Computational protocol: A Comparative Study of Interaction of Tetracycline with Several Proteins Using Time Resolved Anisotropy, Phosphorescence, Docking and FRET

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Protocol publication

[…] The crystal structure of HSA (PDB entry 1AO6) and BSA (PDB entry 4F5S) were downloaded from the Protein Data Bank. The three-dimensional structure of the tetracycline molecule was obtained from Sybyl 6.92 (Tripos Inc., St. Louis, USA) and the energy-minimized structure was achieved using a Tripos force field and Gasteiger-Hückel charges with a gradient of 0.005 kcal/mol. The dielectric constant, number of iteration, maximum displacement, minimum energy change, simplex threshold and simplex iteration were set to 1.0, 1000, 0.01, 0.05, 1000 and 20 respectively. The FlexX single molecule docking software was used to dock tetracycline with chain A of alkaline phosphatase. The ranking of the generated solutions was obtained from a scoring function as mentioned by Rarey et al. PyMol was used to visualize the docked conformation and to measure the distances between the ligand and the protein. . [...] The ASA (accessible surface area) of HSA and BSA (free) and the docked complexes with tetracycline were calculated using NACCESS. The best docked structure according to the minimum energy was chosen to determine the ASA of the docked proteins. The change in accessible surface area for residue i was calculated using the following equation.A residue was considered to be involved in the binding if it lost more than 10 Å2 ASA when going from the free state to the complexed state. PEARLS (Program of Energetic Analysis of Receptor Ligand System) was used to estimate the energetics of the protein-ligand interaction. . […]

Pipeline specifications

Software tools LeadIt, PyMOL, Naccess
Applications Drug design, Protein physicochemical analysis
Organisms Escherichia coli
Chemicals Tetracycline