Book of Abstracts: Albany 2007
June 19-23 2007
Antibiotic Binding to the Ribosome
Some preliminary studies of ribosome-antibiotics interactions have been carried out through the calculation of the binding free energy and characterization of the conformational dynamics. Molecular Dynamics (MD) simulation free energy perturbation (FEP) was used to calculate the binding free energy of antibiotics to the ribosomal large subunit. Generalized Solvent Boundary Potential (GSBP) method, which includes both the solvent-shielded static field from the distant atom of macromolecule and the reaction field from the dielectric solvent acting on the atoms of the simulation region, was used. Because binding specificity is often dominated by local interactions in the vicinity of the ligand while the remote regions of the receptor contribute only in an average manner, GSBP has all atoms in the inner region belonging to ligand, macromolecule or solvent undergo explicit dynamics, whereas the influence of the macromolecule and solvent atom outside this inner region are included implicitly. The results have provided the insight into the mechanism of ribosomal inhibition by antibiotics.
1Biophysics and Physiology,