Yang Changwon, Kulkarni Mandar, Lim Manho, Pak Youngshang
Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 609-735, South Korea.
Nucleic Acids Res. 2017 Dec 15;45(22):12648-12656. doi: 10.1093/nar/gkx1079.
The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10-12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K+ ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers.
利用延长时间尺度（10 - 12微秒）的并行回火元动力学（PTMetaD）模拟方法，结合修改版的AMBER bsc1力场，证明了凝血酶结合DNA适体G-四链体（GQs）（TBA - 15）从完全展开状态开始的可逆折叠。为了对TBA - 15的折叠自由能景观进行无偏描述，对该力场进行了最小程度的修改。通过使用修改后的bsc1力场进行的这种直接折叠模拟，在富含K⁺的水溶液（150 mM）中获得了合理收敛的自由能景观，提供了TBA - 15的GQ折叠机制的详细原子水平图像。该研究发现，在存在G-三链体变体的几个中间状态的情况下，TBA折叠通过多个折叠途径发生，具有两个主要自由能垒，分别为13和15千卡/摩尔。这些中间体的早期形成与单个K⁺离子捕获有关。有趣的是，这些中间状态似乎通过相对较小的能垒在它们自身之间进行容易的转变。
