関連する実験動画
Updated: Jun 22, 2025

10:58
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
17.0K
構造情報型言語モデルによるタンパク質と抗体複合体の無監督進化
Varun R Shanker1,2,3, Theodora U J Bruun2,3,4, Brian L Hie3,4
1Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
まとめ
タンパク質の構造を言語モデルに統合することで タンパク質の設計と進化が促進されます このアプローチは,SARS-CoV-2の変種に対する抗体治療を改善し,タンパク質工学の強力な方法を示した.
科学分野:
- 計算生物学
- タンパク質工学
- 構造生物学
背景:
- 大型言語モデル (LLM) は,配列データだけでタンパク質の設計原理を学ぶのに優れている.
- タンパク質の機能,活動,進化性は 単に配列ではなく 3次元構造によって決定されます
- 既存のLLMには,包括的なタンパク質設計に必要な構造的な文脈がしばしば欠けています.
研究 の 目的:
- タンパク質の進化を導くための構造情報で補完された一般的なタンパク質言語モデルを開発する.
- タンパク質複合体を設計し,治療用抗体を改善するモデルの能力を実証する.
- 構造情報に基づくタンパク質言語モデルの有効性を検証する.
主な方法:
- 一般的なタンパク質言語モデルを タンパク質構造の脊髄座標で拡張する.
- ESM-IF1モデルを拡張し,最初は単鎖構造で訓練され,タンパク質複合体を設計しました.
- SARS-CoV-2に対する2つの治療用抗体の約30の変種をスクリーニング.
主要な成果:
- 構造拡張言語モデルは様々なタンパク質の タンパク質進化を成功裏に導きました
- 拡張されたESM-IF1モデルは,タンパク質複合体の設計を可能にしました.
- SARS-CoV-2の変種BQ.1.1およびXBB.1.5に対する抗体中和 (25倍まで) と親和 (37倍まで) の有意な改善が観察されました.
結論:
- タンパク質言語モデルに構造情報を統合することは,効率的なタンパク質進化経路を特定するのに有利です.
- このアプローチは,タスク固有のトレーニングデータを必要とせずにタンパク質工学を可能にします.
- この発見は,タンパク質の設計と治療開発の改善,特にウイルスの脱出変種を標的とした抗体開発の道を開く.
関連する概念動画
Protein Organization
6.4K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
6.4K
Conservation of Protein Domains Over Different Proteins
10.8K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K
Antibody Structure and Classes
871
Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
871
Protein Complexes with Interchangeable Parts
1.8K
1.8K
Antibody Structure
59.8K
Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
59.8K
Conservation of Protein Domains
3.1K
3.1K

