GSC: a graphical program for NMR chemical shift comparison.

Abstract

Comparison of NMR chemical shift files can provide the researcher with valuable insights. For example, a comparison of NMR chemical shifts obtained for the same protein at various temperatures can provide insights into the protein's thermal stability (Roder, 1989). Also, shift comparisons of a large protein subjected to various detergents can show whether protein tertiary structure is disrupted (Mutter and Altmann, 1985), or the detergent may have an effect on stabilizing the secondary structure in a small protein (Dyson etai, 1988). Chemical shift changes can verify metal bindings in proteins (Shaw et al., 1990) and it can be insightful to compare the overall effect on chemical shifts from protein mutations (Rajarathnam et al., 1994). Chemical shift comparison of two or more similar proteins can identify regions where the global fold and secondary structure are preserved, and where changes can be expected (Kim et al., 1994). Despite its useful nature, chemical shift comparison can be very tedious and error prone. The GSC program has been developed to make it easy to analyze chemical shifts of selected atoms between chemical shift files. We have used GSC with great success to compare predicted chemical shifts with observed ones to gain insight into the accuracy of our new NMR chemical shift prediction program ORB (Gronwald etai, 1997).Figure 1 shows a main screen snapshot of GSC. The program is started by designating one set of shifts as the 'reference shifts' and either one or two other shift sets as 'comparison shifts'. Once the user selects the atom type (e.g. HN, Ha, Ca, etc.) and the region of the sequences to study, the program draws line graph(s) depicting the difference in shifts between the reference and comparison shifts. The Pearson correlation coefficient (Larson and Marx, 1981) and the average error measure overall chemical shift difference. Here the average error is the sum of the absolute values of all chemical shift differences (in p.p.m.) divided by the number of compared atoms.