Overall rotational diffusion and internal mobility in domain II of protein G from Streptococcus determined from ¹⁵N relaxation data

Abstract

The backbone dynamics and overall tumbling of protein G have been investigated using ¹⁵N relaxation. Comparison of measured R₂/R₁ relaxation rate ratios with known three-dimensional coordinates of the protein show that the rotational diffusion tensor is significantly asymmetric, exhibiting a prolate axial symmetry. Extensive Monte Carlo simulations have been used to estimate the uncertainty due to experimental error in the relaxation rates to be D_∥/D_⊥ = 1.68 ± 0.08, while the dispersion in the NMR ensemble leads to a variation of D_∥/D_⊥ = 1.65 ± 0.03. Incorporation of this tensorial description into a Lipari–Szabo type analysis of internal motion has allowed us to accurately describe the local dynamics of the molecule. This analysis differs from an earlier study where the overall rotational diffusion was described by a spherical top. In this previous analysis, exchange parameters were fitted to many of the residues in the alpha helix. This was interpreted as reflecting a small motion of the alpha helix with respect to the beta sheet. We propose that the differential relaxation properties of this helix compared to the beta sheet are due to the near-orthogonality of the NH vectors in the two structural motifs with respect to the unique axis of the diffusion tensor. Our analysis shows that when anisotropic rotational diffusion is taken into account NH vectors in these structural motifs appear to be equally rigid. This study underlines the importance of a correct description of the rotational diffusion tensor if internal motion is to be accurately investigated.