植物核酸结合性白丰富的重复和病原体效应因子相互作用的in silico预测方法
Alicia Fick1,2, Jacobus Lukas Marthinus Fick3, Velushka Swart1,2
1Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa.
The Plant journal : for cell and molecular biology
|April 30, 2025
概括
现在可以预测植物核酸结合性氨酸丰富重复 (NLR) 蛋白与病原体因子的相互作用. 这项研究开发了一种计算方法来识别植物免疫的关键NLR,帮助抵抗策略.
科学领域:
- 植物分子生物学 植物分子生物学
- 计算生物学是一种计算生物学.
- 免疫学 免疫学 免疫学
背景情况:
- 核酸结合性氨酸丰富的重复蛋白 (NLR) 对于植物免疫来说至关重要.
- 确定特定的NLR-效应因子相互作用至关重要,但具有挑战性.
- 推进植物防御机制需要了解NLR功能.
研究的目的:
- 开发和验证一种用于预测植物NLR-effector相互作用的in silico方法.
- 以高精度识别新的NLR-效应因子相互作用.
- 创建一个资源来简化植物免疫研究.
主要方法:
- 使用AlphaFold2-Multimer预测的NLR效应器复杂结构.
- 通过97个机器学习模型评估了绑定亲和力和能量.
- 开发了一种 Ensemble 机器学习模型,用于新型交互预测.
主要成果:
- AlphaFold2-Multimer结构对NLR-效应因子相互作用显示了可接受的准确性.
- 验证的相互作用具有特定的结合亲和力和能量范围.
- 在99%的准确度下确定了新的NLR-效应因子相互作用.
结论:
- 开发的in silico方法准确地预测了跨病理系统的NLR-效应器相互作用.
- 为了激活NLR,可能需要特定的绑定能量变化.
- 该NLR-Effector互动分类 (NEIC) 资源将加速植物免疫研究.
相关概念视频
Protein-protein Interfaces
12.4K
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...
12.4K
Conserved Binding Sites
4.1K
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...
4.1K
Cell Signaling in Plants
5.4K
Plant cells communicate to coordinate their cycle of growth, flowering and fruiting, and activities in roots, shoots, and leaves in response to the changing environmental conditions. Plant signaling is distinct from animal signaling. Plants primarily utilize enzyme-linked receptors, whereas the largest class of cell-surface receptors in animals are G-protein coupled receptors (GPCRs). Unlike animals, receptor tyrosine kinases are rare in plants. Instead, plants have a diverse class of...
5.4K
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
Ligand Binding Sites
12.6K
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...
12.6K


