Dk. Chang et Sf. Cheng, ON THE IMPORTANCE OF VAN-DER-WAALS INTERACTION IN THE GROOVE BINDING OF DNA WITH LIGANDS - RESTRAINED MOLECULAR-DYNAMICS STUDY, International journal of biological macromolecules, 19(4), 1996, pp. 279-285
Comparison of interaction energy between an oligonucleotide and a DNA-
binding ligand in the minor and major groove modes was made by use of
restrained molecular dynamics. Distortion in DNA was found for the maj
or groove mode whereas less significant changes for both ligand and DN
A were detected for the minor groove binding after molecular dynamics
simulation. The conformation of the ligand obtained from the major gro
ove mode resembles that computed with the ligand soaked in water. The
van der Waals contact energy was found to be as significant as electro
static energy and more important for difference in binding energy betw
een these two binding modes. The importance of van der Waals force in
groove binding was supported by computations on the complex formed by
the repressor peptide fragment from the bacteriophage 434 and its oper
ator oligonucleotide. Copyright (C) 1996 Elsevier Science B.V.