Implementation of PaDSAR method on NAMD

Abstract

Pseudoatoms Driven Solvent Accessibility Refinement or PaDSAR is a computational approach for modeling low-resolution membrane protein structure using restraints derived from the solvent accessibility data from site-directed spin labelling and electron paramagnetic resonance spectroscopy. In the PaDSAR method, protein conformations were driven by repulsive and attractive interactions between the spin-label pseudoatoms and the surrounding environment during molecular dynamics (MD) simulations. This work has demonstrated an implementation of PaDSAR on the molecular dynamics simulation program, NAMD for refining the 3D structure of a potassium channel from Streptomyces lividans (KcsA). Working steps in NAMD-PaDSAR that are mainly conducted through the tcl script commands, include i) preparing the initial configuration of the system consisting of protein coordinates, pseudo-spins attaching to the Cα atom and the surrounding particles with pre-generated positions, and ii) performing MD simulations with the restraints. For the initial configuration, the surrounding OXY and NIC particles were randomly placed in the simulation within the specified boundary of membrane and non-membrane regions, respectively. NAMD-PaDSAR was treated the same way as that previously described in the original CHARMM-PaDSAR, except that the incorporation of the type II restraint potential was not successful due to a technical problem. This study also demonstrated that the best solution for the present problem was to take a flexible pseudo- spin into account via modifying the force constant of improper dihedral angle. The results showed that 433 out of 524 decoys which has the structure distortion based on RMSD to the x-ray structure in a range of 3 - 13Å, can refold back to the correct fold with RMSD < 3Å.