Journal: Molecules

Article Title: Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit

doi: 10.3390/molecules28104108

Figure Lengend Snippet: 2D interactions diagram of ligands bound to GluN1 LBD. Hydrophobic residues are shown in green, polar residues are shown in cyan, positively charged residues are shown in purple, and negatively charged residues are shown in orange. Hydrogen bonds are shown as purple arrows, π-cation interactions are shown as red lines, and salt bridges are shown as red-blue lines. The tip of the tear-drop shape points towards the side chain of the residue; dots on a connection indicate a residue not making contact with the ligand. ( A ) Glycine bound to the wild-type GluN1 LBD ( B ) D-serine bound to the wild-type GluN1 LBD. ( C ) Glycine bound to the S688Y GluN1 LBD ( D ) D-serine bound to the S688Y GluN1 LBD. Figure generated using the ligand interaction visualization module in Maestro 2021.4 [ , ].

Article Snippet: Graphs were generated using the Simulation Interactions Diagram module in Desmond 2018-4 [ , ] and GraphPad Prism version 9.5.0 for MacOS, GraphPad Software, San Diego, CA, USA.

Techniques: Residue, Generated

Journal: Molecules

Article Title: Binding and Dynamics Demonstrate the Destabilization of Ligand Binding for the S688Y Mutation in the NMDA Receptor GluN1 Subunit

doi: 10.3390/molecules28104108

Figure Lengend Snippet: Averaged triplicate GluN1 LBD-ligand interactions of the 1 µs simulations. Note that figure scales are different to improve the visibility of the data. Hydrogen bonds are defined as an H-Acceptor distance less than 2.8 Å and a Donor-H-Acceptor angle greater than 120. Hydrophobic interactions include pi-pi stacking, pi-cation interactions, and van der Waals interactions within 3.6 Å of ligand. Ionic interactions are defined as charged interactions within 3.6 Å of the ligand. Water bridges are defined as H-Acceptor distances less than 2.7 Å. Hydrogen bonds are shown in green, hydrophobic interactions are shown in lilac, ionic interactions are shown in magenta, and water bridges are shown in blue. For residues with more than one type of interaction, the interaction fraction can exceed 1. ( A ) Glycine bound to wild-type GluN1 LBD, ( B ) D-serine bound to wild-type GluN1 LBD, ( C ) Glycine bound to S688Y GluN1 LBD, ( D ) D-serine bound to S688Y GluN1 LBD. Graphs were generated using the Simulation Interactions Diagram module of Maestro 2021.4 [ , ].

Article Snippet: Graphs were generated using the Simulation Interactions Diagram module in Desmond 2018-4 [ , ] and GraphPad Prism version 9.5.0 for MacOS, GraphPad Software, San Diego, CA, USA.

Techniques: Generated

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