Programs for computer-assisted sequential assignment of proteins

Abstract

A set of computer programs for assisting in the sequential assignment of proton chemical shifts in proteins is presented. These programs use peak coordinates and intensities directly as input. The major tasks performed by the programs include (1) use of scalar coupling information to find N, C-α, and C-β proton chemical shifts for the spin systems; (2) use of nuclear Overhauser effect data for the identification of pairs of spin systems which may be adjacent in the primary sequence; and (3) assembly of long lists of spin systems which are sequential in the primary sequence. The output of these programs may be combined with knowledge of spin system types obtained manually to quickly and unambiguously assign the majority of the spin systems. Operation of the programs on a test data set acquired for a mutant of bovine pancreatic trypsin inhibitor correctly placed 48% of the spin systems with finger print peaks in sequential lists of length 3 or longer, and lists of possible next and previous spin systems were created for most of the other spin systems. By combining knowledge of the spin system types (determined manually) with the program output, it was possible to assign unambiguously 86% of the spin systems.