Computational protocol: Electrostatic Interactions Guide the Active Site Face of a Structure-Specific Ribonuclease to Its RNA Substrate†

Similar protocols

Protocol publication

[…] Numerical solutions to the nonlinear Poisson−Boltzmann equation were determined using APBS (). Atomic charges were assigned with PDB2PQR () using the AMBER force field (). Protonation states were assigned at pH 7.5 using PROPKA (). The protein and RNA molecules were assigned a low dielectric constant of 2.0 with a solvent dielectric constant of 78.0. Ionic radii of 3.3 Å were used, corresponding to the radius of a hydrated potassium ion. The multigrid solution used a grid size of 161 × 161 × 161 and a solvent radius of 1.6 Å. Binding energies for each RNA−protein complex are the differences between the calculated electrostatic energies of the individual molecules and that of the bound complex. Calculation of the complex energy (E, kilojoules per mole) at multiple salt concentrations ranging from 40 to 100 mM enabled subsequent determination of the salt dependence from a plot of −E/RT versus the natural logarithm of the salt concentration, where T = 310 K. […]

Pipeline specifications

Software tools PDB2PQR, PROPKA
Application Protein structure analysis