The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2 . 相似文献
There is a critical need to evaluate lithium–sulfur (Li–S) batteries with practically relevant high sulfur loadings and minimal electrolyte. Under such conditions, the concentration of soluble polysulfide intermediates in the electrolyte drastically increases, which can alter the fundamental nature of the solution‐mediated discharge and thereby the total sulfur utilization. In this work, an investigation into various high donor number (DN) electrolytes that allow for increased polysulfide dissolution is presented, and the way in which this property may in fact be necessary for increasing sulfur utilization at low electrolyte and high loading conditions is demonstrated. The solvents dimethylacetamide, dimethyl sulfoxide, and 1‐methylimidazole are holistically evaluated against dimethoxyethane as electrolyte co‐solvents in Li–S cells, and they are used to investigate chemical and electrochemical properties of polysulfide species at both dilute and practically relevant conditions. The nature of speciation exhibited by lithium polysulfides is found to vary significantly between these concentrations, particularly with regard to the S3?? species. Furthermore, the extent of the instability in conventional electrolyte solvents and high DN solvents with both lithium metal and polysulfides is thoroughly investigated. These studies establish a basis for future efforts into rationally designing an optimal electrolyte for a lean electrolyte, high energy density Li–S battery. 相似文献
Bone morphogenetic protein-13 (BMP-13) plays an important role in skeletal development. In the light of a recent report that mutations in the BMP-13 gene are associated with spine vertebral fusion in Klippel-Feil syndrome, we hypothesized that BMP-13 signaling is crucial for regulating embryonic endochondral ossification. In this study, we found that BMP-13 inhibited the osteogenic differentiation of human bone marrow multipotent mesenchymal stromal cells (BM MSCs) in vitro. The endogenous BMP-13 gene expression in MSCs was examined under expansion conditions. The MSCs were then induced to differentiate into osteoblasts in osteo-inductive medium containing exogenous BMP-13. Gene expression was analysed by real-time PCR. Alkaline phosphatase (ALP) expression and activity, proteoglycan (PG) synthesis and matrix mineralization were assessed by cytological staining or ALP assay. Results showed that endogenous BMP-13 mRNA expression was higher than BMP-2 or -7 during MSC growth. BMP-13 supplementation strongly inhibited matrix mineralization and ALP activity of osteogenic differentiated MSCs, yet increased PG synthesis under the same conditions. In conclusion, BMP-13 inhibited osteogenic differentiation of MSCs, implying that functional mutations or deficiency of BMP-13 may allow excess bone formation. Our finding provides an insight into the molecular mechanisms and the therapeutic potential of BMP-13 in restricting pathological bone formation. 相似文献
Chronic back pain is a global health problem affecting millions of people worldwide and carries significant economic and social morbidities. Intervertebral disc damage and degeneration is a major cause of back pain, characterised by histological and biochemical changes that have been well documented in animal models. Recently there has been intense interest in early intervention in disc degeneration using growth factors or stem cell transplantation, to replenish the diseased tissues. Bone Morphogenetic Proteins (BMPs) have been approved for clinical use in augmenting spinal fusions, and may represent candidate molecules for intervertebral disc regeneration. 相似文献
The key to understanding the evolutionary origin and modification of phenotypic traits is revealing the responsible underlying developmental genetic mechanisms. An important organismal trait of ray‐finned fishes is the gas bladder, an air‐filled organ that, in most fishes, functions for buoyancy control, and is homologous to the lungs of lobe‐finned fishes. The critical morphological difference between lungs and gas bladders, which otherwise share many characteristics, is the general direction of budding during development. Lungs bud ventrally and the gas bladder buds dorsally from the anterior foregut. We investigated the genetic underpinnings of this ventral‐to‐dorsal shift in budding direction by studying the expression patterns of known lung genes (Nkx2.1, Sox2, and Bmp4) during the development of lungs or gas bladder in three fishes: bichir, bowfin, and zebrafish. Nkx2.1 and Sox2 show reciprocal dorsoventral expression patterns during tetrapod lung development and are important regulators of lung budding; their expression during bichir lung development is conserved. Surprisingly, we find during gas bladder development, Nkx2.1 and Sox2 expression are inconsistent with the hypothesis that they regulate the direction of gas bladder budding. Bmp4 is expressed ventrally during lung development in bichir, akin to the pattern during mouse lung development. During gas bladder development, Bmp4 is not expressed. However, Bmp16, a paralogue of Bmp4, is expressed dorsally in the developing gas bladder of bowfin. Bmp16 is present in the known genomes of Actinopteri (ray‐finned fishes excluding bichir) but absent from mammalian genomes. We hypothesize that Bmp16 was recruited to regulate gas bladder development in the Actinopteri in place of Bmp4. 相似文献
This paper presents a simple multi-band metamaterial absorber for terahertz applications. The unit cell of the proposed structure consists of a single square ring having gaps at the centers on three of its sides. The proposed absorber produces three absorption bands for all polarizations and hence the design can be considered as insensitive to polarization variation. It provides an average absorption of 96.92% for the TE polarization with a peak absorption of 99.44% at 3.87 THz and for the TM polarization, it provides an average absorption of 98.4% with a peak absorption of 99.86% at 3.87 THz. An additional absorption peak is observed for the TE polarization at 1.055 THz that gradually diminishes with the increase in polarization angle and completely vanishes for the TM polarization. Thus, the structure displays a hybrid polarization response with polarization insensitivity in three bands and polarization sensitivity in one band. Parametric analysis has been carried out validating the optimal selection of the design parameters. The simplicity of the design and its combined polarization sensitive and polarization insensitive absorption characteristics can find tremendous applications in the field of terahertz imaging and sensing.
A focused library of rhodanine compounds containing novel substituents at the C5-position was synthesized and tested in vitro against a panel of clinically relevant MRSA strains. The present SAR study was based on our lead compound 1 (MIC = 1.95 μg/mL), with a focus on identifying optimal C5-arylidene substituents. In order to obtain this objective, we condensed several unique aromatic aldehydes with phenylalanine-derived rhodanine intermediates to obtain C5-substituted target rhodanine compounds for evaluation as anti-MRSA compounds. These efforts produced three compounds with significant efficacy: 23, 32 and 44, with MIC values ranging from 0.98 to 1.95 μg/mL against all tested MRSA strains as compared to the reference antibiotics penicillin G (MIC = 15.60–250.0 μg/mL) and ciprofloxacin (MIC = 7.80–62.50 μg/mL) and comparable to that of vancomycin (MIC = 0.48 μg/mL). In addition, compounds 24, 28, 37, 41, 46 and 48 (MIC = 1.95–3.90 μg/mL) were efficacious against all MRSA strains. The majority of the synthesized compounds had bactericidal activity at concentrations only two to fourfold higher than their MIC. Overall, the results suggest that compounds 23, 32 and 44 may be of potential use in the treatment of MRSA infections. 相似文献
Plasmonics - In recent years, novel terahertz (THz) metamaterial sensors are being actively explored by the research community. These structures absorb the incident THz waves, and their absorption... 相似文献
Apicomplexan parasites, such as the malaria-causing Plasmodium species, utilize a unique way of locomotion and host cell invasion. This substrate-dependent gliding motility requires rapid cycling of actin between the monomeric state and very short, unbranched filaments. Despite the crucial role of actin polymerization for the survival of the malaria parasite, the majority of Plasmodium cellular actin is present in the monomeric form. Plasmodium lacks most of the canonical actin nucleators, and formins are essentially the only candidates for this function in all Apicomplexa. The malaria parasite has two formins, containing conserved formin homology (FH) 2 and rudimentary FH1 domains. Here, we show that Plasmodium falciparum formin 1 associates with and nucleates both mammalian and Plasmodium actin filaments. Although Plasmodium profilin alone sequesters actin monomers, thus inhibiting polymerization, its monomer-sequestering activity does not compete with the nucleating activity of formin 1 at an equimolar profilin-actin ratio. We have determined solution structures of P. falciparum formin 1 FH2 domain both in the presence and absence of the lasso segment and the FH1 domain, and show that the lasso is required for the assembly of functional dimers. 相似文献