Molecular modeling of anti-parallel G-quadruplex DNA/TMPyP complexes.
We carried out the molecular modeling of anti-parallel G-quadruplex/TMPyP complex, molecular dynamics simulation and estimation of binding free energy using MM-PBSA method to validate groove binding model in addition to external stacking one. We found that not total electrostatic but van der Waals energy contributes to the negative binding free energies in both models.
Ishikawa
Yoshinobu
Y
Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan.
Tomisugi
Yoshikazu
Y
Uno
Tadayuki
T
D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011166:Porphyrins / Q000737:chemistry*
D011166:Porphyrins; C021096:tetra(4-N-methylpyridyl)porphine; D006147:Guanine; D004247:DNA