Jayapal Prabha, Mayer Günter, Heckel Alexander, Wennmohs Frank
Department of Theoretical Chemistry, Institute for Physical & Theoretical Chemistry, Bonn University, Wegeler Str. 12, D-53115 Bonn, Germany.
J Struct Biol. 2009 Jun;166(3):241-50. doi: 10.1016/j.jsb.2009.01.010. Epub 2009 Mar 11.
15-mer ssDNA aptamers play a vital role in the inhibition of alpha-thrombin in the blood clotting mechanism. It is of high importance to explore the structural factors controlling the inhibitory nature of the aptamer. Here we investigated the structure-function relationship of the anti-thrombin aptamer, as well as its 'caged' variant (2-(2-nitrophenyl)-propyl group (NPP)) by molecular dynamics simulations. The stability of the unmodified aptamer at different temperatures is examined in 2ns all-atom simulations and compared to experiment. The change in structure when introducing the photo-labile caged compound is analyzed, and the regiospecificity of this modification explained on atomic level. Removal of the photo-labile group leads to the reformation of the active aptamer structure from its inactive state. The mechanism for this formation process is a concerted movement of the aptamer backbone and some highly important bases. The binding of the aptamer to thrombin with regard to the 'caged' group is studied in an explicit simulation with the aptamer-thrombin complex and the reason for the binding/unbinding nature of the aptamer shown.
15聚体单链DNA适配体在血液凝固机制中对α-凝血酶的抑制作用中发挥着至关重要的作用。探索控制适配体抑制特性的结构因素具有高度重要性。在此，我们通过分子动力学模拟研究了抗凝血酶适配体及其“笼化”变体（2-(2-硝基苯基)-丙基基团（NPP））的结构-功能关系。在2纳秒的全原子模拟中考察了未修饰适配体在不同温度下的稳定性，并与实验结果进行比较。分析了引入光不稳定笼化化合物时的结构变化，并在原子水平上解释了这种修饰的区域特异性。去除光不稳定基团会导致活性适配体结构从其非活性状态重新形成。这种形成过程的机制是适配体主链和一些非常重要的碱基的协同运动。在与适配体-凝血酶复合物的显式模拟中研究了适配体与凝血酶关于“笼化”基团的结合，并展示了适配体结合/解离性质的原因。
