NOE intensities from multiple conformations in solution analyzed by the complete relaxation matrix approach

Abstract

In the refinement procedure for macromolecular structure determination by NMR, extraction of interproton distances from experimental NOE intensities is crucial. In particular, major problems could arise when NMR experimental data are the result of a weighted average of multiple conformations in solution (rapid exchange). In this case the usual “static” averaged structure derived from the observed spectroscopic data may even be devoid of physical meaning. It is well known that the complete relaxation matrix analysis approach is valuable for calculating distances from NOESY intensities. This approach works by producing hybrid NOE matrices in which the missing experimental intensities are replaced by theoretical values computed from a model and then converted into distances by back-calculation using a standard matrix technique. To verify the capability of such an approach to discern between time-averaged and static coordinate-averaged NOE data, we investigated a DNA oligomer as a test case. In this work, we used “synthetic” NOE intensities obtained by different mixtures of A-form DNA and B-form DNA. The complete relaxation matrix analysis was performed using the program MARDIGRAS. In particular we focused our attention on the intraresidue base H6/H8-H2′ and H6/H8-H3′ distances that are very sensitive to sugar repuckering. These “synthetic” results are then compared with several real cases.