NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths
At. Alexandrescu et al., NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths, PROTEIN SCI, 10(9), 2001, pp. 1856-1868
Hydrogen bonding in cold-shock protein A of Escherichia coli has been inves
tigated using long-range HNCO spectroscopy. Nearly half of the amide proton
s involved in hydrogen bonds in solution show no measurable protection from
exchange in water, cautioning against a direct correspondence between hydr
ogen bonding and hydrogen exchange protection. The N to O atom distance acr
oss 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 N
MR parameters show poorer agreement with the 2.0-Angstrom resolution X-ray
structure of the cold-shock protein studied by NMR than with a 1.2-Angstrom
resolution X-ray structure of a homologous cold-shock protein from the the
rmophile B. caldolyticus. The influence of crystallographic resolution on c
omparisons of, hydrogen bond lengths was further investigated using a datab
ase of 33 X-ray structures of ribonuclease A. For highly similar structures
, both hydrogen bond R-NO distance and C alpha 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 C alpha coordinate root mean squ
are deviations become progressively smaller. The results of this study are
discussed with regard to the influence of data precision on establishing st
ructure similarity relationships between proteins.