PMC-IZ: A Simple Algorithm for the Electrostatics Calculation in Slab Geometric Molecular Dynamics Simulations.

Slab geometric systems are widely utilized in molecular simulations. However, an efficient, straightforward, and accurate method for calculating electrostatic interactions in these systems for molecular dynamics (MD) simulations is still needed. This review introduces a PME-like approach called PMC-IZ, specifically designed for slab geometric systems. Traditional approaches for long-range electrostatic interaction calculations in slab geometry typically involve Ewald summation, where the Gaussian charge density is summed within 3D unit cells and then integrated in the 2D periodic space. In the proposed approach here, the Poisson equation was solved for a single Gaussian charge density within 2Dl periodic space, followed by convolution within 3D unit cells using an effective potential as the convolution kernel for summation. The effective potential ensures that the solution within the region of interest adheres strictly to 2D periodic boundary conditions while inherently possessing 3D periodic boundary condition properties. The PMC-IZ method provides for such systems accurate treatment of electrostatic interactions, overcomes limitations associated with finite vacuum layers, and offers improved computational efficiency. We thus postulate that this method provides a valuable tool for studying electrostatic interactions in slab geometric system MD simulations. It has promising applications in various areas such as surface science, catalysis, and materials research, where accurate modeling of slab geometric electrostatic interactions is essential.

Artificial Intelligence Enhanced Molecular Simulations.

Molecular simulations, which simulate the motions of particles according to fundamental laws of physics, have been applied to a wide range of fields from physics and materials science to biochemistry and drug discovery. Developed for computationally intensive applications, most molecular simulation software involves significant use of hard-coded derivatives and code reuse across various programming languages. In this Review, we first align the relationship between molecular simulations and artificial intelligence (AI) and reveal the coherence between the two. We then discuss how the AI platform can create new possibilities and deliver new solutions to molecular simulations, from the perspective of algorithms, programming paradigms, and even hardware. Rather than focusing solely on increasingly complex neural network models, we introduce various concepts and techniques brought about by modern AI and explore how they can be transacted to molecular simulations. To this end, we summarized several representative applications of molecular simulations enhanced by AI, including from differentiable programming and high-throughput simulations. Finally, we look ahead to promising directions that may help address existing issues in the current framework of AI-enhanced molecular simulations.

Investigating the Activation Mechanism Differences between Human and Mouse cGAS by Molecular Dynamics Simulations.

Cyclic GMP-AMP synthase (cGAS) has been widely investigated as a drug target for its crucial role in innate immunity. However, the inhibitors designed using mouse model were often shown to be ineffective for humans. This outcome indicates that the activation mechanisms of human and mouse cGAS (mcGAS) are different. The cGAS activation is achieved by dimerization via binding to DNA, the detailed mechanism of which, however, is not entirely clear. To investigate these mechanisms, molecular dynamics (MD) simulations were performed on several states of four types of cGAS, namely, the mcGAS, the wild-type and A- and C-type mutations of human cGAS (hcGAS). We find that sequence differences between hcGAS and mcGAS can directly affect the protein structure stability, especially that of the siteB domain. The sequence and structural differences also contribute to DNA-binding differences. In addition, the conformational fluctuations of cGAS are found to correlate with the regulation of catalytic capacity. More importantly, we illustrate that dimerization enhances the correlation among distant residues and significantly reinforces the allosteric signal transmission among the DNA-binding interfaces and the catalytic pocket, which facilitates rapid immune response to cytosolic DNA. We conclude that siteB domain plays a prominent role in mcGAS activation, while siteA domain is key to hcGAS activation.

Accelerating supramolecular aggregation by molecular sliding.

Diffusion-based translocation along DNA or RNA molecules is essential for genome regulatory proteins to execute their biological functions. The reduced dimensionality of the searching process makes the proteins bind specific target sites at a "faster-than-diffusion-controlled rate". We herein report a photoresponsive slider-track diffusion system capable of self-assembly rate acceleration, which consists of (-)-camphorsulfonic acid, 4-(4'-n-octoxylphenylazo)benzenesulfonic acid, and isotactic poly(2-vinylpyridine). The protonated pyridine rings act as the footholds for anionic azo sliders to diffusively bind and slide along polycationic tracks via electrostatic interactions. Ultraviolet light triggers the trans to cis isomerization and aggregation of azo sliders, which can be monitored by multiple spectroscopic methods without labeling. The presence of vinyl polymer track increases the aggregation rate of cis azobenzene up to ∼20 times, depending on the stereoregularity of the polymer chain, the acid/base ratio and the addition of salt. This system has a feature of simplicity, monitorability, controllability, and could find applications in designing molecular machines with desired functionalities.

Inhibitory effects of alpha-lipoic acid on oxidative stress in the rostral ventrolateral medulla in rats with salt-induced hypertension.

Oxidative stress in the rostral ventrolateral medulla (RVLM) plays an important role in the pathophysiology of hypertension. Alpha­lipoic acid (ALA) is widely recognized for its potent superoxide inhibitory properties, and it can safely penetrate deep into the brain. The aim of this study was to explore whether ALA supplementation attenuates hypertensive responses and cardiac hypertrophy by decreasing the NAD(P)H oxidase (NOX)-derived overproduction of reactive oxygen species (ROS) in the mitochondria in the RVLM, and thus attenuating the development of salt­induced hypertension. For this purpose, male Wistar rats were randomly divided into 2 groups and either fed a high-salt diet or not. After 8 weeks, the rats were either administered ALA or an equal volume of the vehicle for 8 weeks. The rats fed a high­salt diet exhibited higher mean arterial pressure (MAP) and higher plasma noradrenaline (NE) levels, as well as cardiac hypertrophy, as evidence by the increased whole heart weight/body weight (WHW/BW) ratio, WHW/tibia length (TL) ratio and left­ventricular weight (LVW)/TL ratio. Compared with the rats in the NS group, the rats in the HS group only exhibited increased levels of superoxide, NOX2, NOX4 and mitochondrial malondialdehyde (MDA), but also decreased levels of copper/zinc (Cu/Zn)-superoxide dismutase (SOD), mitochondrial SOD and glutathione (GSH) in the RVLM. The supplementation of ALA decreased MAP, plasma NE levels and the levels of cardiac hypertrophy indicators. It also decreased the levels of superoxide, NOX2, NOX4 and mitochondrial MDA, and increased the levels of Cu/Zn­SOD, mitochondrial SOD and GSH in the RVLM compared with the rats fed a high-salt diet and not treated with ALA. On the whole, our findings indicate that long­term ALA supplementation attenuates hypertensive responses and cardiac hypertrophy by decreasing the expression of NAD(P)H subunits (NOX2 and NOX4), increasing the levels of mitochondrial bioenergetic enzymes, and enhancing the intracellular antioxidant capacity in the RVLM during the development of hypertension.