HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations

Abstract

The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily shaped particles, by means of bead models, we have constructed a computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure. From the atomic coordinates file used to build the bead model, the orientation of the pertinent dipoles can be extracted and combined with the hydrodynamic information to predict, for each residue in the protein, the relaxation times. All of these developments have been implemented in a computer program, HYDRONMR, which will be of public domain.