Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India.
J Chem Inf Model. 2018 Aug 27;58(8):1638-1651. doi: 10.1021/acs.jcim.8b00155. Epub 2018 Jul 27.
Thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in the noncoding region of mRNA. The aptamer domain of TPP riboswitch detects the high abundance of coenzyme thiamine pyrophosphate (TPP) and modulates the gene expression for thiamine synthetic gene. The mechanistic understanding in recognition of TPP in aptamer domain and ligand-induced compactness for folding of expression platform are most important to designing novel modulators. To understand the dynamic behavior of TPP riboswitch upon TPP binding, molecular dynamics simulations were performed for 400 ns in both apo and TPP bound forms of thiM riboswitch from E. coli and analyzed in terms of eRMSD-based Markov state modeling and residual fluctuation network. Markov state models show good correlations in transition probability among metastable states from simulated trajectory and generated models. Structural compactness in TPP bound form is observed which is correlated with SAXS experiment. The importance of junction of P4 and P5 is evident during dynamics, which correlates with FRET analysis. The dynamic nature of two sensor forearms is due to the flexible P1 helix, which is its intrinsic property. The transient state in TPP-bound form was observed in the Markov state model, along with stable states. We believe that this transient state is responsible to assist the influx and outflux of ligand molecule by creating a solvent channel around the junction region of P4 and P5 and such a structure was anticipated in FRET analysis. The dynamic nature of riboswitch is dependent on the interaction between residues on distal loops L3 and L5/P3 and junction P4 and P5, J3/2 which stabilize the J2/4. It helps in the transfer of allosteric information between J2/4 and P3/L5 tertiary docking region through the active site residues. Understanding such information flow will benefit in highlighting crucial residues in highly dynamic and kinetic systems. Here, we report the residues and segments in riboswitch that play vital roles in providing stability and this can be exploited in designing inhibitors to regulate the functioning of riboswitches.
硫胺素焦磷酸（TPP）核糖开关是 mRNA 非编码区的顺式调控元件。TPP 核糖开关的适体结构域检测辅酶 TPP 的高丰度，并调节硫胺素合成基因的表达。在适体结构域中识别 TPP 的机制理解以及配体诱导表达平台折叠的紧凑性对于设计新型调节剂至关重要。为了了解 TPP 结合后 TPP 核糖开关的动态行为，对来自大肠杆菌的 thiM 核糖开关的 apo 和 TPP 结合形式进行了 400 ns 的分子动力学模拟，并根据 eRMSD 基马尔可夫状态建模和残差波动网络进行了分析。马尔可夫状态模型显示，模拟轨迹和生成模型之间的亚稳态之间的跃迁概率具有很好的相关性。在 TPP 结合形式中观察到结构紧凑性，这与 SAXS 实验相关。在动力学过程中，P4 和 P5 的连接的重要性是明显的，这与 FRET 分析相关。两个传感器前臂的动态性质是由于 P1 螺旋的灵活性，这是其固有性质。在 Markov 状态模型中观察到 TPP 结合形式的瞬态，同时还有稳定状态。我们相信，这种瞬态负责通过在 P4 和 P5 以及 Junction P4 和 P5 的连接区域周围创建溶剂通道来协助配体分子的流入和流出，并且在 FRET 分析中预期存在这种结构。核糖开关的动态性质取决于远端环 L3 和 L5/P3 以及 Junction P4 和 P5、J3/2 上的残基之间的相互作用，这些残基稳定了 J2/4。它通过活性位点残基帮助在 J2/4 和 P3/L5 三级对接区域之间传递变构信息。了解这种信息流将有助于突出高度动态和动力学系统中的关键残基。在这里，我们报告了核糖开关中在提供稳定性方面发挥重要作用的残基和片段，这可以用于设计抑制剂来调节核糖开关的功能。
