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自動化されたRNA構造予測は,ダブルグリシンリボスイッチのキックターンリンクを明らかにした
Wipapat Kladwang1, Fang-Chieh Chou, Rhiju Das
1Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
Journal of the American Chemical Society
|December 24, 2011
まとめ
自動化されたツールは,グリシンリボスイッチ機能に不可欠な新しいRNA構造要素を正確に予測しました. この発見により,RNAの三次構造とリンガンド結合に関する理解が深まる.
科学分野:
- 分子生物学は分子生物学である.
- 構造生物学 構造生物学とは
- バイオインフォマティックス
背景:
- 機能的なRNAの三次構造を解読することは困難です.
- 自動化されたRNA構造予測ツールには,実験的検証が必要です.
研究 の 目的:
- 自動化されたRNA構造予測ツールを実験的に検証するために.
- ダブルグリシンリボスイッチの構造と機能を調査する.
主な方法:
- 4つの予測ツール (BPPalign,RMdetect,JAR3D,ロゼッタ3Dモデリング) を適用する.
- 化学的探査 (N-メチルイサト酸アンヒドリド,ジメチル硫酸塩など) Fusobacterium nucleatum riboswitchに関するニュース記事一覧
- ミューテーション・アンド・マップの研究と,ミューテーション/救出実験.
- RNA構造の破壊の熱力学分析.
主要な成果:
- すべてのツールによって新しい幹 P0 とキックターンのモチーフの一貫した予測.
- アプタマー間の構造化リンク器の実験的検証.
- ヘリックス・ジャンクション・ヘリックス構造の破壊は,グリシン結合を著しく損なう (120倍と6~30倍の解離定数の増加).
- 構造リンク器の量化されたエネルギー効果 (4.3 ± 0.5 kcal/mol).
結論:
- 自動予測ツールは,新しいRNA構造要素を特定するのに有効です.
- 特定された構造化リンク器は,リボスイッチにおける協力性グリシン結合に不可欠である.
- 以前の研究では,RNAの過小縮小により,機能的な要素が欠けていた可能性があります.
- 機能性RNAの未発見の他の要素は,自動予測ツールを使用して検出することができます.
関連する概念動画
Riboswitches
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
Transcriptional Regulation: Riboswitches
Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
RNA Structure
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Types of RNA
Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...

