Pasquali S, Frezza E, Barroso da Silva F L
Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Université Paris Descartes, Paris 75006, France.
Departamento de Física e Química, Faculdade de Ciência s Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do café, s/no, Ribeirão Preto, SP BR-14040-903, Brazil.
Interface Focus. 2019 Jun 6;9(3):20180066. doi: 10.1098/rsfs.2018.0066. Epub 2019 Apr 19.
Electrostatic interactions play a pivotal role in many biomolecular processes. The molecular organization and function in biological systems are largely determined by these interactions. Owing to the highly negative charge of RNA, the effect is expected to be more pronounced in this system. Moreover, RNA base pairing is dependent on the charge of the base, giving rise to alternative secondary and tertiary structures. The equilibrium between uncharged and charged bases is regulated by the solution pH, which is therefore a key environmental condition influencing the molecule's structure and behaviour. By means of constant-pH Monte Carlo simulations based on a fast proton titration scheme, coupled with the coarse-grained model HiRE-RNA, molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local p values for each nucleotide.
静电相互作用在许多生物分子过程中起着关键作用。生物系统中的分子组织和功能在很大程度上由这些相互作用决定。由于RNA带高度负电荷，预计这种效应在该系统中会更加明显。此外，RNA碱基配对取决于碱基的电荷，从而产生不同的二级和三级结构。不带电和带电碱基之间的平衡受溶液pH值调节，因此pH值是影响分子结构和行为的关键环境条件。通过基于快速质子滴定方案的恒pH蒙特卡罗模拟，结合粗粒度模型HiRE-RNA，在恒定pH值下对RNA分子进行分子动力学模拟，使我们能够探索不同pH值下RNA的构象可塑性，并计算每个核苷酸的局部p值等静电性质。
