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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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酵素アーキテクチャ:トリオセフォスファートイソメラーゼによる触媒における水害性クランプの動作をモデル化
Yashraj S Kulkarni1, Qinghua Liao1, Dušan Petrović2
1Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden.
Journal of the American Chemical Society
|July 8, 2017
まとめ
トリオフォスファートイソメラーゼ (TIM) は,触媒を強化するために,水害性クランプを使用します. このクランプは,酵素活性に不可欠な基板の脱プロトン化のためのギブスの自由エネルギーを最小限にします.
科学分野:
- 生物化学
- 酵素触媒
- 計算生物学
背景:
- トリオフォスファートイソメラーゼ (TIM) は,DHAPのGAPへのイソメリゼーションを触媒する,グリコロシスの重要な酵素である.
- TIMの触媒メカニズムは,触媒ベースE165の周りに水性ポケットを形成する形状の変化を含みます.
- 水性残留物I170とL230は,TIM活動にとって重要な"クランプ"を形成しますが,基板の脱プロトン化における正確な役割は不明です.
研究 の 目的:
- DHAPとGAPのTIM触媒によるデプロトネーションにおける水害性クランプ (I170とL230) の役割を計算的に調査する.
- 経験的なバレンスの結合計算を用いて,TIMの触媒メカニズムに対する変異 (I170A,L230A) の影響を定量的に評価する.
- 酵素触媒における基底状態と移行状態の相互作用を解明する.
主な方法:
- ワイルド型TIMおよびそのI170A,L230AおよびI170A/L230A変異体について,詳細な経験的バレンスの結合 (EVB) を計算した.
- 計算は,TIM活性部位内のDHAPとGAPの脱プロトン化段階に焦点を当てた.
- 結果は数値的に実験データと比較して計算モデルを検証した.
主要な成果:
- 野生型と変異型TIMのEVB計算と実験データとの間で例外的な量的な合意が達成されました.
- 活性化バリアとギブス自由エネルギーとの間には,0.8の傾きを持つ線形自由エネルギー関係 (LFER) が確認された.
- ヒドロホビッククランプは基板脱プロトネーションのためのギブス自由エネルギーを最小限に抑え,主に移行状態で効果を示した.
結論:
- I170とL230によって形成された水害性クランプは,TIMにおける基板脱陽子のギブス自由エネルギーを最小限に抑えるために不可欠です.
- クランプによる触媒強化は,大部分が陽子移転の移行状態で表現されます.
- この研究は,計算と実験の発見を統合したTIM触媒における水害性クランプの機能の詳細な分子記述を提供します.
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