Journal
BULLETIN OF THE KOREAN CHEMICAL SOCIETY
Volume 33, Issue 11, Pages 3597-3600Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.5012/bkcs.2012.33.11.3597
Keywords
TBA-15; Thrombin binding aptamer; Umbralla sampling; Potential of mean force
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Funding
- Pusan National University
- National Research Council of Science & Technology (NST), Republic of Korea [K-12-L10-C05] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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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.
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