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- Title
- Potential of Mean Force Simulation by Pulling a DNA Aptamer in Complex with Thrombin
- Author(s)
- ChangwonYang,; 김은애
- Publication Year
- 2012-10-31
- Abstract
-
Thrombinbindingaptamter(TBA-15)isa15-merguanine-richoligonucleotide.ThisDNAapamerspecifically
bindstothethrombinproteininvolvedinbloodcoagulation.Usingextensiveumbrellasamplingmolecular
dynamicssimulationmethodatallatomlevel,weinvestigatedthepotentialofmeanforce(PMF)uponpulling
theDNAaptamerfromthebindingmodeofaptamer/thrombincomplex.Fromthiscalculation,thefreeenergy
costforafulldissociationofthisaptamer/proteincomplexis17kcal/mol,indicatingasubstantialbinding
affinityofTBA-15.Interestingly,thisPMFrevealsnoticeableplateauregionsalongthepullingcoordinate.
Possiblestructuralchangesofthiscomplexintheplateauwereinvestigatedindetails.
- Keyword
- TBA-15; Thrombinbindingaptamer; Umbrallasampling; Potentialofmeanforce
- Journal Title
- BulletinoftheKoreanChemicalSociety
- Citation Volume
- 33
- ISSN
- 0253-2964
- Files in This Item:
- There are no files associated with this item.
- Appears in Collections:
- 7. KISTI 연구성과 > 학술지 발표논문
http://www.ndsl.kr/ndsl/commons/util/ndslOriginalView.do?dbt=JAKO&cn=JAKO201236135722954
