Ishikawa Yoshinobu, Tomisugi Yoshikazu, Uno Tadayuki
Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan.
Nucleic Acids Symp Ser (Oxf). 2006(50):331-2. doi: 10.1093/nass/nrl165.
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.
我们进行了反平行G-四链体/TMPyP复合物的分子建模、分子动力学模拟，并使用MM-PBSA方法估算结合自由能，以验证除外部堆积模型外的沟槽结合模型。我们发现，在这两种模型中，并非总静电能而是范德华能对负结合自由能有贡献。
