使用AlphaFold预测揭示缺失的蛋白质-连接体相互作用
Nahuel Escobedo1, Tadeo Saldaño2, Juan Mac Donagh1
1Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Argentina.
Journal of molecular biology
|November 7, 2024
概括
AlphaFold2 (AF2) 可以预测连接体和无序蛋白质区域之间的"幽灵相互作用",这是传统结构生物学方法经常错过的. 这些发现有助于理解分子识别和开发针对内在无序蛋白质的药物.
科学领域:
- 结构生物学 结构生物学
- 计算生物学 计算生物学
- 药物发现 药物发现 药物发现
背景情况:
- 蛋白质 - 连接体相互作用是分子识别的关键,但在灵活的区域研究具有挑战性.
- 目前的结构生物学技术难以可靠地描述与内在无序蛋白的相互作用.
- 内在无序的蛋白质越来越被认为是重要的药物点,因为它们的生物相关性和疾病参与.
研究的目的:
- 评估AlphaFold2 (AF2) 能够预测蛋白质区域中联结体和残留物之间的相互作用的能力.
- 为了识别和描述这些以前未被描述的相互作用,称为"幽灵相互作用".
主要方法:
- 使用经过实验获得的蛋白质结构,在AlphaFold2的训练后确定.
- 评估了AF2对呈现秩序-混乱转变的区域的预测准确度.
- 分析了预测的残留埋葬和进化保护模式的"幽灵相互作用".
主要成果:
- AlphaFold2模型准确地预测了容易发生顺序-混乱转变的区域.
- AF2成功地预测了与连接体"幽灵相互作用"中的残留物.
- 这些预测的残留物经常被埋葬,与其他灵活的残留物相比,它们显示出明显的进化保护.
结论:
- AlphaFold2在预测与无序蛋白质区域的联结体相互作用方面表现有前途.
- 这种能力可以增强我们对分子识别和内在无序蛋白质的理解.
- 这些发现支持开发针对内在无序蛋白质的新疗法策略.
相关概念视频
01:49Conserved Binding Sites
4.2K
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...
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...
4.2K
02:04Protein-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
02:40Ligand Binding Sites
12.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.7K
00:49Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
01:24Protein Organization
6.3K
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....
6.3K
02:26Protein 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