Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli

Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

“…Consequently, the appropriate choice of reference distance in the calculation of the unknown interproton distances has to be made. This has been discussed and verified in detail previously (Gronenborn et al, 1984a;Gronenborn & Clore, 1985) so only the conclusions will be given here: namely, all unknown distances involving sugar-sugar and sugar-base (with the exception of the H 1' sugar-base) vectors should be calculated by using the H2'-H2" cross-relaxation rate and distance as a reference, while all those involving base-base and sugar H1'-base vectors should be calculated by using the C(H5)-C(H6) or T(CH3)-T(H6) cross-relaxation rates and distances as a reference. This choice is based on the reasoning that the contribution from internal motion to the effective correlation times of the first class of distances will mainly be dominated by motion within the sugar units whereas that of the second class will mainly be dominated by motion about the glycosidic bond.…”

“…The complete list of assignments is given in Table I. The low-resolution solution structure of an oligonucleotide is readily deduced from a qualitative assessment of the relative NOE cross-peak intensities [for a review see Clore and Gronenborn (1985a) and Gronenborn and Clore (1985)l as these are approximately proportional to (rd) at short mixing times. In the case of the hexamer, the pattern of NOE cross-peak intensities is indicative of a right-handed B-type structure.…”

“…These interproton distances can then be used as the basis of a structure determination or refinement. The method we have chosen is restrained molecular dynamics in which the interproton distances are incorporated into the total energy function of the system in the form of effective potentials and energetic considerations are taken into account during the entire course of the structure refinement or determination (Kaptein et al, 0006-2960/87/0426-37 18$01 SO10 1985; Clore et al, 1985). This particular method has been shown to have a large radius of convergence when applied to both proteins Clore et al, 1986a) and oligonucleotides (Nilsson et al, 1986).…”

Two-Dimensional1H and31P NMR Spectra of a Decamer Oligodeoxyribonucleotide Duplex and a Quinoxaline ([MeCys3, MeCys7]TANDEM) Drug Duplex Complex

“…Starting from an idealized model-built duplex structure, we have used NOESY-derived distances to constrain the molecular mechanics/dynamics energy minimization program AMBER (51) to minimize the energy of the decamer duplex. Instead of a simple harmonic potential error function to restrain the NMR-derived distances, we have modified AMBER so as to provide a flat well harmonic function which better reflects the intrinsic accuracy of these NO-ESY distance restraints (62,92). We have generally used an estimated error of ± 15% in the NOESY distances.…”

Automated Assignment of Simulated and Experimental NOESY Spectra of Proteins by Feedback Filtering and Self-correcting Distance Geometry

“…Since the early calculations of three-dimensional protein structures directly from nuclear magnetic resonance data (Arseniev et al, 1984;Kaptein et al, 1985;Williamson et al, 1985;Braun et al, 1986;Kline et al, 1986;Brü nger et al, 1986) the conventional way of solving structures relies on the identification of spin systems (Nagayama & Wü thrich, 1981), sequence specific assignments , assignment of two-dimensional homonuclear or three-and fourdimensional heteronuclear edited NOESY spectra (Fesik & Zuiderweg, 1988;Clore & Gronenborn, 1991) and the calculation of three-dimensional structures from distance constraints (Braun et al, 1981Havel et al, 1983;Clore et al, 1985;Braun & Gō , 1985). Several strategies for sequence specific assignments by combining various heteronuclear experiments have been proposed (Bax & Grzesiek, 1993), which lead to complete assignments of proteins with molecular weight up to 30 kDa (Fairbrother et al, 1992;Stockmann et al, 1992;Grzesiek et al, 1992;Thériault et al, 1993;Spitzfaden et al, 1994;Fogh et al, 1994;Remerowski et al, 1994).…”