Cell-specific polymerization-driven biomolecular condensate formation fine-tunes root tissue morphogenesis.

Formation of biomolecular condensates can be driven by weak multivalent interactions and emergent polymerization. However, the mechanism of polymerization-mediated condensate formation is less studied. We found lateral root cap cell (LRC)-specific SUPPRESSOR OF RPS4-RLD1 (SRFR1) condensates fine-tune primary root development. Polymerization of the SRFR1 N-terminal domain is required for both LRC condensate formation and optimal root growth. Surprisingly, the first intrinsically disordered region (IDR1) of SRFR1 can be functionally substituted by a specific group of intrinsically disordered proteins known as dehydrins. This finding facilitated the identification of functional segments in the IDR1 of SRFR1, a generalizable strategy to decode unknown IDRs. With this functional information we further improved root growth by modifying the SRFR1 condensation module, providing a strategy to improve plant growth and resilience.

In situ rapid synthesis of ionic liquid/ionic covalent organic framework composites for CO2 fixation.

IL/ICOF composites were in situ synthesized via a one-pot route in half an hour under ambient conditions for catalytic cycloaddition of CO2 with epoxides into cyclic carbonates. The prepared composites feature a decent CO2 adsorption capacity of 1.63 mmol g-1 at 273 K and 1 bar and exhibit excellent catalytic performance in terms of yield and durability. This work may pave a new way to design and construct functionalized porous organic frameworks as heterogeneous catalysts for CO2 capture and conversion.

Unique fluorophilic pores engineering within porous aromatic frameworks for trace perfluorooctanoic acid removal.

Perfluorooctanoic acid (PFOA), a representative of per/polyfluorinated alkyl substances, has become a persistent water pollutant of widespread concern due to its biological toxicity and refractory property. In this work, we design and synthesize two porous aromatic frameworks (PAF) of PAF-CF3 and PAF-C2F5 using fluorine-containing alkyl based monomers in tetrahedral geometry. Both PAFs exhibit nanosized pores (∼1.0 nm) of high surface areas (over 800 m2 g-1) and good fluorophilicity. Remarkable adsorption capacity (˃740 mg g-1) and superior efficiency (˃24 g mg-1 h-1) are achieved toward the removal of PFOA with 1 µg L-1 concentration owing to unique C-F···F-C interactions. In particular, PAF-CF3 and PAF-C2F5 are able to reduce the PFOA concentration in water to 37.9 ng L-1 and 43.3 ng L-1, below EPA regulations (70 ng L-1). The reusability and high efficiency give both PAFs a great potential for sewage treatment.

Template-guided method for protein-ligand complex structure prediction: Application to CASP15 protein-ligand studies.

Critical Assessment of Structure Prediction 15 (CASP15) added a new category of ligand prediction to promote the development of protein/RNA-ligand modeling methods, which have become important tools in modern drug discovery. A total of 22 targets were released, including 18 protein-ligand targets and 4 RNA-ligand targets. We applied our recently developed template-guided method to the protein-ligand complex structure predictions. The method combined a physicochemical, molecular docking method, and a bioinformatics-based ligand similarity method. The Protein Data Bank was scanned for template structures containing the target protein, homologous proteins, or proteins sharing a similar fold with the target protein. The binding modes of the co-bound ligands in the template structures were used to guide the complex structure prediction for the target. The CASP assessment results show that the overall performance of our method was ranked second when the top predicted model was considered for each target. Here, we analyzed our predictions in detail, and discussed the challenges including protein conformational changes, large and flexible ligands, and multiple diverse ligands in a binding pocket.

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.

Highly stable Ru-complex-based metal-covalent organic frameworks as novel type of electrochemiluminescence emitters for ultrasensitive biosensing.

Developing novel types of high-performance electrochemiluminescence (ECL) emitters is of great significance for constructing ultrasensitive ECL sensors. Herein, a highly stable metal-covalent organic framework (MCOF), termed Ru-MCOF, has been devised and synthesized by employing a classic ECL luminophore, tris(4,4'-dicarboxylicacid-2,2'-bipyridyl)ruthenium(II) (Ru(dcbpy)32+), as building unit and applied as a novel ECL probe to construct an ultrasensitive ECL sensor for the first time. Impressively, the topologically ordered and porous architectures of the Ru-MCOF not only allow Ru(bpy)32+ units to precisely locate and homogeneously distribute in the skeleton via strong covalent bonds but also facilitate the transport of co-reactants and electrons/ions in channels to promote the electrochemical activation of both external and internal Ru(bpy)32+ units. All these features endow the Ru-MCOF with excellent ECL emission, high ECL efficiency, and outstanding chemical stability. As expected, the constructed ECL biosensor based on the Ru-MCOF as a high-efficiency ECL probe accomplishes the ultrasensitive detection of microRNA-155. Overall, the synthesized Ru-MCOF not only enriches the MCOF family but also displays excellent ECL performance and thus expands the application of MCOFs in bioassays. Considering the structural diversity and tailorability of MCOFs, this work opens a new horizon to design and synthesize high-performance ECL emitters, therefore paving a new way to develop highly stable and ultrasensitive ECL sensors and motivating further research on MCOFs.

Ginkgo biloba extract attenuates cisplatin-induced renal interstitial fibrosis by inhibiting the activation of renal fibroblasts through down-regulating the HIF-1α/STAT3/IL-6 pathway in renal tubular epithelial cells.

BACKGROUND: Activation of renal fibroblasts into myofibroblasts plays an important role in promoting renal interstitial fibrosis (RIF). Ginkgo biloba extract (EGb) can alleviate RIF induced by cisplatin (CDDP). PURPOSE: To elucidate the effect of EGb treatment on cisplatin-induced RIF and reveal its potential mechanism. METHODS: The two main active components in EGb were determined by high-performance liquid chromatography (HPLC) analysis. Rats were induced by CDDP and then treated with EGb, 2ME2 (HIF-1α inhibitor) or amifostine. After HK-2 cells and HIF-1α siRNA HK-2 cells were treated with CDDP, EGb or amifostine, the conditioned medium from each group was cultured with NRK-49F cells. The renal function of rats was detected. The renal damage and fibrosis were evaluated by H&E and Masson trichrome staining. The IL-6 content in the cell medium was detected by ELISA. The expression levels of indicators related to renal fibrosis and signaling pathway were examined by western blotting and qRT-PCR. RESULTS: HPLC analysis showed that the contents of quercetin and kaempferol in EGb were 36.0 µg/ml and 45.7 µg/ml, respectively. In vivo, EGb and 2ME2 alleviated renal damage and fibrosis, as well as significantly decreased the levels of α-SMA, HIF-1α, STAT3 and IL-6 in rat tissues induced by CDDP. In vitro, the levels of HIF-1α, STAT3 and IL-6 were significantly increased in HK-2 cells and HIF-1α siRNA HK-2 cells induced by CDDP. Notably, HIF-1α siRNA significantly decreased the levels of HIF-1α, STAT3 and IL-6 in HK-2 cells, as well as the IL-6 level in medium from HK-2 cells. Additionally, the α-SMA level in NRK-49F cells was significantly increased after being cultured with conditioned medium from HK-2 cells or HIF-1α siRNA HK-2 cells exposed to CDDP. Furthermore, exogenous IL-6 increased the α-SMA level in NRK-49F cells. Importantly, the expression levels of the above-mentioned indicators were significantly decreased after the HK-2 cells and HIF-1α siRNA HK-2 cells were treated with EGb. CONCLUSION: This study revealed that EGb improves CDDP-induced RIF, and the mechanism may be related to its inhibition of the renal fibroblast activation by down-regulating the HIF-1α/STAT3/IL-6 pathway in renal tubular epithelial cells.

A Bipyridyl Covalent Organic Framework with Coordinated Cu(I) for Membrane C3 H6 /C3 H8 Separation.

Covalent organic frameworks (COFs) mixed matrix membranes (MMMs) combining individual attributes of COFs and polymers are promising for gas separation. However, applying COF MMMs for propylene/propane (C3 H6 /C3 H8 ) separation remains a big challenge due to COF inert pores and C3 H6 /C3 H8 similar molecular sizes. Herein, the designed synthesis of a Cu(I) coordinated COF for membrane C3 H6 /C3 H8 separation is reported. A platform COF is synthesized from 5,5'-diamino-2,2'-bipyridine and 2-hydroxybenzene-1,3,5-tricarbaldehyde. This COF possesses a porous 2D structure with high crystallinity. Cu(I) is coordinated to bipyridyl moieties in the COF framework, acting as recognizable sites for C3 H6 gas, as shown by the adsorption measurements. Cu(I) COF is blended with 6FDA-DAM polymer to yield MMMs. This COF MMM exhibits selective and permeable separation of C3 H6 from C3 H8 (C3 H6 permeability of 44.7 barrer, C3 H6 /C3 H8 selectivity of 28.1). The high porosity and Cu(I) species contribute to the great improvement of separation performance by virtue of 2.3-fold increase in permeability and 2.2-fold increase in selectivity compared to pure 6FDA-DAM. The superior performance to those of most relevant reported MMMs demonstrates that the Cu(I) coordinated COF is an excellent candidate material for C3 H6 separation membranes.

An ultrastable La-MOF for catalytic hydrogen transfer of furfural: in situ activation of the surface.

The poor stability of metal-organic frameworks (MOFs) severely limits their catalytic application. The in situ activation of stable MOF catalysts not only simplifies the catalytic process, but also reduces energy consumption. Therefore, it is meaningful to explore the in situ activation of the MOF surface in the actual reaction process. In this paper, a novel rare-earth MOF La2(QS)3(DMF)3 (LaQS) was synthesized, which exhibited ultra-high stability not only in organic solvents but also in aqueous solutions. When LaQS was used as a catalyst for the catalytic hydrogen transfer (CHT) of furfural (FF) to furfuryl alcohol (FOL), the FF conversion and FOL selectivity reached 97.8% and 92.1%, respectively. Meanwhile, the high stability of LaQS ensures an enhanced catalytic cycling performance. The excellent catalytic performance is mainly attributed to the acid-base synergistic catalysis of LaQS. More importantly, it has been confirmed by control experiments and DFT calculation that the in situ activation in catalytic reactions leads to the formation of acidic sites in LaQS, together with the uncoordinated oxygen atoms of sulfonic acid groups in LaQS as Lewis bases, which can synergistically activate FF and isopropanol. Finally, the mechanism of in situ activation-caused acid-base synergistic catalysis of FF is speculated. This work provides meaningful enlightenment for the study of the catalytic reaction path of stable MOFs.

Physicochemical and Functional Changes in Lotus Root Polysaccharide Associated with Noncovalent Binding of Polyphenols.

To promote the functional applications of lotus root polysaccharides (LRPs), the effects of noncovalent polyphenol binding on their physicochemical properties, as well as antioxidant and immunomodulatory activities, were investigated. Ferulic acid (FA) and chlorogenic acid (CHA) were spontaneously bound to the LRP to prepare the complexes LRP-FA1, LRP-FA2, LRP-FA3, LRP-CHA1, LRP-CHA2 and LRP-CHA3, and their mass ratios of polyphenol to LRP were, respectively, 121.57, 61.18, 34.79, 2359.58, 1276.71 and 545.08 mg/g. Using the physical mixture of the LRP and polyphenols as a control, the noncovalent interaction between them in the complexes was confirmed by ultraviolet and Fourier-transform infrared spectroscopy. The interaction increased their average molecular weights by 1.11~2.27 times compared to the LRP. The polyphenols enhanced the antioxidant capacity and macrophage-stimulating activity of the LRP depending on their binding amount. Particularly, the DPPH radical scavenging activity and FRAP antioxidant ability were positively related to the FA binding amount but negatively related to the CHA binding amount. The NO production of the macrophages stimulated by the LRP was inhibited by the co-incubation with free polyphenols; however, the inhibition was eliminated by the noncovalent binding. The complexes could stimulate the NO production and tumor necrosis factor-α secretion more effectively than the LRP. The noncovalent binding of polyphenols may be an innovative strategy for the structural and functional modification of natural polysaccharides.

Cryo-EM structure of adeno-associated virus 4 at 2.2†Šresolution.

Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruses interact exclusively with the polycystic kidney disease-like 1 (PKD1) domain of AAVR, while most other AAVs interact primarily with the PKD2 domain. A comparison of the present AAV4 structure with prior corresponding structures of AAV5, AAV2 and AAV1 in complex with AAVR provides a foundation for understanding why the AAV4-like clade is unable to interact with either PKD1 or PKD2 of AAVR. The conformation of the AAV4 capsid in variable regions I, III, IV and V on the viral surface appears to be sufficiently different from AAV2 to ablate binding with PKD2. Differences between AAV4 and AAV5 in variable region VII appear to be sufficient to exclude binding with PKD1.

Purification, Characterization and Bioactivity of Different Molecular-Weight Fractions of Polysaccharide Extracted from Litchi Pulp.

Litchi polysaccharides are a kind of macromolecular polymers with various biological activities and a wide range of molecular weights. In this study, two separate fractions, with average molecular weights of 378.67 kDa (67.33%) and 16.96 kDa (6.95%), which were referred to as LP1 and LP2, respectively, were separated using an ultrafiltration membrane. Their physicochemical properties, and immunomodulatory and prebiotic activity were compared. The results revealed that LP2 contained more neutral sugar, arabinose, galactose and rhamnose, but less uronic acid, protein, mannose and glucose than LP1. Compared with LP1, LP2 possessed higher solubility and lower apparent viscosity. LP2 exhibited stronger stimulation on macrophage secretion of NO, TNF-α and IL-6, as well as better proliferation of Lactobacillus plantarum, Leuconostoc mesenteroides, Lactobacillus casei and Bifidobacterium adolescentis. These results suggest that an ultrafiltration membrane might be used to prepare a highly-active polysaccharide fraction from litchi pulp that may be used for food or drug development.

Ultramicroporous Covalent Organic Framework Nanosheets with Functionality Pair for Membrane C2 H2 /C2 H4 Separation.

Gas separation efficiency of covalent organic framework (COF) membrane can be greatly elevated through precise functionalization. A pair-functionalized COF membrane of 1,3,5-triformylphloroglucinol (TP) and isoquinoline-5,8-diamine (IQD) monomers in two and three nodes is designed and synthesized. TP-IQD is crystallized in a two-dimensional structure with a pore size of 6.5 Šand a surface area of 289 m2 g-1 . This COF possesses N-O paired groups which cooperatively interact with C2 H2 instead of C2 H4 . TP-IQD nanosheets of ≈10 µm in width and ≈4 nm in thickness are prepared by mechanical exfoliation; they are further processed with 6FDA-ODA polymer into a hybrid membrane. High porosity and functionality pair of TP-IQD offer the membrane with significantly increased C2 H2 permeability and C2 H2 /C2 H4 selectivity which are 160 % and 430 % higher of pure 6FDA-ODA. The boosted performance demonstrates high efficiency of the pair-functionality strategy for the synthesis of separation-led COFs.

Computational Modeling of IN-CTD/TAR Complex to Elucidate Additional Strategies to Inhibit HIV-1 Replication.

HIV-1 integrase (IN) is a key enzyme that is essential for mediating the insertion of retroviral DNA into the host chromosome. IN also exhibits additional functions which are not fully elucidated, including its ability to bind to viral genomic RNA. Lack of binding of IN to RNA within the virions has been shown to be associated with production of morphologically defective virus particles. However, the exact structure of HIV-1 IN bound to RNA is not known. Based on the studies that C-terminal domain (CTD) of IN binds to TAR RNA region and based on the observation that TAR and the host factor INI1 binding to IN-CTD are identical, we computationally modelled the IN-CTD/TAR complex structure. Computational modeling of nucleic acid binding to proteins is a valuable method to understand the macromolecular interaction when experimental methods of solving the complex structures are not feasible. The current model of the IN-CTD/TAR complex may facilitate further understanding of this interaction and may lead to therapeutic targeting of IN-CTD/RNA interactions to inhibit HIV-1 replication.

Fine-Tuned Ultra-Microporous Metal-Organic Framework in Mixed-Matrix Membrane: Pore-Tailoring Optimization for C2 H2 /C2 H4 Separation.

Effective separation of ethyne from ethyne/ethylene (C2 H2 /C2 H4 ) mixtures is a challenging and crucial industrial process. Herein, an ultra-microporous metal-organic framework (MOF) platform, Cd(dicarboxylate)2 (ditriazole), with triangular channels is proposed for high-efficiency separation of C2 H2 from C2 H4 . The targeted structures are constructed via a mixed-ligand strategy by selecting different-sized ligands, allowing for tunable pore sizes and volumes. The pore properties can be further optimized by additional modification via pore environment tailoring. This concept leads to the successful synthesis of three ultra-microporous Cd-MOFs (JLU-MOF87-89). As intended, C2 H2 uptake and C2 H2 /C2 H4 selectivity gradually increase with progressively optimizing the pore structure by adjusting ligand length and substituents. JLU-MOF89, functionalized with methyl groups, features the most optimal pore chemistry and shows selective recognition of C2 H2 over C2 H4 , owing to the framework-C2 H2 host-guest interactions. Furthermore, JLU-MOFs are fabricated into mixed-matrix membranes for C2 H2 /C2 H4 separation. C2 H2 permeability and C2 H2 /C2 H4 permselectivity are substantially enhanced by ≥400% and ≥200%, respectively, after hybridization of JLU-MOF88 and JLU-MOF89 with a polyimide polymer (6FDA-ODA). These membranes can work efficiently and are stable under different conditions, demonstrating their potential in actual ethyne separation.

An allosteric modulator activates BK channels by perturbing coupling between Ca2+ binding and pore opening.

BK type Ca2+-activated K+ channels activate in response to both voltage and Ca2+. The membrane-spanning voltage sensor domain (VSD) activation and Ca2+ binding to the cytosolic tail domain (CTD) open the pore across the membrane, but the mechanisms that couple VSD activation and Ca2+ binding to pore opening  are not clear. Here we show that a compound, BC5, identified from in silico screening, interacts with the CTD-VSD interface and specifically modulates the Ca2+ dependent activation mechanism. BC5 activates the channel in the absence of Ca2+ binding but Ca2+ binding inhibits BC5 effects. Thus, BC5 perturbs a pathway that couples Ca2+ binding to pore opening to allosterically affect both, which is further supported by atomistic simulations and mutagenesis. The results suggest that the CTD-VSD interaction makes a major contribution to the mechanism of Ca2+ dependent activation and is an important site for allosteric agonists to modulate BK channel activation.

Tailoring the pore chemistry in porous aromatic frameworks for selective separation of acetylene from ethylene.

The separation of acetylene from ethylene is a crucial process in the petrochemical industry, because even traces of acetylene impurities can poison the catalysts of ethylene polymerization. Herein, we synthesize a new family of 3D porous aromatic frameworks (PAFs), non-functionalized PAF-28, carbene-functionalized PAF-28 (cPAF-28) and imidazolium-functionalized PAF-28 (iPAF-28), via Sonogashira coupling reactions. These PAFs show high porosity and good thermal stability. Both cPAF-28 and iPAF-28 are proved to be good candidates for C2H2 adsorption, demonstrated by C2H2/C2H4 selectivity of 12.2 and 15.4, and C2H2 capacity of 48 cm3 g-1 and 57 cm3 g-1, which are significantly higher than those of non-functionalized PAF-28 (1.8, 37 cm3 g-1). Furthermore, the cPAF-28 and iPAF-28 display good breakthrough performance and remarkable recyclability for the separation of the C2H2/C2H4 gas mixture. In addition, the C2H2/C2H4 adsorption sites are revealed by DFT calculations. This work sheds a new light on gas molecular recognition by tailoring the pore chemistry of PAFs.

Physicochemical properties and prebiotic activities of polysaccharides from Zizyphus jujube based on different extraction techniques.

Zizyphus jujube polysaccharide was extracted with hot water, ultrahigh pressure, deep eutectic solvent (DES) and ultrahigh pressure-assisted DES. Comparative analyses were conducted on the yield, physicochemical properties and prebiotic activity of four polysaccharides (JP-H, JP-U, JP-D and JP-UD). The yield of JP-UD (10.42 %) was 3.3 times that of JP-H (3.12 %), and its sugar content was the highest. JP-UD possessed the lowest Mw, while JP-H possessed the highest. Four JPs were acidic pyranose and mainly composed of galacturonic acid, arabinose and galactose. NMR results demonstrated that they contained not only similar glycosidic linkage but also the specific glycosidic linkage of →4)-α-D-Glcp-(l→ appeared in JP-U and JP-UD, the esterified units of GalA and CONH2 group appeared in JP-D and JP-UD, and the Terminal ß-D-Galp and →4)-α-GalpA-(1→ appeared in JP-UD. JPs showed different proliferation effects on four lactobacillus strains, among which JP-UD exhibited the strongest prebiotic activity. Zizyphus jujube polysaccharides have great potential for application in the functional food and medical industry.