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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure
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Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure

机译：三甲胺N-氧化物（TMAO）的质子化需要稳定RNA三级结构

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摘要

The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQ_1 riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQ_1. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQ_1 ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent.
机译：渗透液三甲胺N-氧化物（TMAO）可稳定RNA的三级结构，但不能稳定二级结构。但是，对PreQ_1核糖开关进行的分子动力学模拟表明，TMAO使三级核糖开关结构不稳定，从而使我们假设RNA的存在可能导致质子化形式TMAOP的增加。恒定的pH复制副本交换模拟表明，一定比例的TMAO确实已质子化，因此有助于PreQ_1的三级结构而不是二级结构的稳定性。 TMAOP导致磷酸二酯主链的不利脱水，这可通过TMAOP和磷酸基团之间的静电吸引来补偿。此外，TMAOP与第三级RNA结构中的特定位点相互作用，模仿带正电的离子和PreQ_1配体在稳定RNA中的行为。最后，我们预测TMAO诱导的RNA三级结构的稳定应该强烈依赖于pH。

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