移行状態の相互作用は,核塩基のイオン化を中立にシフトさせ,小さなリボ酵素の触媒を容易にします

Joseph A Liberman¹, Man Guo, Jermaine L Jenkins

¹Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine & Dentistry, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, USA.

Journal of the American Chemical Society

|September 20, 2012

まとめ

リボ酵素は塩基イオン化を変化させることで反応を加速する. ラーマン結晶学では,塩基pKを増加させるヘアピンリボ酵素における重要な静電相互作用を明らかにし,触媒を助長した.

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.
構造生物学構造生物学とは

背景:

リボ酵素は,触媒的活性を持つRNA分子である.
核塩基のイオン化状態は,RNAの触媒機構にとって非常に重要です.
RNA構造が反応性にどのように影響するかを理解することは不可欠です.

研究の目的:

特定のリボ酵素活性部位のpK (a) 値を直接測定する.
変化したイオン化状態に起因する構造的特徴を特定する.
リボ酵素触媒における塩基イオン化の役割を明らかにする.

主な方法:

ラーマン結晶学により,異なる構成状態におけるpK (a) 値を測定した.
改変されたリボ酵素の結晶構造が決定されました.
特定の相互作用を調査するために単原子置換が導入されました.

主要な成果:

Ade38 N1イミノ群のpK (a) は,ラマン結晶学を用いて直接測定した.
移行状態のアナログは,pK (((a) が 6.27 ± 0.05.05 であった.
単一の静電相互作用が特定され,pK(a) を0.8 log単位以上増加させた.

結論:

この発見は,Ade38 N1(H) +が一般的な酸性触媒として作用するメカニズムを支持する.
この研究では,単一の静電相互作用が塩基イオン化に与える影響を定量化しています.
この結果は,RNAの構造と機能の関係を理解する上で大きな意味を持ちます.

さらに関連する動画

12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

13:19

Chemical Triphosphorylation of Oligonucleotides

Published on: June 2, 2022

関連する概念動画

02:26

S_N2 Reaction: Transition State

An SN2 reaction of an alkyl halide is a single-step process in which bond formation between the nucleophile and the substrate and bond breaking between the substrate and the halide occurs simultaneously through a transition state without forming an intermediate.
When the nucleophile approaches the electrophilic carbon with its lone pairs, the halide acts as a leaving group and moves away with the electron-pair bonded to the carbon. Dotted partial bonds represent the bonds being formed or broken...

02:47

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.
Ribozymes can be...

02:47

Ribozymes

02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

01:56

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...

01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

関連する実験動画