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Carbocations02:10

Carbocations

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Carbocations are one of the reaction intermediates formed during several nucleophilic substitutions or elimination reactions. A carbocation is an electron-deficient species with the central carbon atom having six electrons and three bonded atoms. The central carbon in a carbocation is sp2 hybridized with trigonal planar geometry. It has an empty p orbital perpendicular to the plane of the structure that can accept electrons. Thus, carbocations act as strong electrophiles and may react with any...
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Enolate Mechanism Conventions01:15

Enolate Mechanism Conventions

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When a carbonyl compound is treated with a strong base, the α position gets deprotonated to give a resonance-stabilized intermediate called an enolate. Enolates are ambident nucleophiles because they possess two nucleophilic sites that can attack an electrophile owing to the delocalization of the negative charge between the α carbon and oxygen atoms. When the oxygen atom attacks an electrophile, it is called O-attack, whereas electrophilic attack via the α carbon is known as...
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Nucleophilic Addition to the Carbonyl Group: General Mechanism01:18

Nucleophilic Addition to the Carbonyl Group: General Mechanism

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The carbonyl carbon in an aldehyde or ketone is the site of a nucleophilic attack due to its electron-deficient nature. Depending on the strength of the incoming nucleophile, the reaction occurs via different mechanistic pathways.
A stronger nucleophile can directly attack the electrophilic center, the carbonyl carbon. The HOMO orbital of the nucleophile interacts with the LUMO (π* antibonding) orbital present on the carbonyl carbon. This interaction breaks the π bond and shifts the...
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Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

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Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Reactivity of Enols01:18

Reactivity of Enols

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Enols are a class of compounds where a hydroxyl group is attached to a carbon–carbon double bond, which implies that it is a vinyl alcohol. A carbonyl compound with an α hydrogen undergoes keto–enol tautomerism and remains in equilibrium with its tautomer, the enol form. Usually, the keto tautomer is present in a higher concentration than the enol tautomer due to the higher bond energy of C=O compared to C=C. Moreover, the direction of the keto–enol equilibrium is...
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プロトグロビン反応カルベンの中間物質のマイクロED構造

Emma Danelius1,2, Nicholas J Porter3, Johan Unge1

  • 1Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States.

Journal of the American Chemical Society
|March 22, 2023
PubMed
まとめ

マイクロクリスタル電子 difraktion (MicroED) は,Aeropyrum pernix protoglobinの変異体の構造を決定した. この突破により タンパク質の構造を 詳細に研究することが可能になりました

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科学分野:

  • 構造生物学
  • 生物化学
  • クリスタルグラフィー

背景:

  • マイクロクリスタル電子 difraktion (MicroED) は,分子構造を決定するための強力な技術です.
  • 小分子やペプチドには成功しているが,新しいタンパク質構造には限られた応用がある.
  • マイクロED技術と タンパク質構造の予測の進歩により 機能が拡大しています

研究 の 目的:

  • MicroEDを用いて工学的に作られたAeropyrum pernix protoglobin (ApePgb) の構造を決定する.
  • マイクロED構造の決定の段階化のためにAlphaFold2モデルを使用します.
  • ApePgb 変異体における 強化されたカルベンの移転活性に対する構造的根拠を調査する.

主な方法:

  • マイクロクリスタル電子 difraktion (MicroED) と先進技術 (より高い電圧,低騒音検出器).
  • AlphaFold2のモデルを利用した.
  • 結晶学とApePgb変種とその中間体の構造分析

主要な成果:

  • Aeropyrum pernix protoglobin (ApePgb) の変種の最初のマイクロED構造を決定した.
  • 変異がアルファヘリクスを ダイナミック・ループに変換し 触媒活性部位のアクセシビリティを向上させる
  • エンジニアリングされたカルベンの移転活動における反応性鉄カルベノイド中間物質を捕まえて特徴づけました.

結論:

  • 改良されたマイクロED技術とタンパク質構造予測モデルは,以前はアクセスできないタンパク質構造の研究を可能にします.
  • 決定された構造は,突然変異がカルベンの移転活動をどのように強化するかについての洞察を提供します.
  • この発見は,複雑な生物学的分子とそのメカニズムを調査するMicroEDの可能性を強調しています.