自然语言提示指导新型功能蛋白序列的设计
bioRxiv : the preprint server for biology
|November 28, 2024
概括
我们介绍了生物多模式模型 (BioM3),这是一个新的AI框架,使用自然语言提示来设计功能性蛋白质. 生物M3可以创建具有特定属性的蛋白质,通过计算和实验测试进行验证.
科学领域:
- 计算生物学 计算生物学
- 人工智能的人工智能
- 蛋白质工程是指蛋白质的工程.
背景情况:
- 自然语言交互正在推动各种领域的文本导向生成创新.
- 设计具有所需属性的功能性蛋白质仍然是生物技术中的一个重大挑战.
研究的目的:
- 引入生物多模式模型 (BioM3),这是使用自然语言提示设计功能性蛋白质的新框架.
- 通过文本描述来实现具有特定属性的新型蛋白质序列的条件生成.
主要方法:
- 生物M3通过三阶段的过程整合了自然语言和蛋白质设计:联合嵌入空间对齐,文本嵌入改进和条件序列生成.
- 使用对比式学习进行表示对齐,并使用离散的自回归扩散模型进行序列生成.
- 用于各种蛋白质性质预测的in silico验证以及对设计的Src-homology 3 (SH3) 域蛋白的体外/体内实验测试.
主要成果:
- 生物M3成功地根据结构,血统和功能的详细文本注释合成了蛋白质序列.
- 在 silico 验证中,在亚细胞局部化预测,反应分类和同质检测方面表现强.
- 实验测试证实,BioM3设计的蛋白质表现出与本地类似的三级折叠和野生类型的功能水平.
结论:
- 生物M3代表了蛋白质设计的重大进步,使得以自然语言为指导的功能性蛋白质的创造成为可能.
- 该框架在零射击预测和同质检测任务中实现了最先进的性能.
- 生物M3有望加速蛋白质工程和开发新的生物技术应用.
更多相关视频
相关概念视频
Protein-protein Interfaces
12.5K
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...
12.5K
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
Protein Families
15.3K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.3K
Protein Networks
3.9K
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,...
3.9K
Mechanical Protein Function
2.0K
2.0K
Protein Organization
6.2K
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....
6.2K


