Distance measurement and structure refinement with NOE data

Abstract

The two-dimensional ‘H NMR nuclear Overhauser experiment is a powerful method to determine the spatial proximity of protons within a macromolecule. Computation of molecular conformation can be based on a set of distances derived from NOESY cross-peak intensities (I-4). Often the cross-peak intensity is taken as inversely proportional to the sixth power of the distance between two spins. Distances so derived are only approximate since the cross-peak intensity due to direct crossrelaxation between spins i and j is modified by additional cross-relaxation with any spin k, especially if spin k exists such that rik < rij or rjk < rij. Accuracy is improved with a proper correction for spin diffusion and since longer distances are affected more than shorter ones, the range of distances can be extended to better define the conformational space covered by the molecule. Spin diffusion effects can be eliminated by two methods that involve the calculation of the NOE from a given structure (5, 6). Distances may be corrected by back-transformation of a combined experimental and calculated NOE matrix ( 7, 8). Alternatively, calculated NOE intensities may be compared directly to observed intensities and the initial structure can be adjusted in an iterative manner so as to minimize the difference between the two sets of NOES ( 9-1 I). However, the computational requirements for a complete NOE calculation are cumbersome and therefore approximate distances have been most often used to determine molecular structure in solution by NMR (4, 10). The first section of this paper evaluates three procedures for the best method to determine inter-proton distances from NOE data. Using the method of highest performance, inter-proton distances are then estimated for a DNA decamer, d ( TCTATCACCG) . d ( CGGTGATAGA ) , which comprises the left 10 base pairs ( LlO) of the bacteriophage X OR3 operator. An initial structure is derived from the basis set of approximate distances, along with a set of allowed torsion angles, by restrained molecular dynamics ( 12). The second part of the paper describes the incorporation of NOE-based refinement into NMR structure determination. The direct comparison between calculated and observed NOE intensities is used as an effective energy potential in a restrained molecular mechanics calculation. The calculated NOES are evaluated using a full matrix