All of the 100 molecules obtained from the DGSA calculations were subjected to NOE-restrained simulated annealing refinement in XPLOR (47 ) with a distance-dependent dielectric constant, as described previously (39 (link),43 (link)). The force constants were scaled at 10–30 and 80–100 kcal mol−1 Å−2 for NOE and hydrogen bond distance restraints, respectively. A total of 727 NOE distance restraints, of which 324 are from inter-residue NOEs, were incorporated into the NOE-restrained structure calculation.
Dihedral angle restraints were used to restrict the glycosidic torsion angle (χ) for the experimentally assigned syn and anti conformations. A dihedral angle restraint of 60(±35)° was applied to the syn G-tetrad guanines, and a dihedral angle restraint of 240(±40)° was applied to the anti G-tetrad guanines. The force constants of dihedral angle restraints were 10 kcal · mol−1 · rad−2.
NOE-restrained simulated annealing refinement calculations were performed as described previously (39 (link),43 (link)). The time steps for all processes of heating, cooling and equilibration were set to 1 fs. The 10 best molecules were selected based both on their minimal energy terms and number of NOE violations and have been deposited in the Protein Data Bank (PDB ID 2JPZ).
Dihedral angle restraints were used to restrict the glycosidic torsion angle (χ) for the experimentally assigned syn and anti conformations. A dihedral angle restraint of 60(±35)° was applied to the syn G-tetrad guanines, and a dihedral angle restraint of 240(±40)° was applied to the anti G-tetrad guanines. The force constants of dihedral angle restraints were 10 kcal · mol−1 · rad−2.
NOE-restrained simulated annealing refinement calculations were performed as described previously (39 (link),43 (link)). The time steps for all processes of heating, cooling and equilibration were set to 1 fs. The 10 best molecules were selected based both on their minimal energy terms and number of NOE violations and have been deposited in the Protein Data Bank (PDB ID 2JPZ).
