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Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
アクティブサイトグアニンは,glmSリボジームのカタリシスに,その陽子化状態で参加する
Júlia Viladoms1, Lincoln G Scott, Martha J Fedor
1Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
Journal of the American Chemical Society
|September 23, 2011
まとめ
この研究では,glmS ribozyme.glmSにおけるグアニン33 (G33) の触媒的役割を調査した. 結果は,G33がRNA分裂において一般的な塩基触媒ではなく,移行状態の安定剤として作用することを示している.
科学分野:
- バイオケミストリー バイオケミストリー
- 分子生物学は分子生物学である.
- RNA触媒によるRNA触媒は,
背景:
- リボ酵素における活性部位グアニンは,一般的塩基触媒として提案されている.
- Bacillus anthracis glmS ribozymeにおけるG33の特定の役割は不明である.
研究 の 目的:
- glmSリボジームにおけるG33の触媒メカニズムを調査する.
- G33が一般的な塩基触媒として機能するか,RNA分裂に別の役割を果たすかどうかを判断する.
主な方法:
- 野生型および変異型glmSリボ酵素の割裂のpH依存度を測定する運動分析.
- 位置33で8-アザグアノシンを用いた,光ベースのpK (a) 測定.
主要な成果:
- 運動分析から得られたpK (a) の値は,G33を一般的ベース触媒として支持しない.
- pK (a) 値の不一致は,G33のデプロトン化がpHに依存するステップではないことを示唆しています.
- G33 (((N1) は,中性,陽子化形態の水素結合により,移行状態を安定させる可能性が高い.
結論:
- glmSリボ酵素のG33は,一般的な塩基触媒として機能しません.
- G33は,水素結合によって触媒的移行状態を安定させる可能性が高い.
- G33の代替的触媒モデルが提案されています.
関連する概念動画
GTPases and their Regulation
Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell signaling, vesicular transport, and the regulation of cell shape and motility. Mutation or dysfunction of these proteins can lead to disease. There are around 40,000 known G-proteins that can broadly be classified into two groups ‒ small G-proteins consisting of a single domain and large multi-domain G-proteins.
Large G-proteins, also known...
Large G-proteins, also known...
GTPases and their Regulation
Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell signaling, vesicular transport, and the regulation of cell shape and motility. Mutation or dysfunction of these proteins can lead to disease. There are around 40,000 known G-proteins that can broadly be classified into two groups ‒ small G-proteins consisting of a single domain and large multi-domain G-proteins.
Large G-proteins, also known...
Large G-proteins, also known...
Activation and Inactivation of G Proteins
Heterotrimeric G proteins are guanine nucleotide-binding proteins. As the name suggests, heterotrimeric G proteins are composed of three subunits: alpha, beta, and gamma. They remain GDP-bound or GTP-bound inside the cells and switch between inactive/active states. The Gα subunit possesses the nucleotide-binding pocket that binds guanine nucleotides and switches between GDP or GTP-bound states. In contrast, the Gꞵ and Gγ subunits are always bound together with high affinity and are together...
Small GTPases - Ras and Rho
Ras and Rho are small monomeric GTPases that act downstream of receptor tyrosine kinase (RTK) and regulate various cellular processes. These GTPases switch between active and inactive states by binding to guanine nucleotides.
Three regulatory proteins control their activity:
Three regulatory proteins control their activity:
Rab Proteins
Rab proteins constitute the largest family of monomeric GTPases, of which 70 members are present in humans. Rab proteins and their effectors regulate consecutive stages of vesicle transport such as vesicle transport, docking, and fusion to the correct recipient membrane.
Rab proteins switch between a cytosolic, GDP-bound inactive state and a membrane-anchored, GTP-bound active state. By themselves, Rabs show slow rates of GDP/GTP exchange and GTP hydrolysis. Thus, Rab proteins are considered...
Rab proteins switch between a cytosolic, GDP-bound inactive state and a membrane-anchored, GTP-bound active state. By themselves, Rabs show slow rates of GDP/GTP exchange and GTP hydrolysis. Thus, Rab proteins are considered...
Enzymes
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...

