Relaxation Matrix Analysis of Spin Diffusion for the NMR Structure Calculation with eNOEs.

Abstract

NMR structure determination is usually based on distance restraints extracted semiquantitatively from cross peak volumes or intensities in NOESY spectra. The recent introduction of exact NOEs (eNOE) by Vogeli et al. opens an avenue for the ensemble-based structure determination of proteins on the basis of eNOE-derived quantitative distance restraints. We present an approach to extract eNOE from build-up curve intensities. For the determination of eNOEs, spin diffusion is a major source of errors. A full relaxation matrix analysis is used to calculate the spin diffusion contribution to the NOESY cross peaks of each individual spin pair of interest. A software program is written, which requires as input the peak intensities from the various NOESY spectra as well as a 3D structure of the protein. This structure can be either an X-ray structure or an NMR structure determined with the conventional approach. The outputs of the program are the eNOE rates, the autorelaxation rates, as well as graphs and quality factors from the individual NOE build-up curves for semiautomated analysis of the derived rates. The protocol is straightforward, and the program integrates well into the current structure calculation workflow.