NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths

Hydrogen bonding in cold-shock protein A of Escherichia coli has been investigated using long-range HNCO spectroscopy. Nearly half of the amide protons involved in hydrogen bonds in solution show no measurable protection from exchange in water, cautioning against a direct correspondence between hydrogen bonding and hydrogen exchange protection. The N to O atom distance across a hydrogen bond, R(NO), is related to the size of the (3h)J(NC') trans hydrogen bond coupling constant and the amide proton chemical shift. Both NMR parameters show poorer agreement with the 2.0-A resolution X-ray structure of the cold-shock protein studied by NMR than with a 1.2-A resolution X-ray structure of a homologous cold-shock protein from the thermophile B. caldolyticus. The influence of crystallographic resolution on comparisons of hydrogen bond lengths was further investigated using a database of 33 X-ray structures of ribonuclease A. For highly similar structures, both hydrogen bond R(NO) distance and Calpha coordinate root mean square deviations (RMSD) show systematic increases as the resolution of the X-ray structure used for comparison decreases. As structures diverge, the effects of coordinate errors on R(NO) distance and Calpha coordinate root mean square deviations become progressively smaller. The results of this study are discussed with regard to the influence of data precision on establishing structure similarity relationships between proteins.