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化学学报
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化学学报 ›› 2009, Vol. 67 ›› Issue (3): 255-260. 上一篇    下一篇

研究论文

应用MM/PBSA方法研究CDK2活性口袋内溶剂水分子对CDK2-配体结合自由能的影响

杨丽君a,b 贾 若a 杨胜勇*,a

  

  1. (a四川大学华西医院 生物治疗国家重点实验室 成都 610041)
    (b西华师范大学化学化工学院 南充 637002)

  • 投稿日期:2008-06-10 修回日期:2008-08-27 发布日期:2009-02-14
  • 通讯作者: 杨胜勇

Influence of the Solvent Water Molecules at the Active Site of CDK2 on the Binding Free Energy of CDK2-ligand Complexes: an MM/PBSA Study

Yang, Lijun a,b Jia, Ruo a Yang, Shengyong *,a   

  1. (a State Key Laboratory of Biotherapy, West China Hospital, West China Medical School,
    Sichuan University, Chengdu 610041)
    (b College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002)
  • Received:2008-06-10 Revised:2008-08-27 Published:2009-02-14
  • Contact: Yang, Shengyong

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被引次数

4

应用MM/PBSA方法研究了CDK2活性口袋内溶剂水分子对CDK2-配体结合自由能的影响. 结果表明, 活性口袋内溶剂水分子对CDK2-配体相互作用自由能有一定的贡献, 其贡献的大小随配体不同而有所差异, 导致这种差异的主要原因是活性位点内溶剂水分子与蛋白残基和配体之间形成了不同的氢键相互作用网络.

关键词: MM/PBSA, CDK2, 结合自由能, 溶剂水分子, 分子动力学

An MM/PBSA method has been used to investigate the influence of the solvent water molecules at the active site of CDK2 on the binding free energy of CDK2-ligand complexes. The results show that the solvent water molecules at the active site of CDK2 have some contribution to the binding free energy of CDK2-ligand complex. However, the magnitude of contribution depends on the characteristic of the corresponding ligand. The difference of the contribution is mainly due to the different hydrogen bonding interaction network formed among the water molecules, the protein residues and ligand.

Key words: MM/PBSA, CDK2, binding free energy, solvent water molecule, molecular dynamics