Solution structure of the octamer motif in immunoglobulin genes via restrained molecular dynamics calculations

Abstract

The solution structure of the DNA decamer d(CATTTGCATC)-d(GATGCAAATG), comprising the octamer motif of immunoglobulin genes, is determined by restrained molecular dynamics (rMD) simulations. The restraint data set includes interproton distances and torsion angles for the deoxyribose sugar ring which were previously obtained by a complete relaxation matrix analysis of the two-dimensional nuclear Overhauser enhancement (2D NOE) intensities and by the quantitative simulation of cross-peaks in double-quantum-filtered correlated (2QF-COSY) spectra. The influence of torsion angles and the number of experimental distance restraints on the structural refinement has been systematically examined. Omitting part of the experimental NOE-derived distances results in reduced restraint violations and lower R factors but impairs structural convergence in the rMD refinement. Eight separate restrained molecular dynamics simulations were carried out for 20 ps each, starting from either energy-minimized A- or B-DNA. Mutual atomic root-mean-square (rms) differences among the refined structures are well below 1 A and comparable to the rms fluctuations of the atoms about their average position, indicating convergence to essentially identical structures. The average refined structure was subjected to an additional 100 ps of rMD simulations and analyzed in terms of average torsion angles and helical parameters. The B-type duplex exhibits clear sequence-dependent variations in its geometry with a narrow minor groove at the T3.A3 tract and a large positive roll at the subsequent TG.CA step. This is accompanied by a noticeable bend of the global helix axis into the major groove. There is also evidence of significant flexibility of the sugar-phosphate backbone with rapid interconversion among different conformers.

Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants

“…22,23 Sprous et al 24 characterized an AMBER MD model for an A-form structure of the Eco RI dodecamer, obtained from a simulation carried out in an 85% ethanol/water mixed solvent. Konderding et al 25 described the use of the Cornell et al force field with PME in restrained MD based on NMR-derived distance and torsional restraints for two previously determined DNA sequences, 26 and compared the resulting conformations to those obtained in free MD simulations. They found the agreement for some structural aspects of the NMR derived structure and the free MD to be quite good, but commented on significant differences in helical twist values.…”

Structural characterization of intrinsically curved AT-rich DNA sequences

“…On the contray, our results indicate that the conformation of most dinucleotide steps is sequence dependent as judged by the different reactivities with DNase I, OH and/or DEPC that they show in different sequence contexts. Recent NMR data also suggest that the conformation of particular dinucleotide steps is sequence dependent (39,40).…”

Interproton distance bounds from 2D NOE intensities: Effect of experimental noise and peak integration errors

“…To investigate this effect, we selected a single-stranded trinucleotide dTTG (Fig. 1C), which is part of a recently solved structure of a DNA duplex in solution (Weisz et al, 1994). An interesting feature of this structure is a sharp bend in the direction of the major groove, localized in the complementary dinucleotide TG : CA (Weisz et al, 1994).…”

“…1C), which is part of a recently solved structure of a DNA duplex in solution (Weisz et al, 1994). An interesting feature of this structure is a sharp bend in the direction of the major groove, localized in the complementary dinucleotide TG : CA (Weisz et al, 1994). Such a bend is a common feature of TG sequences in solution (Ulyanov and James, 1994), in crystals (Gorin et al, 1995), and on polyacrylamide gels (Beutel and Gold, 1992).…”

“…Such a bend is a common feature of TG sequences in solution (Ulyanov and James, 1994), in crystals (Gorin et al, 1995), and on polyacrylamide gels (Beutel and Gold, 1992). For the purpose of this study, the atomic coordinates of the trinucleotide dTTG were calculated using the idealized bond length and bond angle values and the helical parameters of the solution DNA decamer (Weisz et al, 1994). Protons H2', H2" and H6 of the central thymine are positioned almost in line (Fig.…”