BIOPHYSICAL THEORY AND MODELING |
Reorientational Contact-Weighted Elastic Network Model
for the Prediction of Protein Dynamics: Comparison with
NMR Relaxation
Dengming Ming 1 and Rafael Bruschweiler 2*
1 LANL
2 Florida State University
* To whom correspondence should be addressed. E-mail: bruschweiler{at}magnet.fsu.edu.
Submitted on August 2, 2005
Revised on September 2, 2005
Accepted on 13 January 2006
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Abstract |
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A new model for the prediction of protein backbone motions is presented. The model, termed reorientational contact-weighted elastic network model (rCENM), is based on a multi-dimensional 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 inter-vector 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 3D 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 rCENM 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.
Key Words:
NMR order parameters, Protein backbone dynamics, contact model, dynamics prediction, elastic network model, normal mode analysis
