Potential of Mean Force Simulation by Pulling a DNA Aptamer in Complex with Thrombin

Bulletin of the Korean chemical society

Changwon Yang¹  Youngshang Pak¹  Eunae Kim¹ 

关键词: TBA-15;    Thrombin binding aptamer;    Umbralla sampling;    Potential of mean force;   

DOI  :  

学科分类：化学（综合）

来源: Korean Chemical Society

【 摘 要 】

Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specifically binds to the thrombin protein involved in blood coagulation. Using extensive umbrella sampling molecular dynamics simulation method at all atom level, we investigated the potential of mean force (PMF) upon pulling the DNA aptamer from the binding mode of aptamer/thrombin complex. From this calculation, the free energy cost for a full dissociation of this aptamer/protein complex is 17 kcal/mol, indicating a substantial binding affinity of TBA-15. Interestingly, this PMF reveals noticeable plateau regions along the pulling coordinate. Possible structural changes of this complex in the plateau were investigated in details.

【 授权许可】

Unknown