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Updated: May 26, 2026

13:19
Chemical Triphosphorylation of Oligonucleotides
Published on: June 2, 2022
ピロホスファートイオンの放出と,結合されたトリガーループの動きの動態は,RNAポリメラーゼIIにおける閉じた状態から開いた状態に変化する
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
まとめ
RNAポリメラーゼII (pol II) から放出されるピロホスファートイオン (PP(i)) は,転写に極めて重要です. 分子動力学シミュレーションでは,H1085,K752,K619などの特定の残留物が,ホッピングメカニズムを通じてPPの放出を促進することを明らかにしています.
科学分野:
- 分子生物学は分子生物学である.
- バイオフィジックス 生物物理学
- コンピュータ生物学 コンピュータ生物学
背景:
- RNAポリメラーゼII (pol II) は,トランスクリプションの延長のために,ピロホスファートイオン (PP ((i)) の放出を必要とします.
- ポルII残留とトリガーループの正確な役割は,PP ((i)) の放出では完全に理解されていません.
研究 の 目的:
- ポリII転写延長中のPP (i) 放出のメカニズムを解明する.
- トリガー・ループの役割と,PPの放出における特定のポリ・II残留物の役割を調査する.
主な方法:
- 全原子分子動力学 (MD) のシミュレーションは,明示的な溶媒で行われます.
- PPの放出経路を分析するためのマルコフ状態モデル (MSM) の構築.
- キー残留物の機能を評価するための単一変異体シミュレーション.
主要な成果:
- トリガーループは,触媒化後の運動の増加を示し,H1085の相互作用を通じてPPの放出を助長する.
- PP(i) は,保存された残留物 (K752,K619) を含むホッピングメカニズムを介して活性部位を退去します.
- 2次通路を通過するPP (i) トランジットについて,4つの動力的にメタスタブルな状態が特定されました.
結論:
- H1085とK752は,PPのアクティブサイトからの脱出を容易にし,K619は二次チャネルを通過するのを助けます.
- PP(i) の放出はトリガーループの開きを促進するかもしれないが,PP(i) のダイナミクスはより速い.
- シミュレーション結果は,実験的検証のための予測を提供します.
関連する概念動画
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...

