Analysis Of Hydrogen-bond Patterns Research Articles

Database analysis of hydrogen bond patterns in phosphoric triamides completed with seven new compounds: a crystallographic and15N NMR study

We present the synthesis and characterization of seven new phosphoric triamides followed by analysis of hydrogen bond patterns of the new compounds as well as the phosphoric triamides found in the Cambridge Structural Database (CSD). The analysis of hydrogen bond patterns updates the previous work (Toghraee, Pourayoubi and Divjakovic in Polyhedron, 2011, 30, 1680) on phosphoric triamides with a C(O)NHP(O)[N]2 skeleton, and extends the analysis to other phosphoric triamides i.e. ones without a CO attached to the N of N–PO. For the new phosphoric triamides we also investigated their spectroscopic features (31P, 1H, 13C, and 15N NMR, mass spectroscopy, IR spectroscopy), measured the 1J(15N,31P) coupling constants and discussed the effective parameters.

Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction

Molecular dynamics simulation of Escherichia colitrp-repressor/operator complex was performed to elucidate protein–DNA interactions in solution for 800ps on special-purpose computer MD-GRAPE. The Ewald summation method was employed to treat the electrostatic interaction without cutoff. DNA kept stable conformation in comparison with the result of the conventional cutoff method. Thus, the trajectories obtained were used to analyze the protein–DNA interaction and to understand the role of dynamics of water molecules forming sequence specific recognition interface. The dynamical cross-correlation map showed a significant positive correlation between the helix-turn-helix DNA-binding motifs and the major grooves of operator DNA. The extensive contact surface was stable during the simulation. Most of the contacts consisted of direct interactions between phosphates of DNA and the protein, but several water-mediated polar contacts were also observed. These water-mediated interactions, which were also seen in the crystal structure (Z. Otwinowski, et al., Nature, 335 (1998) 321) emerged spontaneously from the randomized initial configuration of the solvent. This result suggests the importance of the water-mediated interaction in specific recognition of DNA by the trp-repressor, consistent with X-ray structural information.