Mg2+在子头核酶催化中的作用来自分子模拟的分子模拟
Tai-Sung Lee1, Carlos Silva López, George M Giambasu
1Consortium for Bioinformatics and Computational Biology, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA.
Journal of the American Chemical Society
|February 15, 2008
概括
(Mg2+) 离子对于头 рибо酶 (HHRz) 催化非常重要,稳定关键结构和过渡状态. 模拟显示Mg2+通过协调必要的催化残留物来促进RNA裂变.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 分子生物物理学 分子生物物理学
背景情况:
- 头核糖酶 (HHRz) 是一种小型催化RNA分子,对于RNA处理至关重要.
- 已知二元金属离子,特别是Mg2+,对于HHRz催化活性至关重要.
- 了解Mg2+在HHRz裂变机制中的精确作用仍然是一个活跃的研究领域.
研究的目的:
- 为了研究Mg2+在全长头核糖酶裂变反应中的结构和催化作用.
- 描述Mg2+结合模式和导致触媒活性状态的构造变化.
- 阐明RNA催化过程中Mg2+对过渡状态的稳定.
主要方法:
- 执行了8个12ns分子动力学 (MD) 模拟与不同的Mg2+结合职业.
- 在RNA催化中利用最近开发的金属离子和反应性中间体的力场参数.
- 在早期和晚期过渡状态上进行混合量子力学/分子力学 (QM/MM) 计算.
主要成果:
- 2+结合稳定了HHRz.的关键结构元素 (茎I和II).
- 2+促进了接近攻击形状的形成和催化残留物之间的相互作用.
- 在过渡状态下,Mg2+与离开组和一般酸催化剂 (2'OH of G8) 形成桥梁.
结论:
- 2+在头核糖酶机制中发挥着深刻的结构和催化作用.
- 2+通过协调离开组并促进质子转移来稳定过渡状态.
- 模拟模型与实验数据保持一致,并为进一步的QM/MM调查提供了基础.
相关概念视频
Ribozymes
The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes can be...
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