Amphiphilic, monolayer-protected gold nanoparticles (NPs) have been shown to enter cells via a non-endocytic, non-disruptive pathway that could be valuable for biomedical applications. The same NPs ...were also found to insert into a series of model cell membranes as a precursor to cellular uptake, but the insertion mechanism remains unclear. Previous simulations have demonstrated that an amphiphilic NP can insert into a single leaflet of a planar lipid bilayer, but in this configuration all charged end groups are localized to one side of the bilayer and it is unknown if further insertion is thermodynamically favorable. Here, we use atomistic molecular dynamics simulations to show that an amphiphilic NP can reach the bilayer midplane non-disruptively if charged ligands iteratively "flip" across the bilayer. Ligand flipping is a favorable process that relaxes bilayer curvature, decreases the nonpolar solvent-accessible surface area of the NP monolayer, and increases attractive ligand-lipid electrostatic interactions. Analysis of end group hydration further indicates that iterative ligand flipping can occur on experimentally relevant timescales. Supported by these results, we present a complete energy landscape for the non-disruptive insertion of amphiphilic NPs into lipid bilayers. These findings will help guide the design of NPs to enhance bilayer insertion and non-endocytic cellular uptake, and also provide physical insight into a possible pathway for the translocation of charged biomacromolecules.
Understanding how material properties affect hydrophobic interactionsthe water-mediated interactions that drive the association of nonpolar materialsis vital to the design of materials in contact ...with water. Conventionally, the magnitude of the hydrophobic interactions between extended interfaces is attributed to interfacial chemical properties, such as the amount of nonpolar solvent-exposed surface area. However, recent experiments have demonstrated that the hydrophobic interactions between uniformly nonpolar self-assembled monolayers (SAMs) also depend on molecular-level SAM order. In this work, we use atomistic molecular dynamics simulations to investigate the relationship between SAM order, water structure, and hydrophobic interactions to explain these experimental observations. The SAM–SAM hydrophobic interactions calculated from the simulations increase in magnitude as SAM order increases, matching experimental observations. We explain this trend by showing that the molecular-level order of the SAM impacts the nanoscale structure of interfacial water molecules, leading to an increase in water structure near disordered SAMs. These findings are consistent with a decrease in the solvation entropy of disordered SAMs, which is confirmed by measuring the temperature dependence of hydrophobic interactions using both simulations and experiments. This study elucidates how hydrophobic interactions can be influenced by an interfacial physical property, which may guide the design of synthetic materials with fine-tuned interfacial hydrophobicity.
The separation of desired monomers from a liquid-phase mixture of lignin depolymerization products is necessary to facilitate their upscaling and upgrading for industrial applications. One effective ...method to separate multiple liquid-phase products is countercurrent chromatography (CCC), which is a common liquid chromatography technique that separates target solutes based on differences in their partitioning in a biphasic solvent system. Effective CCC separation requires the selection of solvent compositions to tune solute partition coefficients. To alleviate the experimental burden of selecting optimal solvent systems, we apply the conductor-like screening model for real solvents (COSMO-RS) method to compute partition coefficients of representative lignin monomers from four currently used depolymerization strategies in standard solvent systems. We further design new ternary and quaternary solvent systems that are predicted to further improve separation efficacy. On the basis of these predicted partition coefficients and empirical solvent selection criteria for CCC measurements, we suggest a range of solvent systems that would be suitable for the effective separation of aromatic lignin-derived products via CCC or similar liquid–liquid extraction methods.
Neurofibromatosis type 1 associates with multiple neoplasms, and the Schwann cell tumor neurofibroma is the most prevalent. A hallmark feature of neurofibroma is mast cell infiltration, which is ...recruited by chemoattractant stem cell factor (SCF) and has been suggested to sustain neurofibroma tumorigenesis. In the present study, we use new, genetically engineered Scf mice to decipher the contributions of tumor-derived SCF and mast cells to neurofibroma development. We demonstrate that mast cell infiltration is dependent on SCF from tumor Schwann cells. However, removal of mast cells by depleting the main SCF source only slightly affects neurofibroma progression. Other inflammation signatures show that all neurofibromas are associated with high levels of macrophages regardless of Scf status. These findings suggest an active inflammation in neurofibromas and partly explain why mast cell removal alone is not sufficient to relieve tumor burden in this experimental neurofibroma model. Furthermore, we show that plexiform neurofibromas are highly associated with injury-prone spinal nerves that are close to flexible vertebras. In summary, our study details the role of inflammation in neurofibromagenesis. Our data indicate that prevention of inflammation and possibly also nerve injury at the observed tumor locations are therapeutic approaches for neurofibroma prophylaxis and that such treatment should be explored.
Exposure of subendothelial extracellular matrix (ECM) proteins to the circulation is the key event that initiates platelet accumulation and clot formation after vessel injury. Soluble ECM proteins ...are also essential for support and regulation of these events. This review discusses the current understanding of ECM proteins in thrombosis and hemostasis.
Fibrinogen and von Willebrand factor (VWF) are considered essential for thrombosis and hemostasis. Interestingly, αIIbβ3 integrin-dependent thrombus formation persists in the absence of fibrinogen and VWF, suggesting that other αIIbβ3 ligand (s), likely ECM proteins, can still mediate thrombosis. Fibronectin increases in platelets of fibrinogen-deficient humans and mice. This ECM protein can rapidly deposit onto the injured vessel wall prior to platelet accumulation. By switching from the soluble to insoluble form, plasma fibronectin supports hemostasis and inhibits excessive thrombosis. Fibrin, fibronectin, VWF, vitronectin, neutrophil extracellular traps, and other ECM proteins in the blood clot form a de-facto ECM, which interacts with various types of blood cells to regulate the evolution and resolution of the clot.
ECM proteins are intricately involved in major steps of thrombus formation. Further investigations of ECM proteins will reveal new therapeutic targets for treatment of thrombosis and bleeding disorders.
http://links.lww.com/COH/A12
Hydrological connections between river channels and their adjacent floodplains facilitate the flux of organisms and nutrients and access to increased habitat and new resources. Hydrological ...connections also deliver water subsidy and potentially disturb (through hydraulic forces) floodplain ecosystems. This study investigates the role of hydrological connectivity as a driver of patterns in wetland plant assemblages in billabongs on the floodplain of an Australian dryland river, exploring indirectly the relative importance of the mechanisms of flux, subsidy and disturbance. Wetland plants were surveyed in billabongs across gradients of hydrological connectivity and depth. Surveys were accompanied by experiments examining germination from the soil seed banks of each site under submerged and waterlogged conditions. The patterns in extant and germinant plant communities in relation to connectivity and depth gradients were used to infer the relative importance of the connectivity-related mechanisms of flux, subsidy and hydraulic disturbance in structuring wetland plant communities. Depth influenced both extant and germinating plant communities. Shallow billabongs supported a greater diversity and abundance of plants, and greater numbers and diversity of germinable seeds in the seed bank. Germination of seeds was greater in waterlogged soils than submerged soils. Thus, the main controls of plant abundance in wetlands appear to be availability of waterlogged soil habitat for germination and absence of light limitation for growth. Hydrological connectivity did not influence the abundance of plants or germinable seeds, but did influence species presence-absence in growing vegetation; this effect did not extend to the germinating community. Thus, hydrological connection does not appear to influence wetland vegetation by facilitating the movement of propagules between habitats. Instead, the patterns observed are consistent with hydrological connection providing a cue for germination through the delivery of water, and by modifying hydraulic habitat.
The Atlantic cod (Gadus morhua L.) has been overexploited in the North Sea since the late 1960s and great concern has been expressed about the decline in cod biomass and recruitment. Here we show ...that, in addition to the effects of overfishing, fluctuations in plankton have resulted in long-term changes in cod recruitment in the North Sea (bottom-up control). Survival of larval cod is shown to depend on three key biological parameters of their prey: the mean size of prey, seasonal timing and abundance. We suggest a mechanism, involving the match/mismatch hypothesis, by which variability in temperature affects larval cod survival and conclude that rising temperature since the mid-1980s has modified the plankton ecosystem in a way that reduces the survival of young cod.
The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein. The ...presence of a polybasic cleavage site in SARS-CoV-2 spike at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-CoV-2 compared to SARS-CoV-1 by facilitating maturation of the spike precursor by furin-like proteases in the producer cells rather than endosomal cathepsins in the target. We investigate the relevance of the polybasic cleavage site in the route of entry of SARS-CoV-2 and the consequences this has for sensitivity to interferons (IFNs) and, more specifically, the IFN-induced transmembrane (IFITM) protein family that inhibit entry of diverse enveloped viruses. We found that SARS-CoV-2 is restricted predominantly by IFITM2, rather than IFITM3, and the degree of this restriction is governed by route of viral entry. Importantly, removal of the cleavage site in the spike protein renders SARS-CoV-2 entry highly pH and cathepsin dependent in late endosomes, where, like SARS-CoV-1 spike, it is more sensitive to IFITM2 restriction. Furthermore, we found that potent inhibition of SARS-CoV-2 replication by type I but not type II IFNs is alleviated by targeted depletion of IFITM2 expression. We propose that the polybasic cleavage site allows SARS-CoV-2 to mediate viral entry in a pH-independent manner, in part to mitigate against IFITM-mediated restriction and promote replication and transmission. This suggests that therapeutic strategies that target furin-mediated cleavage of SARS-CoV-2 spike may reduce viral replication through the activity of type I IFNs.
The furin cleavage site in the spike protein is a distinguishing feature of SARS-CoV-2 and has been proposed to be a determinant for the higher transmissibility between individuals, compared to SARS-CoV-1. One explanation for this is that it permits more efficient activation of fusion at or near the cell surface rather than requiring processing in the endosome of the target cell. Here, we show that SARS-CoV-2 is inhibited by antiviral membrane protein IFITM2 and that the sensitivity is exacerbated by deletion of the furin cleavage site, which restricts viral entry to low pH compartments. Furthermore, we find that IFITM2 is a significant effector of the antiviral activity of type I interferons against SARS-CoV-2 replication. We suggest that one role of the furin cleavage site is to reduce SARS-CoV-2 sensitivity to innate immune restriction, and thus, it may represent a potential therapeutic target for COVID-19 treatment development.
The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic ...nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of approximately 65 degrees , and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.
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