH) is a promising solution where clean water is collected from the air through various approaches, including dropwise condensation. However, designing surfaces that balance rapid condensation with efficient water removal is challenging. To address this issue, inspired by the efficient water collection mechanisms in the skin of cold-blooded tree frogs, we propose an eco-friendly approach to collect fresh water from cooled window glass. We fabricated various planar and TiO2 nanostructured surfaces including surfaces mimicking a lotus leaf and a hybrid surface mimicking a desert beetle and a cactus, with different wettability levels such as superhydrophilic, hydrophilic, hydrophobic, superhydrophobic, and biphilic. Sub-cooling of glass substrates between 5 and 15 °C using a Peltier device significantly enhanced the condensation process for all surfaces, with modest dependency on surface properties. This cooling temperature regime could be achieved by geothermal cooling methods that consume little energy. To improve visibility for window applications, we developed hydrophobic polymer nanofilm-modified glass substrates using a simple spin-coating technique, and achieved comparable water harvesting efficiency to that of nanostructured substrates. Our study provides insight into the optimal surface structures and cooling temperature for window glass AWH systems that could be used with an underground cooling system.

Isolation of Bovine Milk Exosome Using Electrophoretic Oscillation Assisted Tangential Flow Filtration with Antifouling of Micro-ultrafiltration Membrane Filters.

Tangent flow-driven ultrafiltration (TF-UF) is an efficient isolation process of milk exosomes without morphological deformation. However, the TF-UF approach with micro-ultrafiltration SiNx membrane filters suffers from the clogging and fouling of micro-ultrafiltration membrane filter pores with large bioparticles. Thus, it is limited in the long term, continuous isolation of large quantities of exosomes. In this work, we introduced electrophoretic oscillation (EPO) in the TF-UF approach to remove pore clogging and fouling of with micro-ultrafiltration SiNx membrane filters by large bioparticles. As a result, the combined EPO-assisted TF (EPOTF) filtration can isolate large quantities of bovine milk exosomes without deformation. Furthermore, several morphological and biological analyses confirmed that the EPOTF filtration approach could isolate the milk exosomes in high concentrations with high purity and intact morphology. In addition, the uptake test of fluorescent-labeled exosomes by the keratinocyte cells visualized the biological function of purified exosomes. Hence, compared to the TF-UF process, the EPOTF filtration produced a higher yield of bovine milk exosomes without stopping the filtering process for over 200 h. Therefore, this isolation process enables scalable and continuous production of morphologically intact exosomes from bovine milk, suggesting that high-quality exosome purification is possible for future applications such as drug nanocarriers, diagnosis, and treatments.

Flexible linkers in CaMKII control the balance between activating and inhibitory autophosphorylation.

The many variants of human Ca2+/calmodulin-dependent protein kinase II (CaMKII) differ in the lengths and sequences of disordered linkers connecting the kinase domains to the oligomeric hubs of the holoenzyme. CaMKII activity depends on the balance between activating and inhibitory autophosphorylation (on Thr 286 and Thr 305/306, respectively, in the human α isoform). Variation in the linkers could alter transphosphorylation rates within a holoenzyme and the balance of autophosphorylation outcomes. We show, using mammalian cell expression and a single-molecule assay, that the balance of autophosphorylation is flipped between CaMKII variants with longer and shorter linkers. For the principal isoforms in the brain, CaMKII-α, with a ~30 residue linker, readily acquires activating autophosphorylation, while CaMKII-ß, with a ~200 residue linker, is biased towards inhibitory autophosphorylation. Our results show how the responsiveness of CaMKII holoenzymes to calcium signals can be tuned by varying the relative levels of isoforms with long and short linkers.

Breakage of the oligomeric CaMKII hub by the regulatory segment of the kinase.

Ca2+/calmodulin-dependent protein kinase II (CaMKII) is an oligomeric enzyme with crucial roles in neuronal signaling and cardiac function. Previously, we showed that activation of CaMKII triggers the exchange of subunits between holoenzymes, potentially increasing the spread of the active state (Stratton et al., 2014; Bhattacharyya et al., 2016). Using mass spectrometry, we show now that unphosphorylated and phosphorylated peptides derived from the CaMKII-α regulatory segment bind to the CaMKII-α hub and break it into smaller oligomers. Molecular dynamics simulations show that the regulatory segments dock spontaneously at the interface between hub subunits, trapping large fluctuations in hub structure. Single-molecule fluorescence intensity analysis of CaMKII-α expressed in mammalian cells shows that activation of CaMKII-α results in the destabilization of the holoenzyme. Our results suggest that release of the regulatory segment by activation and phosphorylation allows it to destabilize the hub, producing smaller assemblies that might reassemble to form new holoenzymes.

Lipid-Rich Necrotic Core of Basilar Artery Atherosclerotic Plaque: Contrast-Enhanced Black Blood Imaging on Vessel Wall Imaging.

PURPOSE: We wished to evaluate the lipid-rich necrotic core (LRNC) using contrast-enhanced T1-weighted (CE-T1W) black-blood (BB) imaging for vessel walls. METHODS: Ninety-five patients with basilar artery (BA) stenosis who underwent magnetic resonance angiography between January 2016 and August 2018 were enrolled into this present study. CE-T1W BB imaging was considered as a reference method for identifying an LRNC. RESULTS: Ten (10.5%) patients were identified as having an LRNC on CE-T1W BB imaging. Of these patients, 9 had acute symptoms. The extent of stenosis in patients with an LRNC on CE-T1W BB imaging was significantly greater than that of patients without an LRNC (p < 0.001). The maximum wall thickness in patients with an LRNC on CE-T1W imaging was significantly thicker than that of patients without an LRNC (p = 0.008). CONCLUSIONS: Identification of an LRNC on CE-T1W BB imaging was associated with high-grade stenosis and massive plaque burden from BA atherosclerosis.

N-glycans of bovine submaxillary mucin contain core-fucosylated and sulfated glycans but not sialylated glycans.

Bovine submaxillary mucin (BSM) is a heavily-glycosylated macromolecular (approximately 4 MDa) protein and is used in various biomaterial applications in light of its high viscosity and biocompatibility, in addition to use as a biochemical substrate or inhibitor as a result of its abundant O-glycans. Although it has been reported that N-glycosylation provides stability of human mucins, most BSM research has been focused on its O-glycans, while N-glycans have not been reported to date. In this study, a common N-glycan core component was detected by monosaccharide analysis of BSM, and the structures of the N-glycans and their relative quantities were determined by liquid chromatography-tandem mass spectrometry. Seventeen N-glycans comprising ten complex-type [Fucose0~2Hexose3~4N-acetylhexosamine1~6Sulfate0~1; 61.1% (the sum of the relative quantities of each N-glycan out of the total N-glycans)], two high-mannose-type (Hexose5~6N-acetylhexosamine2; 12.0%), and five paucimannose type (Fucose0~1Hexose3~4N-acetylhexosamine2~3; 26.9%) were identified, but no hybrid-type or sialylated N-glycans were found. Additionally, these are less-branched structures compared to human mucins. Of these, ten glycans (77.2%), including two sulfated glycans (8.0%), were core fucosylated, which confer unique biological functions to glycoproteins. The N-glycosylation sites were identified from the analysis of glycopeptides from BSM. This study is the first confirmation of N-glycan attachment to BSM.

A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS.

The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) is a key Ras activator that is autoinhibited in the cytosol and activates upon membrane recruitment. Autoinhibition release involves structural rearrangements of the protein at the membrane and thus introduces a delay between initial recruitment and activation. In this study, we designed a single-molecule assay to resolve the time between initial receptor-mediated membrane recruitment and the initiation of GEF activity of individual SOS molecules on microarrays of Ras-functionalized supported membranes. The rise-and-fall shape of the measured SOS activation time distribution and the long mean time scale to activation (~50 seconds) establish a basis for kinetic proofreading in the receptor-mediated activation of Ras. We further demonstrate that this kinetic proofreading is modulated by the LAT (linker for activation of T cells)-Grb2-SOS phosphotyrosine-driven phase transition at the membrane.