Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
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DOI：
10.1016/j.jmb.2005.06.016
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发表时间：
2005-08-26
影响因子：
5.6
通讯作者：
Walter, NG
中科院分区：
文献类型：
--
作者：
Krasovska, MV;Sefcikova, J;Walter, NG
丁型肝炎病毒（HDV）核酶是一种参与人类病原体丁型肝炎病毒复制的自切割RNA酶。最近对自裂前体和产物的晶体结构以及详细的动力学分析，对HDV核酶采用的催化策略提出了假设。我们报告了分子动力学（MD）模拟（类似于120 ns的总模拟时间）来测试特定构象重排参与催化的合理性。位点特异性自裂需要胞苷在75位（C75）。未质子化C75的前驱体模拟表明，C75在催化孔内的动态结合相当弱，U-1（O2’）和C75（N3）之间自发、短暂形成氢键。这个氢键是C75作为一般碱所必需的。在前驱体中质子化后，C75H（+）倾向于向其产物位置移动，并在催化口袋内建立牢固的氢键网络。然而，在目前的模拟时间尺度上，没有观察到C75作为一般酸催化剂时预期的C75H(+)(N3)-G1（O5'）氢键。相邻的环路L3是相对动态的，可以作为一个灵活的结构元素，可能由闭合的U20进行门控（）。G25碱基对，以促进质子化C75H（+）引起的构象转换。L3还控制催化核的静电环境，进而调节C75碱强度和金属离子结合。我们发现涉及质子化胞苷（C41）的远端RNA三级相互作用在未质子化时变得不稳定，导致催化核心附近的破坏性构象重排。Na离子暂时补偿了质子化氢键的损失，这与实验观察到的低pH和高Na+浓度在没有二价体时介导HDV核酶残余自裂的协同作用惊人地一致。(c) 2005 Elsevier Ltd版权所有。
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme involved in the replication of a human pathogen, the hepatitis delta virus. Recent crystal structures of the precursor and product of self-cleavage, together with detailed kinetic analyses, have led to hypotheses on the catalytic strategies employed by the HDV ribozyme. We report molecular dynamics (MD) simulations (similar to 120 ns total simulation time) to test the plausibility that specific conformational rearrangements are involved in catalysis. Site-specific self-cleavage requires cytidine in position 75 (C75). A precursor simulation with unprotonated C75 reveals a rather weak dynamic binding of C75 in the catalytic pocket with spontaneous, transient formation of a H-bond between U-1(O2') and C75(N3). This H-bond would be required for C75 to act as the general base. Upon protonation in the precursor, C75H(+) has a tendency to move towards its product location and establish a firm H-bonding network within the catalytic pocket. However, a C75H(+)(N3)-G1(O5') H-bond, which would be expected if C75 acted as a general acid catalyst, is not observed on the present simulation timescale. The adjacent loop L3 is relatively dynamic and may serve as a flexible structural element, possibly gated by the closing U20(.)G25 base-pair, to facilitate a conformational switch induced by a protonated C75H(+). L3 also controls the electrostatic environment of the catalytic core, which in turn may modulate C75 base strength and metal ion binding. We find that a distant RNA tertiary interaction involving a protonated cytidine (C41) becomes unstable when left unprotonated, leading to disruptive conformational rearrangements adjacent to the catalytic core. A Na ion temporarily compensates for the loss of the protonated hydrogen bond, which is strikingly consistent with the experimentally observed synergy between low pH and high Na+ concentrations in mediating residual self-cleavage of the HDV ribozyme in the absence of divalents. (c) 2005 Elsevier Ltd. All rights reserved.