Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation.
A new model for the prediction of protein backbone motions is presented. The model, termed reorientational contact-weighted elastic network model, is based on a multidimensional reorientational harmonic potential of the backbone amide bond vector orientations and it is applied to the interpretation of dynamics parameters obtained from NMR relaxation data. The individual energy terms are weighted as a function of the intervector distances and by the contact strengths of each bond vector with respect to its local environment. Correlated reorientational motional properties of the bond vectors are obtained by means of normal mode analysis. Application to a set of proteins with known three-dimensional structures yields good to excellent agreement between predicted and experimental NMR order parameters presenting an improvement over the local contact model. The reorientational eigenmodes of the reorientational contact-weighted elastic network model method provide direct information on the collective nature of protein backbone motions. The dominant eigenmodes have a notably low collectivity, which is consistent with the behavior found for reorientational eigenmodes from molecular dynamics simulations.
Ming
Dengming
D
Computer and Computational Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
Brüschweiler
Rafael
R
D001665:Binding Sites; D003198:Computer Simulation; D004548:Elasticity; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011485:Protein Binding; D011487:Protein Conformation