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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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The Nucleosome01:19

The Nucleosome

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Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
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DNA Base Pairing02:27

DNA Base Pairing

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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配列平均化による高安定性およびDNA結合親和性を持つホメオドメインの作成

Katherine W Tripp1, Matt Sternke1, Ananya Majumdar1

  • 1The T. C. Jenkins Department of Biophysics and ‡Biomolecular NMR Center, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.

Journal of the American Chemical Society
|March 23, 2017
PubMed
まとめ

コンセンサス・デザインは機能を維持する 超安定した球状タンパク質 (ホメオドメイン) を生み出しました この安定したタンパク質は,より高い親和度でDNAを結合し,安定性がタンパク質の機能と相容れることを示しています.

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関連する実験動画

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科学分野:

  • タンパク質工学
  • 構造生物学
  • バイオ物理学

背景:

  • コンセンサス・デザインは 線形繰り返しのタンパク質の安定性を 向上させるのに成功しました
  • 球状タンパク質に対するコンセンサス・デザインの適用性とその機能への影響は不明である.

研究 の 目的:

  • 安定した機能的な球状タンパク質を作るためのコンセンサスデザインの可能性を調査する.
  • コンセンサスで設計されたホメオドメインの構造的および機能的特性を特徴付ける.

主な方法:

  • ホメオドメイン配列に適用されたコンセンサス設計戦略.
  • 安定性の評価のための円形二重化と微分スキャニングカロメトリー
  • 機能的および動的特徴化のためのDNA結合アッセイと15Nリラックス研究.

主要な成果:

  • コンセンサスで設計されたホメオドメイン (HD) は,安定した折りたたみ構造を採用します.
  • コンセンサス-HDは,天然のエングリルされた-HDよりも5 kcal·mol-1高い展開自由エネルギーを示します.
  • コンセンサス-HDは,約100倍高いDNA結合親和性を示し,バックボンのダイナミクスを減少させた.

結論:

  • コンセンサス・デザインは 超安定した球状タンパク質を作るのに有効です
  • 大きく安定したタンパク質は,基板親和度の増加などの機能的特性を表すことができます.
  • 高いタンパク質の安定性は,タンパク質の機能と互換性があり,改善することができる.