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1.
The calcium pump (sarco/endoplasmic reticulum Ca2+-ATPase, SERCA) plays a major role in calcium homeostasis in muscle cells by clearing cytosolic Ca2+ during muscle relaxation. Active Ca2+ transport by SERCA involves the structural transition from a low-Ca2+ affinity E2 state toward a high-Ca2+ affinity E1 state of the pump. This structural transition is accompanied by the countertransport of protons to stabilize the negative charge and maintain the structural integrity of the transport sites and partially compensate for the positive charges of the two Ca2+ ions passing through the membrane. X-ray crystallography studies have suggested that a hydrated pore located at the C-terminal domain of SERCA serves as a conduit for proton countertransport, but the existence and function of this pathway have not yet been fully characterized. We used atomistic simulations to demonstrate that in the protonated E2 state and the absence of initially bound water molecules, the C-terminal pore becomes hydrated in the nanosecond timescale. Hydration of the C-terminal pore is accompanied by the formation of water wires that connect the transport sites with the cytosol. Water wires are known as ubiquitous proton-transport devices in biological systems, thus supporting the notion that the C-terminal domain serves as a conduit for proton release. Additional simulations showed that the release of a single proton from the transport sites induces bending of transmembrane helix M5 and the interaction between residues Arg762 and Ser915. These structural changes create a physical barrier against full hydration of the pore and prevent the formation of hydrogen-bonded water wires once proton transport has occurred through this pore. Together, these findings support the notion that the C-terminal proton release pathway is a functional element of SERCA and also provide a mechanistic model for its operation in the catalytic cycle of the pump. 相似文献
2.
Shraddha Parate Vikas Kumar Danishuddin Jong Chan Hong Keun Woo Lee 《International journal of molecular sciences》2021,22(10)
Heparanase (Hpse) is an endo-β-D-glucuronidase capable of cleaving heparan sulfate side chains. Its upregulated expression is implicated in tumor growth, metastasis and angiogenesis, thus making it an attractive target in cancer therapeutics. Currently, a few small molecule inhibitors have been reported to inhibit Hpse, with promising oral administration and pharmacokinetic (PK) properties. In the present study, a ligand-based pharmacophore model was generated from a dataset of well-known active small molecule Hpse inhibitors which were observed to display favorable PK properties. The compounds from the InterBioScreen database of natural (69,034) and synthetic (195,469) molecules were first filtered for their drug-likeness and the pharmacophore model was used to screen the drug-like database. The compounds acquired from screening were subjected to molecular docking with Heparanase, where two molecules used in pharmacophore generation were used as reference. From the docking analysis, 33 compounds displayed higher docking scores than the reference and favorable interactions with the catalytic residues. Complex interactions were further evaluated by molecular dynamics simulations to assess their stability over a period of 50 ns. Furthermore, the binding free energies of the 33 compounds revealed 2 natural and 2 synthetic compounds, with better binding affinities than reference molecules, and were, therefore, deemed as hits. The hit compounds presented from this in silico investigation could act as potent Heparanase inhibitors and further serve as lead scaffolds to develop compounds targeting Heparanase upregulation in cancer. 相似文献
3.
Dr. Laurent David Dr. Mark Wenlock Dr. Patrick Barton Dr. Andreas Ritzén 《ChemMedChem》2021,16(17):2669-2685
Chameleonic properties, i. e., the capacity of a molecule to hide polarity in non-polar environments and expose it in water, help achieving sufficient permeability and solubility for drug molecules with high MW. We present models of experimental measures of polarity for a set of 24 FDA approved drugs (MW 405-1113) and one PROTAC (MW 1034). Conformational ensembles in aqueous and non-polar environments were generated using molecular dynamics. A linear regression model that predicts chromatographic apparent polarity (EPSA) with a mean unsigned error of 10 Å2 was derived based on separate terms for donor, acceptor, and total molecular SASA. A good correlation (R2=0.92) with an experimental measure of hydrogen bond donor potential, Δlog Poct-tol, was found for the mean hydrogen bond donor SASA of the conformational ensemble scaled with Abraham's A hydrogen bond acidity. Two quantitative measures of chameleonic behaviour, the chameleonic efficiency indices, are introduced. We envision that the methods presented herein will be useful to triage designed molecules and prioritize those with the best chance of achieving acceptable permeability and solubility. 相似文献
4.
5.
Tallison O. Abreu Roterdan F. Abreu Felipe F. do Carmo Wellington V. de Sousa Helenilson de O. Barros José E.V. de Morais João P.C. do Nascimento Marcelo A.S. da Silva Sergei Trukhanov Alex Trukhanov Larissa Panina Charanjeet Singh Antonio S.B. Sombra 《Ceramics International》2021,47(11):15424-15432
This work presents the dielectric properties of YNbO4 (YNO)–TiO2 composites in the microwave range. X-ray diffraction analysis demonstrates that the addition of TiO2 to YNO results in the formation of a Y(Nb0.5Ti0.5)2O6 phase. In the microwave range, the values of permittivity and dielectric loss did not present major changes with the increment of TiO2. Moreover, the addition of TiO2 results in an improvement in the thermal stability of YNO, with YNO63 demonstrating a resonant frequency of ?8.96 ppm.°C?1. We utilised numerical simulations to evaluate the behaviour of these materials as dielectric resonator antennae and it is found that they exhibit a reflection coefficient below ?10 dB at the resonant frequency, with a realised gain of 4.94 – 5.76 dBi, a bandwidth of 665–1050 MHz and a radiation efficiency above 84%. Our results indicate that YNO–TiO2 composites are interesting candidates for microwave operating devices. 相似文献
6.
The design of a liquid/liquid contact apparatus necessitates the knowledge of fluid dynamics and mass transfer in the dispersion. Prediction of process parameters is challenging due to swarm and interfacial effects. Single drop investigations are suitable to enable a sophisticated dimensioning based on few simple experiments combined with published theories and correlations. In the first part of this article, the fundamentals of fluid dynamics and mass transfer in absence of interfacial effects were explained. Here, an overview of relevant interfacial phenomena and the influence of different substances typically occurring in technical applications as impurities or accompanying components is given. 相似文献
7.
The weeping phenomenon was investigated using some experimental tests and a numerical model. The tests were performed within a 1.22‐m‐diameter pilot‐scale column including two chimney trays and two Nye test trays with an air‐water system. The rates of weeping were measured in the Nye trays with two heights of the weir and a hole area of 5 %. Moreover, the weeping rates in the outlet and inlet halves of the Nye tray and the total weeping rate were calculated. In the next step, an Eulerian‐Eulerian computational fluid dynamics (CFD) technique was used. The results show good agreement between the attained CFD findings and the experimental data. 相似文献
8.
《Ceramics International》2021,47(22):31886-31893
In this contribution, SnFe2O4 nanoparticles were prepared by the solvothermal method, the structural properties were performed using X-Ray Diffraction (DRX) to prove the success of tin ferrite formation and to determine de crystals parameters. The size and morphological study were build using Scanning Electron Microscopy (SEM) and Transmission Electron microscopy (TEM), the results showed that the size of particles is uniform with a range of particles (5–7 nm). The magnetic properties were carried out using the SQUID device, the SnFe2O4 nanoparticles have a magnetic transition at 750 K. In addition, the hysteresis loops at low temperature displayed Ms and Mr equals to 23 emu/g and 6 emu/g, respectively. The magnetoresistance properties were investigated, the SnFe2O4 nanoparticles present a large magnetoresistance effect (80%). The experimental results are supplemented by model calculations utilizing density functional theory and Monte-Carlo simulations. 相似文献
9.
平台支持船由于作业需要通常配备有动力定位系统,其在侧推工况下舱室噪声超标较为严重。针对这个问题采用计算流体力学(CFD)方法,得到侧推螺旋桨作用在导管上的脉动压力,并将时域计算结果转换成噪声计算的激励条件。采用有限元(FE)与统计能量分析(SEA)混合方法建立船体中频段FE-SEA耦合模型并建立船体高频段SEA模型,对某65 m AHTS船侧推工况下全频段(63 Hz~8000 Hz)舱室噪声进行预报,分析该船噪声分布规律及主要影响因素。并建立起全船的SEA模型,在中频段对比SEA与FE-SEA两种方法得到的舱室声压级频谱曲线,验证了使用混合模型的必要性。 相似文献
10.
N. Clament Sagaya Selvam Lijie Du Bao Yu Xia Pil J. Yoo Bo You 《Advanced functional materials》2021,31(12):2008190
Electroreduction of small molecules such as H2O, CO2, and N2 for producing clean fuels or valuable chemicals provides a sustainable approach to meet the increasing global energy demands and to alleviate the concern on climate change resulting from fossil fuel consumption. On the path to implement this purpose, however, several scientific hurdles remain, one of which is the low energy efficiency due to the sluggish kinetics of the paired oxygen evolution reaction (OER). In response, it is highly desirable to synthesize high-performance and cost-effective OER electrocatalysts. Recent advances have witnessed surface reconstruction engineering as a salient tool to significantly improve the catalytic performance of OER electrocatalysts. In this review, recent progress on the reconstructed OER electrocatalysts and future opportunities are discussed. A brief introduction of the fundamentals of OER and the experimental approaches for generating and characterizing the reconstructed active sites in OER nanocatalysts are given first, followed by an expanded discussion of recent advances on the reconstructed OER electrocatalysts with improved activities, with a particular emphasis on understanding the correlation between surface dynamics and activities. Finally, a prospect for clean future energy communities harnessing surface reconstruction-promoted electrochemical water oxidation will be provided. 相似文献