ON THE IMPORTANCE OF VAN-DER-WAALS INTERACTION IN THE GROOVE BINDING OF DNA WITH LIGANDS - RESTRAINED MOLECULAR-DYNAMICS STUDY

Authors
Citation
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
Citations number
29
Categorie Soggetti
Biology
ISSN journal
01418130
Volume
19
Issue
4
Year of publication
1996
Pages
279 - 285
Database
ISI
SICI code
0141-8130(1996)19:4<279:OTIOVI>2.0.ZU;2-2
Abstract
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.