title: Spectral densities of nitrogen nuclei in Escherichia coli ribonuclease HI obtained by 15N NMR relaxation and molecular dynamics.
abstract: Spectral densities of the 15N amide in Escherichia coli ribonuclease HI, obtained from NMR relaxation experiments, were compared with those calculated using a molecular dynamics (MD) simulation. All calculations and comparisons assumed that the auto-correlation function describing the internal motions of the molecule was independent of the auto-correlation function associated with overall rotational diffusion. Comparisons were limited to those residues for which the auto-correlation function of internal motions rapidly relaxed and reached a steady state within 205 ps. The results show the importance of frequency components as well as amplitudes of internal motions in order to obtain a meaningful comparison of MD simulations with NMR data.
authors.affiliation: Nagayama Protein Array Project, ERATO, JRDC, Tsukuba Research Consortium, Pilot Laboratory, Japan.
authors.forename: R
authors.initials: R
authors.lastname: Ishima
authors.forename: K
authors.initials: K
authors.lastname: Yamasaki
authors.forename: M
authors.initials: M
authors.lastname: Saito
authors.forename: K
authors.initials: K
authors.lastname: Nagayama
mesh_terms: D003198:Computer Simulation; D004926:Escherichia coli / Q000201:enzymology*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry*; D009587:Nitrogen Isotopes; D016914:Ribonuclease H / Q000737:chemistry*
chemical_list: D009587:Nitrogen Isotopes; D016914:Ribonuclease H; C078856:ribonuclease HI; D009584:Nitrogen