マイクロアレイにおけるタンパク質の多様性によって引き起こされる問題を回避する:タンパク質の相互作用ネットワークへの影響
Andrew Gordus1, Gavin MacBeath
1Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.
Journal of the American Chemical Society
|October 19, 2006
まとめ
タンパク質マイクロアレイは,物理的性質の変動により,タンパク質の相互作用を不正確に表現することがあります. 飽和結合曲線を取得することで,信頼性の高いタンパク質相互作用ネットワーク分析のための正確な定量データが得られます.
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.
- システム生物学 システム生物学
背景:
- タンパク質マイクロアレイは,タンパク質とタンパク質の相互作用を研究するための高通量ツールです.
- タンパク質の物理的性質の変動は,マイクロアレイのような標準化されたアッセイからの結果をバイアスすることができます.
- 単純な値ベースの分析は,誤解を招くバイナリ相互作用ネットワークにつながる可能性があります.
研究 の 目的:
- マイクロアレイのタンパク質相互作用ドメインの変動性を調査する.
- 表面密度の変動が相互作用データに与える影響を評価する.
- タンパク質マイクロアレイから正確な定量データを取得するための方法を特定する.
主な方法:
- 単体Srcホモロジー2 (SH2) ドメインを均一な濃度で印刷する.
- 光で標識されたフォスフォペプチドによる値ベースの結合測定を行う.
- タンパク質-ペプチド相互作用の飽和結合曲線を取得する.
主要な成果:
- モノメリックSH2ドメインは,同じ濃度で印刷されたとき,活性表面密度の最大50倍の変化を示した.
- 値ベースのアッセイは,誤解を招くような生体物理学的相互作用データを生成した.
- 飽和度曲線から得られた均衡解離定数は,表面密度とは無関係であった.
結論:
- タンパク質の物理的性質の変動は,マイクロアレイベースの相互作用研究に大きく影響する.
- 飽和結合曲線を用いた定量分析は,表面密度のバイアスを克服する.
- 将来の大規模なタンパク質相互作用ネットワークの研究では,定量的データ取得を優先すべきである.
関連する概念動画
Protein-protein Interfaces
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Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-Protein Interfaces
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...


