Tutorial Files and Methods

  • Pseudoatom-driven solvent accessibility refinement (PaDSAR) Method ( pdf, 483 kb) (required tutorial files [.tar, 11.7 mb])

    This suite of NAMD input files is to support the application of the PaDSAR method for membrane protein refinement based on EPR data. This method is used for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (O(2)) and nickel-ethylenediaminediacetic acid (NiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual “solvent” particles corresponding to O(2) and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment.

Solvent accessibility-based structural refinement

Animation depicting the process of structural refinement based on the parametrization of solvent accessibilities derived from EPR experiments as constraints in MD simulations. The approach, "Pseudoatom-Driven Solvent Accessibility Refinement" (PaDSAR), relies on attractive and repulsive forces from embedded pseudo-atoms (blue or red spheres) to the protein backbone (green spheres). Click to enlarge.