Dynamics of the DNA binding domain of the fructose repressor from the analysis of linear correlations between the 15N-1H bond spectral densities obtained by nuclear magnetic resonance spectroscopy.
The spectral densities of the backbone and arginine side chain NH bonds of the DNA binding domain of the fructose repressor (FruR) were extensively analyzed in order to extract reliable motions parameters. An accurate measurement of 15N NMR relaxation rates allowed their calculation at three frequencies, zero, omegaN, and omegaH + omegaN, using a reduced matrix approach. Linear correlations were found between J(omegaN) and J(0) and between <J(omegaH)> and J(0). The analysis of the compatibility between the motions parameters obtained independently from the two correlation lines allowed further development of the linear correlation approach proposed recently [Lefèvre, J. F., Dayie, K. T., Peng, J. W., and Wagner, G. (1996) Biochemistry 35, 2674-2686]. The results demonstrate (i) the existence of a concerted motion along the whole backbone with a global correlation time equal to 5.95 ns.rad-1, and (ii) the presence of complex internal movements at an intermediate time scale around 1 ns. The extracted motion parameters have been related to those obtained with the extended Lipari and Szabo approach but are incompatible with those obtained using the usual simple Lipari and Szabo approach. They were correlated to the features of the NMR structure of FruR(1-57)*. Some residues in the turns and in the third helix experience slow motions in the micro- to millisecond time scale. Side-chain motions are not correlated to the backbone dynamics. A direct examination of spectral densities reveals a higher flexibility for the side chains of arginines that are not involved in ionic bridges.
van Heijenoort
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C
Institut de Chimie des Substances Naturelles, Laboratoire de Résonance Magnétique Nucléaire, 1 Avenue de la Terrasse, Centre National de la Recherche Scientifique, F-91190 Gif sur Yvette, France.
Penin
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F
Guittet
E
E
D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D006859:Hydrogen; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry*; D013997:Time Factors; D056968:Lac Repressors
D001120:Arginine; D001426:Bacterial Proteins; D006859:Hydrogen; D009587:Nitrogen Isotopes; D010446:Peptide Fragments; D012097:Repressor Proteins; C068837:FruR protein, Bacteria; D056968:Lac Repressors