Charged nucleobases and their potential for RNA catalysis.
Charged nucleobases and their potential for RNA catalysis.
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带电的核仁酶及其RNA催化的潜力。
DOI：
10.1021/ar2000452
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发表时间：
2011-12-20
影响因子：
18.3
通讯作者：
Bevilacqua, Philip C.
中科院分区：
文献类型：
--
作者：
Wilcox, Jennifer L.;Ahluwalia, Amarpreet K.;Bevilacqua, Philip C.
活细胞中的催化作用是由蛋白质和RNA共同完成的。蛋白质酶已经被发现了200多年，但RNA酶，或“核酶”，仅在30年前被发现。深入了解RNA酶的机制对于更好地理解现存的生物催化以及早期RNA催化生命中设想的原始催化都是非常宝贵的。天然核酶包括大的rna，如I和II组内含子；小rna，如丁型肝炎病毒和发夹核酶、锤头核酶、VS核酶和glmS核酶；核糖体和剪接体的RNA部分。RNA酶使用许多与蛋白质酶相同的催化策略，但使用更简单的侧链。其中有金属离子催化、一般酸碱催化和静电催化。在这篇文章中，我们研究了带电核碱基参与RNA催化的证据。我们的总体方法是将催化rna的直接测量与寡核苷酸模型系统的热力学研究相结合。带电氨基酸对几乎所有蛋白质酶的机制都有重要贡献。电离的核碱基对于RNA催化也是至关重要的。事实上，带电荷的核碱基在RNA催化中与一般的酸碱和氧阴离子空穴有关。我们提供了核酶研究涉及核碱基催化和并发症参与开发这些机制的概述。我们还考虑了引起碱的pKa值扰动的驱动力。pKa值向中性转移的机制包括静电稳定和氢键的加入。这两种机制将质子化与RNA折叠结合起来，我们用热力学形式和概念模型来处理。此外，核酶的反应机制可以是多通道的，这证明了核酶的多功能性，但也给实验数据的分析带来了挑战。我们研究了测量和分析RNA中扰动pKa值的进展。拉曼晶体学和荧光光谱学对pKa测量尤为重要。这些方法显示核碱基A或C的pKa值等于或大于中性，赋予它们潜在的组氨酸，赖氨酸/精氨酸样行为。核碱基电离的结构支持也存在：本文对数据库中RNA结构的分析表明，在细胞条件下，碱基的充电既不是特别罕见，也不是很难实现。我们的主要结论是，核碱基的阳离子和阴离子电荷状态发生在RNA酶中，这些状态对核酶活性起重要的催化作用。最后，我们考虑了悬而未决的问题和可能的实验和理论方法，以进一步推进。
Catalysis in living cells is carried out by both proteins and RNA. Protein enzymes have been known for over 200 years, but RNA enzymes, or ‘ribozymes,’ were discovered only 30 years ago. Developing insight into RNA enzyme mechanisms is invaluable for better understanding both extant biological catalysis as well as the primitive catalysis envisioned in an early RNA-catalyzed life. Natural ribozymes include large RNAs such as the group I and II introns; small RNAs such as the hepatitis D virus and the hairpin, hammerhead, VS, and glmS ribozymes; and the RNA portion of the ribosome and spliceosome. RNA enzymes use many of the same catalytic strategies as protein enzymes, but do so with much simpler sidechains. Among these strategies are metal ion, general acid–base, and electrostatic catalysis. In this Account, we examine evidence for participation of charged nucleobases in RNA catalysis. Our overall approach is to integrate direct measurements on catalytic RNAs with thermodynamic studies on oligonucleotide model systems. The charged amino acids make critical contributions to the mechanisms of nearly all protein enzymes. Ionized nucleobases should be critical for RNA catalysis as well. Indeed, charged nucleobases have been implicated in RNA catalysis as general acid–bases and oxyanion holes. We provide an overview of ribozyme studies involving nucleobase catalysis and the complications involved in developing these mechanisms. We also consider driving forces for perturbation of the pKa values of the bases. Mechanisms for pKa values shifting towards neutrality involve electrostatic stabilization and the addition of hydrogen bonding. Both mechanisms couple protonation with RNA folding, which we treat with a thermodynamic formalism and conceptual models. Furthermore, ribozyme reaction mechanisms can be multichannel, which demonstrates the versatility of ribozymes but makes analysis of experimental data challenging. We examine advances in measuring and analyzing perturbed pKa values in RNA. Raman crystallography and fluorescence spectroscopy have been especially important for pKa measurement. These methods reveal pKa values for the nucleobases A or C equal to or greater than neutrality, conferring potential histidine-, lysine/arginine-like behavior on them. Structural support for ionization of the nucleobases also exists: an analysis of RNA structures in the databases conducted herein suggests that charging of the bases is neither especially uncommon nor difficult to achieve under cellular conditions. Our major conclusions are that cationic and anionic charge states of the nucleobases occur in RNA enzymes and that these states make important catalytic contributions to ribozyme activity. We conclude by considering outstanding questions and possible experimental and theoretical approaches for further advances.
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影响因子：
15
作者：
Cerrone-Szakal, Andrea L.;Siegfried, Nathan A.;Bevilacqua, Philip C.
通讯作者：
Bevilacqua, Philip C.
影响因子：
4.8
作者：
Cottrell, Joseph W.;Scott, Lincoln G.;Fedor, Martha J.
通讯作者：
Fedor, Martha J.
影响因子：
15
作者：
Lupták, A;Ferré-D'Amaré, AR;Doudna, JA
通讯作者：
Doudna, JA
影响因子：
4.5
作者：
Moody, EM;Lecomte, JTJ;Bevilacqua, PC
通讯作者：
Bevilacqua, PC
分子动力学揭示了关键活性位点残基的质子化状态和 glmS 核糖开关的结构动力学。
影响因子：
3.3
作者：
Banas, Pavel;Walter, Nils G.;Sponer, Jiri;Otyepka, Michal
通讯作者：
Otyepka, Michal