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

Citation
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
Citations number
47
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEIN SCIENCE
ISSN journal
0961-8368 → ACNP
Volume
10
Issue
9
Year of publication
2001
Pages
1856 - 1868
Database
ISI
SICI code
0961-8368(200109)10:9<1856:NOHBIC>2.0.ZU;2-9
Abstract
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.