AUTOMATED ASSIGNMENT OF SIMULATED AND EXPERIMENTAL NOESY SPECTRA OF PROTEINS BY FEEDBACK FILTERING AND SELF-CORRECTING DISTANCE GEOMETRY

A new method for automatically assigning proton-proton NOESY spectra i s described and demonstrated for simulated and experimental spectra of the proteins dendrotoxin K, alpha-amylase inhibitor tendamistat and t he DNA-binding domain of the 434 repressor protein. The method assigns the NOESY spectrum and calculates three-dimensional protein structure s simultaneously, using a list of proton chemical shifts and (3)J(NH a lpha) coupling constants. An ensemble of structures is iteratively cal culated by self-correcting distance geometry from unambiguous and sele cted ambiguous NOESY cross peaks. New structure based filters recogniz e the correct constraints from the ambiguous cross peak list. For the first round of assignment neither a preliminary initial structure nor a sufficient set of unambiguous NOESY cross peaks is needed. The metho d can also be applied to cross peak lists containing hundreds of noise peaks. For an assumed tolerance of +/- 0.01 ppm in the chemical shift s of the peak positions, only about 10% of the NOESY cross peaks can b e unambiguously assigned based on their chemical shifts alone. Our aut omated method assigned about 80% of all cross peaks with this chemical shift tolerance, and 95 to 99% of the assignments were correct. The a verage pairwise RMSD for the backbone atoms of the ten best final stru ctures is about 1.5 Angstrom in all three proteins and the previously determined NMR solution structures are always embedded in this structu re bundle. We regard our method as a highly practical tool for automat ic calculation of three-dimensional protein structures from NMR spectr a with minimal human interference. (C) 1995 Academic Press Limited