Paper Citing NAMD - Abstract
Lakkaraju, Sirish Kaushik; Xue, Fengtian; Faden, Alan I.; MacKerell, Alexander D., Jr.
Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:1337-1349, JUN 2013
Group 1 metabotropic glutamate receptors (mGluR) are G-protein coupled receptors with a large bilobate extracellular ligand binding region (LBR) that resembles a Venus fly trap. Closing of this LBR in the presence of a ligand is associated with the activation of the receptor. From conformational sampling of the LBR-ligand complexes using all molecular dynamics (MD) simulations, we characterized the conformational minima related to the hinge like motion associated with the LBR closing/opening in the presence of known agonists and antagonists. By applying a harmonic restraint on the LBR, we also determined the conformational forces generated by the different ligands. The change in the location of the minima and the conformational forces were used to quantify the efficacies of the ligands. This, analysis shows that efficacies can be estimated from the forces of a single conformation of the receptor indicating the potential of; MD simulations as an efficient and useful technique to quantify efficacies, thereby facilitating the rational design of mGluR agonists and antagonists.
