Molecular Docking_BBR@Mp-AgNP-CsgA/B
Description
ReadMe - Computational Docking Analysis of Curli Protein CsgA & B with Silver Nanoparticles-Berberine nanocomplex. Software: AutoDock Vina 1.2.5 Protein: Enterobacter hormaechei curli proteins CsgA and CsgB was retrieved from the UniProt database (AlphaFold ID: AF-A0A155BS15-F1; CsgB: AF-A0A431SJI7-F1). Docking parameters: Grid center: A docking grid of 44 × 18 × 40 with a grid spacing of 0.375 Å. Lamarckian Genetic Algorithm was used with 100 runs and a maximum of 27,000 GA operations, and conformational clustering was performed at an RMSD tolerance of 1 Å. Nanoparticle model: A silver nanocluster (Ag8) model was used as a computational representative of the experimentally characterized AgNPs, which showed a mean hydrodynamic size of approximately 34 nm by NTA.
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Curli proteins involved in biofilm formation were selected as receptor targets for molecular docking studies. The three-dimensional structure of the Enterobacter hormaechei curli proteins CsgA and CsgB was retrieved from the UniProt database (AlphaFold ID: AF-A0A155BS15-F1; CsgB: AF-A0A431SJI7-F1). Receptor preparation was carried out using AutoDock Tools 1.5.6 by adding polar hydrogens and assigning Kollman united atom charges, and the processed structures were saved in PDBQT format [21]. BBR (CID: 2353) structure was obtained from the PubChem database in SDF format and converted into PDB format, while the Ag8 octahedral nanoparticle was constructed using BIOVIA Discovery Studio Visualizer. Energy minimization of the nanoparticle was performed in PyRx using the Universal Force Field with the steepest descent algorithm, after which the minimized structures were converted to PDBQT format. Initial docking of BBR with the Ag8 nanoparticle was conducted using AutoDock Tools, employing a docking grid of 44 × 18 × 40 with a grid spacing of 0.375 Å. The Lamarckian Genetic Algorithm was used with 100 runs and a maximum of 27,000 GA operations, and conformational clustering was performed at an RMSD tolerance of 1 Å. The most favorable BBR-Ag8 complex was selected based on the lowest binding energy conformation from highest populated cluster. The optimized nanocomplex and BBR alone were subsequently docked against curli proteins CsgA and CsgB. Docking of the BBR-Ag8 complex with E. hormaechei CsgA was performed using a grid size of 100 × 124 × 126 with a grid spacing of 0.397 Å, while docking with CsgB employed a grid size of 126 × 126 × 126 with a grid spacing of 0.375. Similarly, the docking calculation has been performed for BBR with CsgA and CsgB in PyRx using AutoDock4. For all docking runs, AutoDock Tools evaluated binding affinities and clustered poses based on conformational overlap, with the best docked conformations selected according to the lowest binding free energy (ΔG, kcal/mol) and highest cluster population. The resulting docked complexes were analyzed for hydrogen bonding, hydrophobic interactions, and metal coordination using BIOVIA Discovery Studio Visualizer to elucidate potential mechanisms of biofilm inhibition.