This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. By running MD simulations, we demonstrated that GluR2 adopts the open form. To estimate the free energy differences between two conformations we used the pathway of the opening transition as has been determined in our previous study. We employed the combined approach, which includes Thermodynamics integration (TI) in which the protein is mutated in one conformation and Umbrella Sampling (US), along the pathway of the opening transition as has been determined in our previous study. To get the free energy profile from the closed to the open form we kept the closed conformation in the absence of ligand with harmonic constrains during mutation the E705 residue to E705-0.75. Then umbrella sampling MD simulations were performed to determine free energy of the structural transition from the closed to open structure for GluR2 with the E705-0.75 mutant. Next the open GluR2 with E705-0.75 was mutated to E705 to adopt its previous electrostatic environment. A combination of computational methods has been employed here to model the opening transition and compute the free energy differences using a thermodynamic cycle
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