相关实验视频
Updated: May 26, 2026

13:19
Chemical Triphosphorylation of Oligonucleotides
Published on: June 2, 2022
在RNA聚合酶II中,酸盐离子释放及其合触发环运动从封闭状态到开放状态的动态
Lin-Tai Da1, Dong Wang, Xuhui Huang
1Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
Journal of the American Chemical Society
|December 31, 2011
概括
从RNA聚合酶II (pol II) 中释放的酸盐离子 (PP(i)) 对转录至关重要. 分子动力学模拟显示特定的残留物,如H1085,K752和K619,通过跳跃机制促进PP的释放.
科学领域:
- 分子生物学分子生物学
- 生物物理学的生物物理.
- 计算生物学 计算生物学
背景情况:
- RNA聚合酶II (pol II) 需要酸盐离子 (PP ((i)) 释放以进行转录延长.
- 聚二醇残留物和触发环在PP (i) 释放中的确切作用尚未完全理解.
研究的目的:
- 阐明在pol II转录延长过程中PP (i) 释放的机制.
- 调查触发环和特定的pol II残留物在PP (i) 释放中的作用.
主要方法:
- 在明确溶剂中进行全原子分子动力学 (MD) 模拟.
- 构建一个马尔科夫状态模型 (MSM) 来分析PP(i) 释放通路.
- 单个突变模拟来评估关键残留物的功能.
主要成果:
- 触发环在催化后表现出增加的运动,帮助PP(i) 通过H1085相互作用释放.
- PP(i) 通过涉及保存残留物的跳跃机制离开活性部位 (K752,K619).
- 通过二次通道传递PP的四个动态转稳态被确定.
结论:
- H1085和K752有助于PP(i) 离开活动部位,而K619则有助于通过二次通道.
- PP(i) 释放可能会促进触发环的打开,尽管PP(i) 动态更快.
- 模拟结果为实验验证提供了预测.
相关概念视频
Bacterial Transcription
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
RNA Polymerase II Accessory Proteins
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
RNA Polymerase II Accessory Proteins
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
Eukaryotic RNA Polymerases
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
Eukaryotic RNA Polymerases
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
Bacterial RNA Polymerase
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

