Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.
Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.
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DOI：
10.1021/acs.biochem.6b00203
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发表时间：
2016-07-12
期刊：
影响因子：
2.9
通讯作者：
Hammes-Schiffer, Sharon
中科院分区：
文献类型：
--
作者：
Ucisik, Melek N.;Bevilacqua, Philip C.;Hammes-Schiffer, Sharon
最近发现的扭扭核酶的自裂机制被认为是利用一般的酸碱催化，但核碱基和金属离子在其自裂机制中的作用尚不清楚。本文对env22扭扭核酶进行了分子动力学模拟，以阐明其结构和平衡动力学特性，并研究了Mg2+离子和一般碱和酸的可能候选物在自裂机制中的作用。活性位点区域和假结的末端被发现比核酶的其他区域更不容易移动，很可能提供了结构稳定性并可能促进催化。一个所谓的催化Mg2+离子和最邻近的Mg2+离子在整个微秒的运动轨迹中保持螯合和相对不动，尽管这些Mg2+离子的去除并没有导致核酶在微秒时间尺度上的结构或平衡运动的任何显著变化。此外，在大多数微秒轨迹中，第三个金属离子Na+离子保持在离基原子A1（O5’）附近，这表明它可能在自裂过程中稳定A1（O5’）上的负电荷。这些阳离子的位置及其与活性位点关键核苷酸的相互作用表明它们可能具有催化作用。P1杆在晶体结构的顶部和底部部分熔化，并在轨迹上进一步展开。模拟还揭示了一个由氢键和π堆积相互作用组成的相互连接的网络，在自解理位点周围形成了一个相对刚性的网络。该网络中涉及的核苷酸是扭曲核酶中高度保守的核苷酸，这表明该相互作用网络可能对结构和功能很重要。
The recently discovered twister ribozyme is thought to utilize general acid–base catalysis in its self-cleavage mechanism, but the roles of nucleobases and metal ions in the mechanism are unclear. Herein, molecular dynamics simulations of the env22 twister ribozyme are performed to elucidate the structural and equilibrium dynamical properties, as well as to examine the role of Mg2+ ions and possible candidates for the general base and acid in the self-cleavage mechanism. The active site region and the ends of the pseudoknots were found to be less mobile than other regions of the ribozyme, most likely providing structural stability and possibly facilitating catalysis. A purported catalytic Mg2+ ion and the closest neighboring Mg2+ ion remained chelated and relatively immobile throughout the microsecond trajectories, although removal of these Mg2+ ions did not lead to any significant changes in the structure or equilibrium motions of the ribozyme on the microsecond time scale. In addition, a third metal ion, a Na+ ion remained close to A1(O5′), the leaving group atom, during the majority of the microsecond trajectories, suggesting that it might stabilize the negative charge on A1(O5′) during self-cleavage. The locations of these cations and their interactions with key nucleotides in the active site suggest that they may be catalytically relevant. The P1 stem is partially melted at its top and bottom in the crystal structure and further unwinds in the trajectories. The simulations also revealed an interconnected network comprised of hydrogen-bonding and π-stacking interactions that create a relatively rigid network around the self-cleavage site. The nucleotides involved in this network are among the highly conserved nucleotides in twister ribozymes, suggesting that this interaction network may be important to structure and function.
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DOI：
10.1261/rna.052514.115
发表时间：
2015-11
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Harris KA;Lünse CE;Li S;Brewer KI;Breaker RR
通讯作者：
Breaker RR
DOI：
10.1073/pnas.1414571111
发表时间：
2014-09-09
影响因子：
11.1
作者：
Eiler, Daniel;Wang, Jimin;Steitz, Thomas A.
通讯作者：
Steitz, Thomas A.
DOI：
10.1073/pnas.86.18.7054
发表时间：
1989-09-01
影响因子：
11.1
作者：
BENNER, SA;ELLINGTON, AD;TAUER, A
通讯作者：
TAUER, A
影响因子：
64.8
作者：
BUZAYAN, JM;GERLACH, WL;BRUENING, G
通讯作者：
BRUENING, G
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML