Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins

Abstract

We introduce the torsional network model (TNM), an elastic network model whose degrees of freedom are the torsion angles of the protein backbone. Normal modes of the TNM displace backbone atoms including C(β) maintaining their covalent geometry. For many proteins, low frequency TNM modes are localized in torsion space yet collective in Cartesian space, reminiscent of hinge motions. A smaller number of TNM modes than anisotropic network model modes are enough to represent experimentally observed conformation changes. We observed significant correlation between the contribution of each normal mode to equilibrium fluctuations and to conformation changes, and defined the excess correlation with respect to a simple neutral model. The stronger this excess correlation, the lower the predicted free energy barrier of the conformation change and the fewer modes contribute to the change.