Mesodynamics in the SARS nucleocapsid measured by NMR field cycling

Clarkson, Michael W.; Lei, Ming; Eisenmesser, Elan Z.; Labeikovsky, Wladimir; Redfield, Alfred; Kern, Dorothee

Solvent molecules and counter-ions were added to the PDB file 2OFZ (Saikatendu et al. 2007 ) by the program solvate 1.0 (Grubmuller 1995) . Atoms beyond 42 Ã… from the center were deleted; the minimum distance between any protein atom and the spherical surface was 16 Ã… . The stochastic boundary condition (Brooks and Karplus 1983; Brunger et al. 1984 ) was imposed to prevent solvent from departing from the water sphere. The CHARMM program (Brooks et al. 1983 ) with the all-atom force field (MacKerell et al. 1998 ) and CMAP correction (Mackerell et al. 2004 ) was used for minimization and simulation. The non-bonded interaction cut-off distance was set to be 14 Ã… , and the simulation timestep was 2 fs. Hydrogen atoms were constrained by the SHAKE algorithm. The system was minimized, then heated from 50 to 300 K in 200 ps. The two production runs were 15 ns in duration.