USE OF GRAPH-THEORY FOR SECONDARY STRUCTURE RECOGNITION AND SEQUENTIAL ASSIGNMENT IN HETERONUCLEAR (C-13, N-15) NMR-SPECTRA - APPLICATION TO HU PROTEIN FROM BACILLUS-STEAROTHERMOPHILUS

A computer-assisted procedure, based upon a branch of mathematics know n as graph theory, has been developed to recognize secondary structure elements in proteins from their corresponding nuclear Overhauser effe ct spectroscopy (NOESY)-type spectra and to carry out their sequential assignment. In the method, NOE connectivity templates characteristic of regular secondary structures are identified in the spectra. Resonan ce assignment is then achieved by connecting these NOE patterns of sec ondary structure together, and thereby matching connected spin systems to specific pacts of the primary sequence. The range of NOE-graph tem plates of secondary structure motifs, incorporating alpha-helices and beta-strand motifs, has been examined for reliability and extent of se condary structure identification in a data base composed of the high r esolution structures of 20 proteins. The analysis identified several r obust NOE-graph templates and supports the implementation of an ordere d search strategy. The method, known as SERENDIPITY, has been applied to the analysis of nuclear Overhauser effect data from a three-dimensi onal time-shared nuclear Overhauser effect spectroscopy (C-13, N-15) h eteronuclear single quantum correlation spectrum of the (alpha + beta) type protein HU from Bacillus stearothermophilus. The arrangement of the elucidated elements of secondary structure is very similar to that of the x-ray and nmr structures of HU. In addition, our analysis reve aled a pattern of interstrand nuclear Overhauser effect in the beta-ar m region (residues 53-76) of HU, which suggest irregularities, not rep orted in the x-ray structure, in both strands of the beta-arm at Ala57 and Pro72, respectively. At these residues, both strands of the beta- arm appear to flip inside out before continuing as a regular antiparal lel beta-sheet. (C) 1996 John Wiley & Sons, Inc.