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

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...

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Bibliographic Details
Published inBulletin of the Korean Chemical Society Vol. 33; no. 11; pp. 3597 - 3600
Main Authors Yang, Changwon, Kim, Eunae, Pak, Youngshang
Format Journal Article
LanguageEnglish
Published 대한화학회 20.11.2012
Subjects
화학
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Summary: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. KCI Citation Count: 5
Bibliography:G704-000067.2012.33.11.050
http://journal.kcsnet.or.kr/main/j_search/j_abstract_view.htm?code=B121114&qpage=j_search&spage=b_bkcs&dpage=ar
ISSN:0253-2964
1229-5949
DOI:10.5012/bkcs.2012.33.11.3597