| Abstract: | To elucidate potentialities of two-dimensional homonuclear Overhauser effect (NOESY) spectra of peptides and proteins for their spatial structure determination, impact of experimental parameters and intrinsic properties of the investigated molecule on proton cross-peak volumes in NOESY spectra was analysed. Recommendations which could increase accuracy of cross-peak volume measurements were suggested. Influence of intrinsic properties of a molecule (spin-lattice relaxation times T1, correlation time tau C and surrounding protons) on the volume of cross-peak for particular protons was analyzed using a complete relaxation matrix of the (formula; see text) helix of gramicidin A. Nonselective relaxation time T1 of the protons was found to affect only slightly the results of cross-peak volumes computer simulation, whereas correlation time tau C and surrounding protons seriously influenced cross-peak volumes. Nevertheless, cross-peak volumes between NH, C alpha H and C beta H protons of a dipeptide fragment of the entire molecule could be accurately simulated using the relaxation matrix of the individual dipeptide. Thus local conformations (torsion angles phi, psi and chi 1) of amino acid residues could be deduced independently of one another and prior to the complete analysis of a molecular structure. The result can be obtained even in the presence of spin-diffusion at mixing times providing maximal volumes of cross-peaks in NOESY spectra. |
