INTERPROTON DISTANCE BOUNDS FROM 2D NOE INTENSITIES - EFFECT OF EXPERIMENTAL NOISE AND PEAK INTEGRATION ERRORS

The effect of experimental and integration errors on the calculation o f interproton distances from NOE intensities is examined, It is shown that NOE intensity errors can have a large impact on the distances det ermined. When multiple spin ('spin diffusion') effects are significant , the calculated distances are often underestimated, even when using a complete relaxation matrix analysis. In this case, the bias of distan ces to smaller values is due to the random errors in the NOE intensiti es. We show here that accurate upper and lower bounds of the distances can be obtained if the intensity errors are properly accounted for in the complete relaxation matrix calculations, specifically the MARDIGR AS algorithm. The basic MARDIGRAS algorithm has been previously descri bed [Borgias, B.A. and James, T.L. (1990) J. Magn. Reson., 87, 475-487 ]. It has been shown to provide reasonably good interproton distance b ounds, but experimental errors can compromise the quality of the resul ting restraints, especially for weak cross peaks. In a new approach in troduced here, termed RANDMARDI (random error MARDIGRAS), errors due t o random noise and integration errors are mimicked by the addition of random numbers from within a specified range to each input intensity. interproton distances are then calculated for the modified intensity s et using MARDIGRAS. The distribution of distances that define the uppe r and lower distance bounds is obtained by using N randomly modified i ntensity sets. RANDMARDI has been used in the solution structure deter mination of the interstrand cross-link (XL) formed between 4'-hydroxym ethyl-4,5',8-trimethylpsoralen (HMT) and the DNA oligomer d(5'-GCGTACG C-3')(2) [Spielmann, H.P. et al. (1995) Biochemistry, 34, 12937-12953] . RANDMARDI generates accurate distance bounds from the experimental N OESY cross-peak intensities for the fixed (known) interproton distance s in XL. This provides an independent internal check for the ability o f RANDMARDI to accurately fit the experimental data. The XL structure determined using RANDMARDI-generated restraints is in good agreement w ith other biophysical data that indicate that there is no bend introdu ced into the DNA by the cross-link. In contrast, isolated spin-pair ap proximation calculations give distance restraints that, when applied i n a restrained molecular dynamics protocol? produce a bent structure.