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molecular dynamics simulation diagrams  (Molecular Dynamics Inc)

 
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    Molecular Dynamics Inc molecular dynamics simulation diagrams
    Lachnospirin-1 can specifically bind to LPS to target bacterial cell membrane. (A) <t>Molecular</t> <t>dynamics</t> <t>simulation</t> <t>diagrams</t> of lachnospirin-1 interacting with cell membranes. The upper diagram shows bacterial membranes, and the lower diagram shows mammalian membranes. From left to right: simulation initiation, membrane attachment, membrane penetration, and the equilibrium state of lachnospirin-1 interacting with the cell membrane. (B) Energy analysis during molecular dynamics simulation. The upper left panel shows the van der Waals interaction energy between the antimicrobial peptide and the cell membrane; the upper right panel shows the electrostatic interaction energy (coulomb) between the antimicrobial peptide and the cell membrane; the lower left panel shows the binding free energy between the antimicrobial peptide and the cell membrane; the lower right panel shows the binding free energy contribution of amino acid residues of the antimicrobial peptide in the mixed cell membrane system of DOPC and DOPG. Membrane1 refers to the mixed cell membrane system of DOPC and DOPG; Membrane2 refers to the mixed cell membrane system of POPC and Cholesterol. (C) Details of the interaction between the amp and the mixed cell membrane of DOPC and DOPG during molecular dynamics simulation. (D) Detection of bacterial cell membrane permeability after lachnospirin-1 treatment using NPN probe. (E) Competitive inhibition experiment of lachnospirin-1 with cell membrane components POPC, POPG, and cl. (F) Schematic diagram of the interaction structure between LPS and lachnospirin-1. Blue sticks represent lachnospirin-1 residues; magenta sticks represent LPS molecules; green dashed lines represent hydrogen bond interactions; light green dashed lines represent C-H bond interactions; red dashed lines represent electrostatic interactions; orange dashed lines represent salt bridge interactions; blue dashed lines represent hydrophobic interactions. (G) Detection of the binding affinity between lachnospirin-1 and LPS by ITC.
    Molecular Dynamics Simulation Diagrams, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dynamics+simulation+diagram/gromacs+package+simulation/pmc13007424-287-12-12
    Average 86 stars, based on 1 article reviews
    molecular dynamics simulation diagrams - by Bioz Stars, 2026-10
    86/100 stars

    Images

    1) Product Images from "Antibacterial efficacy and mechanism of the novel antimicrobial peptide lachnospirin-1 against Acinetobacter baumannii"

    Article Title: Antibacterial efficacy and mechanism of the novel antimicrobial peptide lachnospirin-1 against Acinetobacter baumannii

    Journal: Virulence

    doi: 10.1080/21505594.2026.2646808

    Lachnospirin-1 can specifically bind to LPS to target bacterial cell membrane. (A) Molecular dynamics simulation diagrams of lachnospirin-1 interacting with cell membranes. The upper diagram shows bacterial membranes, and the lower diagram shows mammalian membranes. From left to right: simulation initiation, membrane attachment, membrane penetration, and the equilibrium state of lachnospirin-1 interacting with the cell membrane. (B) Energy analysis during molecular dynamics simulation. The upper left panel shows the van der Waals interaction energy between the antimicrobial peptide and the cell membrane; the upper right panel shows the electrostatic interaction energy (coulomb) between the antimicrobial peptide and the cell membrane; the lower left panel shows the binding free energy between the antimicrobial peptide and the cell membrane; the lower right panel shows the binding free energy contribution of amino acid residues of the antimicrobial peptide in the mixed cell membrane system of DOPC and DOPG. Membrane1 refers to the mixed cell membrane system of DOPC and DOPG; Membrane2 refers to the mixed cell membrane system of POPC and Cholesterol. (C) Details of the interaction between the amp and the mixed cell membrane of DOPC and DOPG during molecular dynamics simulation. (D) Detection of bacterial cell membrane permeability after lachnospirin-1 treatment using NPN probe. (E) Competitive inhibition experiment of lachnospirin-1 with cell membrane components POPC, POPG, and cl. (F) Schematic diagram of the interaction structure between LPS and lachnospirin-1. Blue sticks represent lachnospirin-1 residues; magenta sticks represent LPS molecules; green dashed lines represent hydrogen bond interactions; light green dashed lines represent C-H bond interactions; red dashed lines represent electrostatic interactions; orange dashed lines represent salt bridge interactions; blue dashed lines represent hydrophobic interactions. (G) Detection of the binding affinity between lachnospirin-1 and LPS by ITC.
    Figure Legend Snippet: Lachnospirin-1 can specifically bind to LPS to target bacterial cell membrane. (A) Molecular dynamics simulation diagrams of lachnospirin-1 interacting with cell membranes. The upper diagram shows bacterial membranes, and the lower diagram shows mammalian membranes. From left to right: simulation initiation, membrane attachment, membrane penetration, and the equilibrium state of lachnospirin-1 interacting with the cell membrane. (B) Energy analysis during molecular dynamics simulation. The upper left panel shows the van der Waals interaction energy between the antimicrobial peptide and the cell membrane; the upper right panel shows the electrostatic interaction energy (coulomb) between the antimicrobial peptide and the cell membrane; the lower left panel shows the binding free energy between the antimicrobial peptide and the cell membrane; the lower right panel shows the binding free energy contribution of amino acid residues of the antimicrobial peptide in the mixed cell membrane system of DOPC and DOPG. Membrane1 refers to the mixed cell membrane system of DOPC and DOPG; Membrane2 refers to the mixed cell membrane system of POPC and Cholesterol. (C) Details of the interaction between the amp and the mixed cell membrane of DOPC and DOPG during molecular dynamics simulation. (D) Detection of bacterial cell membrane permeability after lachnospirin-1 treatment using NPN probe. (E) Competitive inhibition experiment of lachnospirin-1 with cell membrane components POPC, POPG, and cl. (F) Schematic diagram of the interaction structure between LPS and lachnospirin-1. Blue sticks represent lachnospirin-1 residues; magenta sticks represent LPS molecules; green dashed lines represent hydrogen bond interactions; light green dashed lines represent C-H bond interactions; red dashed lines represent electrostatic interactions; orange dashed lines represent salt bridge interactions; blue dashed lines represent hydrophobic interactions. (G) Detection of the binding affinity between lachnospirin-1 and LPS by ITC.

    Techniques Used: Membrane, Binding Assay, Permeability, Inhibition

    Related Articles

    Binding Assay:

    Article Title: Rapid screening, isolation, and activity evaluation of potential xanthine oxidase inhibitors in Polyporus umbellatus and mechanism of action in the treatment of gout.
    Article Snippet: Funding information the Natural Science Foundation of Jilin Province, Grant/Award Number: no. YDZJ202201ZYTS514 Abstract Introduction: Studies show that Polyporus umbellatus has some pharmacological effects in enhancing immunity and against gout.. Objectives: We aimed to establish new techniques for extraction, biological activity screening, and preparation of xanthine oxidase inhibitors (XODIs) from P. umbellatus.. Methods: First, the extraction of P. umbellatus was investigated using the back propagation (BP) neural network genetic algorithm mathematical regression model, and the extraction variables were optimised to maximise P. umbellatus yield.

    Conjugation Assay:

    Article Title: Rapid screening, isolation, and activity evaluation of potential xanthine oxidase inhibitors in Polyporus umbellatus and mechanism of action in the treatment of gout.
    Article Snippet: Funding information the Natural Science Foundation of Jilin Province, Grant/Award Number: no. YDZJ202201ZYTS514 Abstract Introduction: Studies show that Polyporus umbellatus has some pharmacological effects in enhancing immunity and against gout.. Objectives: We aimed to establish new techniques for extraction, biological activity screening, and preparation of xanthine oxidase inhibitors (XODIs) from P. umbellatus.. Methods: First, the extraction of P. umbellatus was investigated using the back propagation (BP) neural network genetic algorithm mathematical regression model, and the extraction variables were optimised to maximise P. umbellatus yield.

    Solvent:

    Article Title: Rapid screening, isolation, and activity evaluation of potential xanthine oxidase inhibitors in Polyporus umbellatus and mechanism of action in the treatment of gout.
    Article Snippet: Funding information the Natural Science Foundation of Jilin Province, Grant/Award Number: no. YDZJ202201ZYTS514 Abstract Introduction: Studies show that Polyporus umbellatus has some pharmacological effects in enhancing immunity and against gout.. Objectives: We aimed to establish new techniques for extraction, biological activity screening, and preparation of xanthine oxidase inhibitors (XODIs) from P. umbellatus.. Methods: First, the extraction of P. umbellatus was investigated using the back propagation (BP) neural network genetic algorithm mathematical regression model, and the extraction variables were optimised to maximise P. umbellatus yield.

    other:

    Article Title: Fast and Efficient Screening and Separation Based on AUF-MS Combined With Molecular Docking Technology and Network Pharmacology Method for Potential Xanthine Oxidase Inhibitors From Pinelliae Rhizoma Praeparatum.
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    Image Search Results


    Lachnospirin-1 can specifically bind to LPS to target bacterial cell membrane. (A) Molecular dynamics simulation diagrams of lachnospirin-1 interacting with cell membranes. The upper diagram shows bacterial membranes, and the lower diagram shows mammalian membranes. From left to right: simulation initiation, membrane attachment, membrane penetration, and the equilibrium state of lachnospirin-1 interacting with the cell membrane. (B) Energy analysis during molecular dynamics simulation. The upper left panel shows the van der Waals interaction energy between the antimicrobial peptide and the cell membrane; the upper right panel shows the electrostatic interaction energy (coulomb) between the antimicrobial peptide and the cell membrane; the lower left panel shows the binding free energy between the antimicrobial peptide and the cell membrane; the lower right panel shows the binding free energy contribution of amino acid residues of the antimicrobial peptide in the mixed cell membrane system of DOPC and DOPG. Membrane1 refers to the mixed cell membrane system of DOPC and DOPG; Membrane2 refers to the mixed cell membrane system of POPC and Cholesterol. (C) Details of the interaction between the amp and the mixed cell membrane of DOPC and DOPG during molecular dynamics simulation. (D) Detection of bacterial cell membrane permeability after lachnospirin-1 treatment using NPN probe. (E) Competitive inhibition experiment of lachnospirin-1 with cell membrane components POPC, POPG, and cl. (F) Schematic diagram of the interaction structure between LPS and lachnospirin-1. Blue sticks represent lachnospirin-1 residues; magenta sticks represent LPS molecules; green dashed lines represent hydrogen bond interactions; light green dashed lines represent C-H bond interactions; red dashed lines represent electrostatic interactions; orange dashed lines represent salt bridge interactions; blue dashed lines represent hydrophobic interactions. (G) Detection of the binding affinity between lachnospirin-1 and LPS by ITC.

    Journal: Virulence

    Article Title: Antibacterial efficacy and mechanism of the novel antimicrobial peptide lachnospirin-1 against Acinetobacter baumannii

    doi: 10.1080/21505594.2026.2646808

    Figure Lengend Snippet: Lachnospirin-1 can specifically bind to LPS to target bacterial cell membrane. (A) Molecular dynamics simulation diagrams of lachnospirin-1 interacting with cell membranes. The upper diagram shows bacterial membranes, and the lower diagram shows mammalian membranes. From left to right: simulation initiation, membrane attachment, membrane penetration, and the equilibrium state of lachnospirin-1 interacting with the cell membrane. (B) Energy analysis during molecular dynamics simulation. The upper left panel shows the van der Waals interaction energy between the antimicrobial peptide and the cell membrane; the upper right panel shows the electrostatic interaction energy (coulomb) between the antimicrobial peptide and the cell membrane; the lower left panel shows the binding free energy between the antimicrobial peptide and the cell membrane; the lower right panel shows the binding free energy contribution of amino acid residues of the antimicrobial peptide in the mixed cell membrane system of DOPC and DOPG. Membrane1 refers to the mixed cell membrane system of DOPC and DOPG; Membrane2 refers to the mixed cell membrane system of POPC and Cholesterol. (C) Details of the interaction between the amp and the mixed cell membrane of DOPC and DOPG during molecular dynamics simulation. (D) Detection of bacterial cell membrane permeability after lachnospirin-1 treatment using NPN probe. (E) Competitive inhibition experiment of lachnospirin-1 with cell membrane components POPC, POPG, and cl. (F) Schematic diagram of the interaction structure between LPS and lachnospirin-1. Blue sticks represent lachnospirin-1 residues; magenta sticks represent LPS molecules; green dashed lines represent hydrogen bond interactions; light green dashed lines represent C-H bond interactions; red dashed lines represent electrostatic interactions; orange dashed lines represent salt bridge interactions; blue dashed lines represent hydrophobic interactions. (G) Detection of the binding affinity between lachnospirin-1 and LPS by ITC.

    Article Snippet: Lachnospirin-1 can specifically bind to LPS to target bacterial cell membrane. (A) Molecular dynamics simulation diagrams of lachnospirin-1 interacting with cell membranes.

    Techniques: Membrane, Binding Assay, Permeability, Inhibition