Hydrodynamic Models and Computational Methods for NMR Relaxation

Abstract

Interpretation of NMR relaxation data of macromolecules is based on the analysis of their dynamic behavior in solution. For quasirigid molecules, in addition to a minor, separable contribution from local mobility, the main contribution corresponds to the overall rotational diffusion of the complete molecule. Therefore, theoretical descriptions and computational methodologies for hydrodynamic calculations, which yield the full, anisotropic rotational diffusion tensor of rigid molecules, are extremely helpful in the analysis of NMR relaxation. Recent approaches allow realistic predictions of the rotational diffusion tensor from structures at atomic detail. This enables measured relaxation rates and structural models to be compared. Such a comparison (1) provides an independent test of the structural model, (2) provides a framework for the interpretation of local motion, even for highly anisotropic systems, (3) provides a simple method for the detection of additional sources of relaxation, such as chemical exchange, and (4) provides a sensitive method for the detection of nonspecific aggregation or oligomer formation. Although hydrodynamic calculations usually assume a rigid structure, Brownian dynamics simulations extend their range of applications to flexible multidomain structures. Hydrodynamic applications are not restricted to globular proteins. Small DNA fragments, which could be otherwise considered cylindrical objects, can also be treated with atomic detail using the same methodology used for proteins.