Genetic Algorithm Workflow for Parameterization of a Water Model Using the Vashishta Force Field

Water participates in countless processes on Earth, and the properties of mineral surfaces can be drastically changed in the presence of water. For example, the fracture toughness of silica glass is reduced by 25% for water-filled cracks than for dry cracks [Geophys. Res.: Solid Earth 2018, 123, 9341-9354]. An accurate description of water is therefore essential for modeling the behavior of minerals in aqueous environments and, in particular, for modeling dynamic processes such as fracture, where the mechanical response of water may play an important role. On the molecular scale, molecular dynamics simulations with empirical force field methods provide a way to study large molecular systems at a relatively low computational cost. Many water models have been developed previously; however, a computationally cheap water model capable of describing reactions with minerals is lacking. Here, we present a parametrization of the water potential using the Vashishta potential form [Phys. Rev. B 1990, 41, 12197-12209]. For this 3-point water model, we obtain good agreement with experimental transport and liquid-vapor properties. Importantly, the Vashishta form opens up compatibility with existing silica glass models, thus enabling the simulation of mineral-water interactions.

Modelling bulk and surface characteristics of cubic CeO2, Gd2O3, and gadolinium-doped ceria using a partial charge framework

The development and characterization of materials for solid oxide fuel cells (SOFC) is an important step towards sustainable energy technologies. This present study models cubic CeO2, Gd2O3, and gadolinium-doped ceria (GDC) using newly constructed interaction potentials based on a partial atom charge framework. The interaction model was validated by comparing the structural properties with experimental reference data, which were found to be in good agreement. Validation of the potential model was conducted considering the surface stability of CeO2 and Gd2O3. Additionally, the accuracy of the novel potential model was assessed by comparing the oxygen diffusion coefficient in GDCn (n = 4-15) and the associated activation energy. The results demonstrate that the novel potential model is capable of describing the oxygen diffusion in GDC. In addition, this study compares the vibrational properties of the bulk with density functional theory (DFT) calculations, using a harmonic frequency analysis that avoids the need for computationally expensive quantum mechanical molecular dynamics (QM MD) simulations. The potential is compatible with a reactive water model, thus providing a framework for the simulation of solid-liquid interfaces.

Pyruvate kinase deficiency and PKLR gene mutations: Insights from molecular dynamics simulation analysis

Pyruvate kinase deficiency is a rare hereditary erythrocyte enzyme disease caused by mutations in the pyruvate kinase liver and red blood cell gene. The clinical presentations of pyruvate kinase deficiency are significantly heterogeneous, ranging from just mild anemia to hemolytic crisis or even death. The proband in our study was a 2-year-old girl for severe skin and scleral icterus with progressive aggravation. We collected the family's data for further analysis. Whole exome genome sequencing of the pedigree revealed a novel compound heterozygous mutation, c.1097del (p.P366Lfs*12) and c.1493G > A (p.R498H), in the pyruvate kinase liver and red blood cell gene. Furthermore, molecular dynamics simulations were employed to uncover differences between the wild type and mutant pyruvate kinase liver and red blood cell proteins, focusing on structural stability, protein flexibility, secondary structure, and overall conformation. The combined bioinformatic tools were also utilised to assess the effects of the missense mutation on protein function. Thereafter, wild type and mutant plasmids were constructed and transfected into 293T cells, and Western blot assay was conducted to validate the impact of the mutations on the expression of pyruvate kinase liver and red blood cell protein. The data presented in our study enriches the genotype database and provides evidence for genetic counseling and molecular diagnosis of pyruvate kinase deficiency.

Network pharmacology analysis combined with experimental validation to explore the therapeutic mechanism of salidroside on intestine ischemia reperfusion

ETHNOPHARMACOLOGICAL RELEVANCE

Salidroside (SAL), a phenolic natural product present in Rhodiola rosea, are commonly used in the treatment of various ischemic-hypoxic diseases, including intestinal ischemia-reperfusion (IR) injury. However, their efficacy and potential mechanisms in the treatment of intestinal IR injury have not been investigated.

OBJECTIVE

The objective of the present study is to investigate the pharmacological mechanism of action of SAL on intestinal IR injury using a network pharmacology approach combined with experimental validation.

METHODS

In the present study, we used the Traditional Chinese Medicine Systematic Pharmacology (TCMSP) database and analysis platform and Comparative Toxicogenomics Database (CTD) to predict possible target genes of SAL, collected relevant target genes of intestinal IR injury from GeneCards and DisGenet websites, and collected summary data to screen common target genes. Then, the protein-protein interaction (PPI) target network was constructed and analyzed by STRING database and Cytoscape 3.8.2 with the above intersecting genes. Then, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed and the component-target-pathway network was constructed, followed by the use of molecular docking and molecular dynamic simulation to verify the possible binding conformation between SAL and candidate targets to further explore the potential targets of SAL in the treatment of intestinal IR injury. Finally, an in vivo model of mouse superior mesenteric artery ligation was established to assess the anti-intestinal IR injury effect of SAL by assessing histopathological changes in mouse small intestine by HE staining, detecting inflammatory factor expression by ELISA kit, and detecting the expression of key protein targets by Western blotting.

RESULTS

A total of 166 SAL target genes and 1740 disease-related targets were retrieved, and 88 overlapping proteins were obtained as potential therapeutic targets. The pathway enrichment analysis revealed that the pharmacological effects of SAL on intestinal IR injury were anti-hypoxic, anti-inflammatory and metabolic pathway related, and the molecular docking and molecular dynamic simulation results showed that the core bioactive components had good binding affinity for TXNIP and AMPK, and the immunoblotting results indicated that the expression levels of TXNIP and AMPK in the small intestinal tissues of mice in the drug-treated group compared with the model group were significantly changed.

CONCLUSION

SAL may target AMPK and TXNIP domains to act as a therapeutic agent for intestinal IR. These findings comprehensively reveal the potential therapeutic targets for SAL against intestinal IR and provide theoretical basis for the clinical application of SAL in the treatment of intestinal IR.

An Efficient Reactive Force Field without Explicit Coordination Dependence for Studying Caustic Aluminum Chemistry

Reactive force fields (RFFs) are an expedient approach to sample chemical reaction paths in complex systems, relative to density functional theory. However, there is continued need to improve efficiencies, specifically in systems that have slow transverse degrees of freedom, as in highly viscous and superconcentrated solutions. Here, we present an RFF that is differentiated from current models (e.g., ReaxFF) by omitting explicit dependence on the atom coordination and employing a small parameter set based on Lennard-Jones, Gaussian, and Stillinger-Weber potentials. The model was parametrized from AIMD simulation data and is used to model aluminate reactivity in sodium hydroxide solutions with extensive validation against experimental radial distribution functions, computed free energy profiles for oligomerization, and formation energies. The model enables simulation of early stage Al(OH)₃ nucleation which has significant relevance to industrial processing of aluminum and has a computational cost that is reduced by 1 order of magnitude relative to ReaxFF.

Verification of sortase for protein conjugation by single-molecule force spectroscopy and molecular dynamics simulations

SMFS and MD simulations revealed a closed conformation and a decreased stability of sortase-mediated polyprotein I27 when a linker with a high content of glycine is used.

An effective partial charge model for bulk and surface properties of cubic ZrO2, Y2O3 and yttrium-stabilised zirconia

In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO₂, Y₂O₃ and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO₂ and Y₂O₃ under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO₂ and Y₂O₃, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO₂ case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.