Conformational Entropy Analysis of Ligand Binding

The normal-mode analysis was performed to evaluate the conformational entropy change upon ligand binding (−TΔS) using the nmode program in AMBER9.0.46 (link) Because the normal mode analysis is computationally expensive, we only considered the residues within a 12 Å sphere centered at the ligand and these residues were retrieved from an MD snapshot for each ligand-protein complex. The open valences were saturated by adding hydrogen atoms using the tleap program of AMBER9.0.46 (link) The corresponding ligand and receptor were extracted from the reduced complex structure. Then each structure was fully minimized for 100,000 steps using a distance-dependent dielectric of 4r_ij (r_ij is the distance between two atoms) to mimic the solvent dielectric change from the solute to solvent until the root-mean-square of the elements of the gradient vector was less than 5 × 10⁻⁴ kcal·mol⁻¹·Å⁻¹. To reduce the computational demand, 125 snapshots were taken from 0 to 5 ns to estimate the contribution of the entropy to binding. The final conformational entropy was obtained from the average over the snapshots. It should be noted that different from the other energy terms the entropy contribution is computed in a way independent of the internal dielectric constant.