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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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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Abstract 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
AbstractList 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
Author Yang, Changwon
Kim, Eunae
Pak, Youngshang
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Cites_doi 10.1529/biophysj.106.097782
10.1021/ja010008o
10.1093/nar/gkr639
10.1021/ct100253m
10.1021/ct900200k
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10.1107/S0907444995013977
10.1021/jp901540t
10.1080/07391102.2004.10506977
10.1107/S0907444907029976
10.1063/1.445869
10.1093/nar/28.9.1969
10.1038/3949
10.1529/biophysj.107.117382
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Snippet Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specifically binds to the thrombin protein involved in blood...
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Title Potential of Mean Force Simulation by Pulling a DNA Aptamer in Complex with Thrombin
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