Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.

ABSTRACT

Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift tolerance windows (delta), which allow for the compensation of badly matching chemical shifts in the assignment-list and peak-lists, and the maximum number of assignment possibilities allowed per peak (n(max)). Here, we test the influence of different values for Delta and n(max) on the performance of automated assignment of NOESY spectra by ARIA. Using Cesta.py (a Python script available from http//pasteur.fr/binfs/), we analyse the number of rejected peaks and the average number of assignments as a function of Delta and derive criteria for optimising delta and n(max) prior to structure calculation. The analysis also makes it possible to detect inconsistencies in the dataset, e.g., badly matching frequencies in the NOESY peak-lists and in the provided assignment-list. We show that ARIA can deal with a large number of assignment possibilities for each peak, provided the correct option is present, and that consequently narrow tolerances should be avoided.