Protein self-assembly is one of the formation mechanisms of biomolecular condensates. However, most phase-separating systems (PS) demand multiple partners in biological conditions. In this study, we divided PS proteins into two groups according to the mechanism by which they undergo PS: PS-Self proteins can self-assemble spontaneously to form droplets, while PS-Part proteins interact with partners to undergo PS. Analysis of the amino acid composition revealed differences in the sequence pattern between the two protein groups. Existing PS predictors, when evaluated on two test protein sets, preferentially predicted self-assembling proteins. Thus, a comprehensive predictor is required. Herein, we propose that properties other than sequence composition can provide crucial information in screening PS proteins. By incorporating phosphorylation frequencies and immunofluorescence image-based droplet-forming propensity with other PS-related features, we built two independent machine-learning models to separately predict the two protein categories. Results of independent testing suggested the superiority of integrating multimodal features. We performed experimental verification on the top-scored proteins DHX9, K i -67, and NIFK. Their PS behavior in vitro revealed the effectiveness of our models in PS prediction. Further validation on the proteome of membraneless organelles confirmed the ability of our models to identify PS-Part proteins. We implemented a web server named PhaSePred ( http://predict.phasep.pro/ ) that incorporates our two models together with representative PS predictors. PhaSePred displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins.
The study investigated the protective effect of walnut oligopeptides (WOPs) against ethanol-induced gastric injury using Sprague-Dawley (SD) rats. Rats were randomly divided into seven groups based on body weight (10/group), normal group, ethanol group, whey protein group (220 mg/kg body weight), omeprazole group (20 mg/kg body weight), and three WOPs groups (220, 440, 880 mg/kg body weight). After 30 days of treatment with WOPs, rats were given 5 mL/kg absolute ethanol by gavage to induce gastric mucosal injury. Gastric ulcer index (GUI) were determined and the following measured; gastric content pH, gastric mucin, endogenous pepsinogens (PG), prostaglandin E2 (PGE2), inflammatory cytokines, oxidative stress indicators, and the expression of apoptosis-related proteins were measured to evaluate the gastroprotective effect of WOPs. The results showed that the administration with WOPs markedly mitigated the hemorrhagic gastric lesions caused by ethanol in rats, and decreased the GUI, the gastric content pH, PG1, PG2, and NO levels, enhanced mucin and PGE2. Also, WOPs repressed gastric inflammation through the reduction of TNF-α, IL-6, IL-1β and increase IL-10 levels, and revealed antioxidant properties with the enhancement of superoxide dismutase, glutathione, and catalase activity, while reduction of malondialdehyde. Moreover, WOPs treatment significantly down-regulated Bax, caspase-3 and nuclear factor-κB p65 (NF-κB p65) expression, while up-regulating the expression of Bcl-2 and inhibitor kappa Bα (IκBα) protein. These results indicated that WOPs have protective effects against ethanol-induced gastric mucosal injury in rats through anti-inflammatory, anti-oxidation, and anti-apoptosis mechanisms.
In this study, silver nanoparticles were formed on a natural macroporous matrix, the stem of rice-paper plant, by reducing Ag+ in aqueous solution through in situ processing without using any other stabilizers. The pores of the matrix, with their size of about 100 µm, were thought to act as reaction compartments for the nucleation and growth of silver nanoparticles, and the control of nucleation of silver crystal during the reduction reaction was found to be important to the successful formation of nanosized silver particles onto the matrix. The diameter and amount of resultant silver particles can be controlled by changing the reaction conditions. Under optimized conditions, the content of silver particles in the matrix can reach as high as 1.8 wt% with the particle diameters being kept below 100 nm. The anti-microbial activities in terms of minimum inhibitory concentration (MIC) for the silver nanoparticle composites against Escherichia coli and Candida albicans were assayed in agar gel, and the results show that MIC values for silver nanoparticle composites are 14.1 mg(Ag) l−1 and 28.1 mg(Ag) l−1 for Escherichia coli and Candida albicans respectively, which are comparable to the value for colloidal nanosilver.
Submicron-sized poly(N-isopropyl acrylamide)/polyethyleneimine core-shell microgels were prepared in aqueous media by using tert-butyl hydroperoxide (TBHP) as an initiator, and then the gold nanoparticles (∼8 nm) were formed on the surface of the microgels. The amino groups on the polyethyleneimine (PEI) chains act as the binder for the assembly of the gold nanoparticles/microgel complex. In aqueous media the microgels are highly stable with the gold nanoparticles on their extended PEI chains, and this multi-scale nanoparticle complex can be recovered from water and redispersed in water. The nanogold/microgel particles were conjugated with the enzymes horseradish peroxidase (HRP) and urease. It is found that under identical assay conditions the enzyme/nanogold/microgel systems exhibit enhanced biocatalytic activity over free enzymes in solution, especially at lower enzyme concentrations. In addition, compared to free HRP, the HRP/nanogold/microgel systems show higher activity at varied pHs and temperatures, as well as higher storage stability. Thus the novel nanogold/microgel particles can serve as an excellent support for enzymes.
Phase separation (PS) proteins form droplets to regulate myriad membraneless organelles (MLOs) and cellular pathways such as transcription, signaling transduction and protein degeneration. PS droplets are usually liquid-like and can convert to hydrogel/solid-like under certain conditions. The PS behavior of proteins is regulated by co-PS partners and mutations, modifications, oligomerizations, repeat regions and alternative splicing of the proteins. With growing interest in PS condensates and associated proteins, we established PhaSepDB 1.0, which provided experimentally verified PS proteins and MLO-related proteins. The past few years witnessed a surge in PS-related research works; thus, we kept updating PhaSepDB. The current PhaSepDB contains 1419 PS entries, 770 low-throughput MLO-related entries and 7303 high-throughput MLO-related entries. We provided more detailed annotations of PS proteins, including PS verification experiments, regions used in experiments, phase diagrams of different experimental conditions, droplet states, co-PS partners and PS regulatory information. We believe that researchers can go further in studying PS proteins with the updated PhaSepDB (http://db.phasep.pro/).
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