Reshetnikov Roman, Golovin Andrey, Spiridonova Vera, Kopylov Alexei, Šponer Jiří
Department of Boiengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation.
A.N.Belozersky Institute of Physical Chemical Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation.
J Chem Theory Comput. 2010 Oct 12;6(10):3003-14. doi: 10.1021/ct100253m.
The thrombin-binding aptamer (15-TBA) is a 15-mer DNA oligonucleotide with sequence d(GGTTGGTGTGGTTGG). 15-TBA folds into a quadruplex DNA (G-DNA) structure with two planar G-quartets connected by three single-stranded loops. The arrangement of the 15-TBA-thrombin complex is unclear, particularly with respect to the precise 15-TBA residues that interact with the thrombin structure. Our present understanding suggests either the 15-TBA single stranded loops containing sequential thymidines (TT) or alternatively a single-stranded loop, containing a guanine flanked by 2 thymidines (TGT), physically associates with thrombin protein. In the present study, the explicit solvent molecular dynamics (MD) simulation method was utilized to further analyze the 15-TBA-thrombin three-dimensional structure. Functional annotation of the loop residues was made with long simulations in the parmbsc0 force field. In total, the elapsed time of simulations carried out in this study exceeds 12 microseconds, substantially surpassing previous G-DNA simulation reports. Our simulations suggest that the TGT-loop function is to stabilize the structure of the aptamer, while the TT-loops participate in direct binding to thrombin. The findings of the present report advance our understanding of the molecular structure of the 15-TBA-thrombin structure further enabling the construction of biosensors for aptamer bases and the development of anticoagulant agents.
凝血酶结合适体（15-TBA）是一种15聚体DNA寡核苷酸，序列为d(GGTTGGTGTGGTTGG)。15-TBA折叠成一种四链体DNA（G-DNA）结构，由两个平面G-四联体通过三个单链环连接。15-TBA-凝血酶复合物的排列尚不清楚，特别是与凝血酶结构相互作用的精确15-TBA残基方面。我们目前的理解表明，要么是含有连续胸腺嘧啶（TT）的15-TBA单链环，要么是含有一个被两个胸腺嘧啶（TGT）侧翼的鸟嘌呤的单链环，与凝血酶蛋白发生物理结合。在本研究中，利用显式溶剂分子动力学（MD）模拟方法进一步分析15-TBA-凝血酶的三维结构。在parmbsc0力场中通过长时间模拟对环残基进行功能注释。本研究中进行的模拟总耗时超过12微秒，大大超过了之前的G-DNA模拟报告。我们的模拟表明，TGT环的功能是稳定适体的结构，而TT环参与与凝血酶的直接结合。本报告的研究结果推进了我们对15-TBA-凝血酶结构分子结构的理解，进一步推动了适体碱基生物传感器的构建和抗凝剂的开发。
