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kainic acid  (MedChemExpress)
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MedChemExpress kainic acid
HADDOCK cluster analysis and transmission electron microscopy (TEM) observations of <t>kainic</t> <t>acid</t> (KA) cells and hippocampus samples from the TLE mice. A) Selected LC3 ─ ROCK2 docked complex where LC3 and ROCK2 are shown in blue and pink, respectively. The HADDOCK docked models were plotted against their interface‐RMSDs (i‐RMSDs); the color filled triangle corresponds to the individual cluster. B) i‐RMSDs versus air energy ( E air) plot for CPB─P2×7 complex model. The i‐RMSDs were calculated on the backbone (CA, C, N, O, P) atoms of all residues involved in intermolecular contact using a 10 Å cutoff. C) The HADDOCK scores of clusters were plotted against their i‐RMSDs. The HADDOCK score corresponds to the weighted sum of D) intermolecular electrostatic, E) van der Waals contacts, Desolvation, E air, and a buried surface area. HADDOCK differs for the various docking stages (rigid body (it0), semiflexible refinement (it1), and explicit solvent refinement (water)). It uses the following weights: HADDOCKscore‐it0 = 0.01 E vdw + 1.0 E elec + 1.0 E desol + 0.01 E air – 0.01BSA; HADDOCKscore‐it1 = 1.0 E vdw + 1.0 E elec + 1.0 E desol + 0.1 E air – 0.01BSA; HADDOCKscore‐water = 1.0 E vdw + 0.2 E elec + 1.0 E desol + 0.1 E air. And z _score_cluster_ i = (HADDOCKscore‐water – µ _all)/ σ _all.
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HADDOCK cluster analysis and transmission electron microscopy (TEM) observations of kainic acid (KA) cells and hippocampus samples from the TLE mice. A) Selected LC3 ─ ROCK2 docked complex where LC3 and ROCK2 are shown in blue and pink, respectively. The HADDOCK docked models were plotted against their interface‐RMSDs (i‐RMSDs); the color filled triangle corresponds to the individual cluster. B) i‐RMSDs versus air energy ( E air) plot for CPB─P2×7 complex model. The i‐RMSDs were calculated on the backbone (CA, C, N, O, P) atoms of all residues involved in intermolecular contact using a 10 Å cutoff. C) The HADDOCK scores of clusters were plotted against their i‐RMSDs. The HADDOCK score corresponds to the weighted sum of D) intermolecular electrostatic, E) van der Waals contacts, Desolvation, E air, and a buried surface area. HADDOCK differs for the various docking stages (rigid body (it0), semiflexible refinement (it1), and explicit solvent refinement (water)). It uses the following weights: HADDOCKscore‐it0 = 0.01 E vdw + 1.0 E elec + 1.0 E desol + 0.01 E air – 0.01BSA; HADDOCKscore‐it1 = 1.0 E vdw + 1.0 E elec + 1.0 E desol + 0.1 E air – 0.01BSA; HADDOCKscore‐water = 1.0 E vdw + 0.2 E elec + 1.0 E desol + 0.1 E air. And z _score_cluster_ i = (HADDOCKscore‐water – µ _all)/ σ _all.

Journal: Advanced Science

Article Title: Targeting ROCK2 to Restore Epileptic Synaptic Networks via Mitophagy Activation: Insights from Translational Imaging of SV2A In Vivo

doi: 10.1002/advs.202508161

Figure Lengend Snippet: HADDOCK cluster analysis and transmission electron microscopy (TEM) observations of kainic acid (KA) cells and hippocampus samples from the TLE mice. A) Selected LC3 ─ ROCK2 docked complex where LC3 and ROCK2 are shown in blue and pink, respectively. The HADDOCK docked models were plotted against their interface‐RMSDs (i‐RMSDs); the color filled triangle corresponds to the individual cluster. B) i‐RMSDs versus air energy ( E air) plot for CPB─P2×7 complex model. The i‐RMSDs were calculated on the backbone (CA, C, N, O, P) atoms of all residues involved in intermolecular contact using a 10 Å cutoff. C) The HADDOCK scores of clusters were plotted against their i‐RMSDs. The HADDOCK score corresponds to the weighted sum of D) intermolecular electrostatic, E) van der Waals contacts, Desolvation, E air, and a buried surface area. HADDOCK differs for the various docking stages (rigid body (it0), semiflexible refinement (it1), and explicit solvent refinement (water)). It uses the following weights: HADDOCKscore‐it0 = 0.01 E vdw + 1.0 E elec + 1.0 E desol + 0.01 E air – 0.01BSA; HADDOCKscore‐it1 = 1.0 E vdw + 1.0 E elec + 1.0 E desol + 0.1 E air – 0.01BSA; HADDOCKscore‐water = 1.0 E vdw + 0.2 E elec + 1.0 E desol + 0.1 E air. And z _score_cluster_ i = (HADDOCKscore‐water – µ _all)/ σ _all.

Article Snippet: At DIV 10, neurons were treated with 50 μ m kainic acid (MedChemExpress, HY‐N2309) in Mg2+‐free N ‐(2‐hydroxyethyl)piperazine‐29‐(2‐ethane‐sulfonic acid)‐buffered saline for 30 min, followed by three washes and 24 h recovery in a conditioned medium.

Techniques: Transmission Assay, Electron Microscopy, Solvent