ArticleJournal of chemical theory and computation2020
Lipopolysaccharide Simulations Are Sensitive to Phosphate Charge and Ion Parameterization.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed.
- Experimental and Monte Carlo Insights into the Biofilm Control ofNanomaterials (Basel, Switzerland) · 2026Article
- Scalable Production of Transfection-Grade Plasmid DNA by Liquid-Liquid Extraction Without Chromatography: Application to CAR-T Vector Packaging.Bioengineering (Basel, Switzerland) · 2026Article
- Martini 3 as a Transferable Force Field for Lipopolysaccharide Parametrization.The journal of physical chemistry. B · 2026Article
- Biophysical Modeling of Lipopolysaccharides in Gram-Negative Bacteria: From Atomic to Colloidal Models.International journal of molecular sciences · 2026Review
- Array-based specific classification of bacterial species via the redox state transition of riboflavin.Mikrochimica acta · 2025Article
- Cryogel scaffolds for localised delivery of lipopolysaccharide in organotypic spinal cord slice cultures: A novelMaterials today. Bio · 2025Article
- Role of Divalent Ions in Membrane Models of Polymyxin-Sensitive and Resistant Gram-Negative Bacteria.Journal of chemical information and modeling · 2025Article
- Biomass-Derived Nanoporous Carbon Honeycomb Monoliths for Environmental Lipopolysaccharide Adsorption from Aqueous Media.International journal of molecular sciences · 2025Article
- A versatile nanoplatform with excellent biofilm permeability and spatiotemporal ROS regulation for peri-implantitis treatment.Theranostics · 2025Article
- Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations.Current opinion in structural biology · 2024Review
- Diversity, Complexity, and Specificity of Bacterial Lipopolysaccharide (LPS) Structures Impacting Their Detection and Quantification.International journal of molecular sciences · 2024Article
- High Antiparasitic and Antimicrobial Performance of Biosynthesized NiO Nanoparticles via Wasted Olive Leaf Extract.International journal of nanomedicine · 2024Article
- Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics.Journal of chemical theory and computation · 2023Article
- Investigation into the Antibacterial Mechanism of Biogenic Tellurium Nanoparticles and Precursor Tellurite.International journal of molecular sciences · 2022Article
- Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation.The journal of physical chemistry. B · 2022Article
- Review
- CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides.Journal of chemical information and modeling · 2021Article
- Molecular dynamics simulations informed by membrane lipidomics reveal the structure-interaction relationship of polymyxins with the lipid A-based outer membrane of Acinetobacter baumannii.The Journal of antimicrobial chemotherapy · 2020Article
- Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers.Molecules (Basel, Switzerland) · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The high proportion of lipopolysaccharide (LPS) molecules in the outer membrane of Gram-negative bacteria makes it a highly effective barrier to small molecules, antibiotic drugs, and other antimicrobial agents. Given this vital role in protecting bacteria from potentially hostile environments, simulations of LPS bilayers and outer membrane systems represent a critical tool for understanding the mechanisms of bacterial resistance and the development of new antibiotic compounds that circumvent these defenses. The basis of these simulations is parameterizations of LPS, which have been developed for all major molecular dynamics force fields. However, these parameterizations differ in both the protonation state of LPS and how LPS membranes behave in the presence of various ion species. To address these discrepancies and understand the effects of phosphate charge on bilayer properties, simulations were performed for multiple distinct LPS chemotypes with different ion parameterizations in both protonated or deprotonated lipid A states. These simulations show that bilayer properties, such as the area per lipid and inter-lipid hydrogen bonding, are highly influenced by the choice of phosphate group charges, cation type, and ion parameterization, with protonated LPS and monovalent cations with modified nonbonded parameters providing the best match to the experiments. Additionally, alchemical free energy simulations were performed to determine theoretical p
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Registered trials
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