Paper Citing NAMD - Abstract
Anderson, Janet S.; LeMaster, David M.
Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation
BIOPHYSICAL CHEMISTRY, 168:28-39, JUL 2012
Rotational velocity rescaling (RVR) enables N-15 relaxation data for the anisotropically tumbling B3 domain of Protein G (GB3) to be accurately predicted from 1 mu s of constant energy molecular dynamics simulation without recourse to any system-specific adjustable parameters. Superposition of adjacent trajectory frames yields the unique rotation axis and angle of rotation that characterizes each transformation. By proportionally scaling the rotation angles relating each consecutive pair of frames, the rotational diffusion in the RVR-MD trajectory was adjusted to correct for the elevated self-diffusion rate of TIP3P water. N-15 T-1 and T-2 values for 32 residues in the regular secondary structures of GB3 were predicted with an rms deviation of 22%, modestly larger than the estimated experimental uncertainties. Residue-specific chemical shift anisotropy (CSA) values reported from isotropic solution, liquid crystal and microcrystalline solid measurements less accurately predict GB3 relaxation than does applying a constant CSA value, potentially indicating structure-dependent correlated variations in H-1- N-15 bond length and N-15 CSA. By circumventing the quasi-static analysis of NMR order parameters often applied in MD studies, a more direct test is provided for assessing the accuracy with which molecular simulations predict protein motion in the ps-ns timeframe. Since no assumption of separability between global tumbling and internal motion is required, utility in analyzing simulations of mobility in disordered protein segments is anticipated. (c) 2012 Elsevier B.V. All rights reserved.
