通过氨基酸背景预测聚Q-和聚A在蛋白质-蛋白质相互作用中的参与
Pablo Mier1, Miguel A Andrade-Navarro1
1Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany.
Heliyon
|September 26, 2024
概括
我们开发了一种机器学习方法来预测多重重复蛋白质 (polyQ) 和多重复氨酸 (polyA) 的蛋白质-蛋白质相互作用 (PPI) 参与. 这种方法在人类蛋白质组中确定了新的相互作用区域.
科学领域:
- * 计算生物学 * 计算生物学
- * 生物信息学是一门学科.
- * 分子相互作用
背景情况:
- *同重复物,如多重胺 (polyQ) 和多氨酸 (polyA) 序列,经常参与蛋白质与蛋白质相互作用 (PPI).
- * 没有预测方法来识别对PPI的同类重复参与,这阻碍了该领域的研究.
研究的目的:
- * 开发和验证一种机器学习模型,用于预测人类蛋白质组中PPI参与的polyQ和polyA区域.
- * 确定可能调解蛋白相互作用的新型同重复区域.
主要方法:
- * 机器学习模型使用人类同源重复的数据集进行训练,结合氨基酸背景和同源重复的长度.
- *随机森林模型使用周围的氨基酸位置 (-10到+10) 进行评估,然后进行优化 (-6到+6为多Q).
- * 线圈-线圈重叠信息被整合,以提高多A区域的预测.
主要成果:
- * 模型在预测PPI参与方面实现了高精度 (0.90-0.98),但可变回忆 (0.42-0.85).
- *随机森林模型显示,polyQ的AUC值为0.686,polyA的AUC值为0.732.
- *优化的模型实现了polyQ的AUC为0.715和polyA的AUC为0.745 (具有卷轴卷轴重叠).
- *应用模型确定了157个多Q和745个多A区域,可能涉及PPI.
结论:
- *开发的机器学习方法有效地预测了多Q和多A同类重复的PPI参与.
- * 该研究确定了许多新的同源重复区域,这些区域可能在蛋白质相互作用中发挥作用.
- *这种方法为探索同重复介导相互作用及其功能影响提供了有价值的工具.
更多相关视频
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
7.3K
08:38Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
Published on: March 3, 2015
13.3K
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
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
Conserved 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
Protein Folding
7.8K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
7.8K
Protein 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
Ligand Binding Sites
12.8K
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...
12.8K
