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

In the refinement procedure for macromolecular structure determination by N MR, extraction of interproton distances from experimental NOE intensities i s crucial. In particular, major problems could arise when NMR experimental data are the result of a weighted average of multiple conformations in solu tion (rapid exchange). In this case the usual "static" averaged structure d erived from the observed spectroscopic data may even be devoid of physical meaning. It is well known that the complete relaxation matrix analysis appr oach is valuable for calculating distances from NOESY intensities. This app roach works by producing hybrid NOE matrices in which the missing experimen tal intensities are replaced by theoretical values computed from a model an d 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 D NA oligomer as a test case. In this work, we used "synthetic" NOE intensiti es obtained by different mixtures of A-form DNA and B-form DNA. The complet e 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 "sy nthetic" results are then compared with several real cases.