DETERMINATION OF STEREOSPECIFIC ASSIGNMENTS, TORSION-ANGLE CONSTRAINTS, AND ROTAMER POPULATIONS IN PROTEINS USING THE PROGRAM ANGLESEARCH

A general program, AngleSearch, which calculates coupling constants an d interproton distances for any molecular fragment and does a grid sea rch to find torsion angles, rotamer populations, and stereospecific as signments which fit the measured data has been developed. The program takes full advantage of the fact that ratios of cross-peak intensities (measured in HNHB and HN(CO)HB experiments) can provide accurate rati os of coupling constants even for large molecules, AngleSearch is capa ble of: (a) analyzing any type of residue including protein, RNA, DNA, and ligand residues; (b) conformational grid searching in dihedral-an gle space using 6 degrees steps; (c) averaging coupling constants and [1/r(6)] distances for rotamers undergoing fast exchange; (d) grid or Monte Carlo searching for populations of staggered rotamers; (e) using all available distance-related data from ROESY and/or NOESY spectra; (f) using any available coupling constant data having known relationsh ips to corresponding dihedral angles; and (g) directly using cross-pea k intensities related to values of coupling constants. The program can also assist in the stereospecific assignment of the alpha-CH2, proton s of glycine residues. The effects of the quality of the input data on the results of the AngleSearch calculations have been assessed. (C) 1 995 Academic Press, Inc.