On the importance of van der Waals interaction in the groove binding of DNA with ligands: restrained molecular dynamics study.
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 major groove mode whereas less significant changes for both ligand and DNA were detected for the minor groove binding after molecular dynamics simulation. The conformation of the ligand obtained from the major groove modes resembles that computed with the ligand soaked in water. The van der Waals contact energy was found to be as significant as electrostatic energy and more important for difference in binding energy between 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 operator oligonucleotide.
Chang
D K
DK
Institute of Chemistry, Academia Sinica, Taipei, Taiwan, ROC. dkc@chem.sinica.edu.tw
Cheng
S F
SF
D001435:Bacteriophages / Q000737:chemistry / Q000235:genetics; D001665:Binding Sites; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D009429:Netropsin / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
D009692:Nucleic Acid Heteroduplexes; D012097:Repressor Proteins; D009429:Netropsin; D004247:DNA