Structural Basis for the Function of the C-Terminal Proton Release Pathway in the Calcium Pump

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.     

Computational Investigation Identified Potential Chemical Scaffolds for Heparanase as Anticancer Therapeutics

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.     

Prediction of Chameleonic Efficiency

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 Ų 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 P_oct-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.     

Tropfenbewegung und Stofftransport in technischen Flüssig/flüssig-Systemen. Teil 2: Auswirkung von Grenzflächeneffekten und Verunreinigungen

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.     

Computational Fluid Dynamics versus Experiment: An Investigation on Liquid Weeping of Nye Trays

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.     

FE-SEA方法在平台支持船噪声预报中的应用

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。     

Reconstructed Water Oxidation Electrocatalysts: The Impact of Surface Dynamics on Intrinsic Activities

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.     

Free energy of conformational change in a single chain of polyvinylidene fluoride using molecular simulations

Polyvinylidene fluoride (PVDF) has several crystal forms of which the α-form is nonpolar, while the β-form is polar and has the highest piezoelectric constant. α PVDF, when stretched, transforms into the β form, which has wide applications in sensors and actuators. Steered molecular dynamics simulations are used to study the transformation of a single chain of PVDF from a trans–gauche conformation to an all trans one. The Helmholtz free energy change (∆F) is estimated using Jarzynski's equality. The transformation starts at the chain ends followed by the transformation of the remaining chain. The free energy change for the transformation is found to be always positive, indicating that the TGTG' form has higher thermodynamic stability than the all trans form throughout the studied temperature range. With increasing temperature, free energy change for the transformation increases monotonically.     

Mitochondrial and Autophagic Regulation of Adult Neurogenesis in the Healthy and Diseased Brain

Adult neurogenesis is a highly regulated process during which new neurons are generated from neural stem cells in two discrete regions of the adult brain: the subventricular zone of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Defects of adult hippocampal neurogenesis have been linked to cognitive decline and dysfunction during natural aging and in neurodegenerative diseases, as well as psychological stress-induced mood disorders. Understanding the mechanisms and pathways that regulate adult neurogenesis is crucial to improving preventative measures and therapies for these conditions. Accumulating evidence shows that mitochondria directly regulate various steps and phases of adult neurogenesis. This review summarizes recent findings on how mitochondrial metabolism, dynamics, and reactive oxygen species control several aspects of adult neural stem cell function and their differentiation to newborn neurons. It also discusses the importance of autophagy for adult neurogenesis, and how mitochondrial and autophagic dysfunction may contribute to cognitive defects and stress-induced mood disorders by compromising adult neurogenesis. Finally, I suggest possible ways to target mitochondrial function as a strategy for stem cell-based interventions and treatments for cognitive and mood disorders.     

Mechanical Properties of Single-Layer Diamond Reinforced Poly(vinyl alcohol) Nanocomposites through Atomistic Simulation

Low-dimensional carbon nanostructures are ideal nanofillers to reinforce the mechanical performance of polymer nanocomposites due to their excellent mechanical properties. Through molecular dynamics simulations, the mechanical performance of poly(vinyl alchohol) (PVA) nanocomposites reinforced with a single-layer diamond – diamane is investigated. It is found the PVA/diamane exhibits similar interfacial strengths and pull-out characteristics with the PVA/bilayer-graphene counterpart. Specifically, when the nanofiller is fully embedded in the nanocomposite, it is unable to deform simultaneously with the PVA matrix due to the weak interfacial load transfer efficiency, thus the enhancement effect is not significant. In comparison, diamane can effectively promote the tensile properties of the nanocomposite when it has a laminated structure as it deforms simultaneously with the matrix. With this configuration, the interlayer sp³ bonds endows diamane with a much higher resistance under compression and shear tests, thus the nanocomposite can reach very high compressive and shear stress. Overall, enhancement on the mechanical interlocking at the interface as triggered by surface functionalization is only effective for the fully embedded nanofiller. This work provides a fundamental understanding of the mechanical properties of PVA nanocomposites reinforced by diamane, which can shed lights on the design and preparation of next generation high-performance nanocomposites.