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相关概念视频

Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Networks02:26

Protein Networks

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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,...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Protein Organization01:24

Protein Organization

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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.
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Ligand Binding Sites

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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...
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深度学习的预测提出了大量的蛋白质-碳水化合物相互作用.

Samuel W Canner1, Ronald L Schnaar2,3, Jeffrey J Gray1,4

  • 1Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States.

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概括

我们开发了计算工具,碳水化合物预测蛋白相互作用 (PiCAP) 和碳水化合物蛋白位点识别器2 (CAPSIF2),以识别蛋白质碳水化合物相互作用. 这些工具可以高精度地预测碳水化合物结合蛋白及其相互作用部位,揭示关键蛋白质组中的广泛相互作用.

关键词:
葡萄糖甘是什么? 葡萄糖甘是什么碳水化合物是一种碳水化合物.葡萄糖的葡萄糖是什么?互动的作用组.莱克托马是指一个乳房.蛋白质组是蛋白质组的组成部分.

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科学领域:

  • 生物化学和分子生物学
  • 计算生物学 计算生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 识别蛋白质-碳水化合物相互作用对于理解生物过程至关重要,但实验方法资源密集.
  • 目前的估计表明,只有1.5-5%的蛋白质与碳水化合物结合,与已知的50-70%的蛋白质糖化相比.
  • 在准确预测碳水化合物结合蛋白及其相互作用部位方面存在很大的差距.

研究的目的:

  • 开发新的计算工具来预测蛋白质-碳水化合物结合,并识别特定的相互作用部位.
  • 建立一个强大的数据集,用于培训和验证蛋白质碳水化合物相互作用的预测模型.
  • 评估不同蛋白质组中碳水化合物结合蛋白的流行程度,并调查它们的生物学相关性.

主要方法:

  • 开发了碳水化合物预测器 (PiCAP) 的蛋白相互作用,这是一个在已知的碳水化合物结合剂和非结合剂上训练的神经网络模型.
  • 创建了碳水化合物蛋白位点标识符2 (CAPSIF2) 模型,以预测参与碳水化合物结合的特定蛋白质残留物.
  • 利用一个精心策划的数据集,包括已知的结合剂,DNA结合蛋白,细胞骨成分,抗体和小分子结合剂,用于训练和验证.

主要成果:

  • 在预测蛋白质水平碳水化合物结合/非结合方面,PiCAP实现了90%的平衡精度.
  • 在CAPSIF2中,残留物水平预测的Dice系数为0.57,表现优于现有模型.
  • 对人类神经细胞和蛋白质组 (大肠杆菌,肌肉菌,智人菌) 的应用预测了35-40%的蛋白质与碳水化合物结合.

结论:

  • PiCAP 和 CAPSIF2 是有效的计算工具,用于预测蛋白质-碳水化合物相互作用和结合部位.
  • 预计各种蛋白质组中的大量蛋白质参与碳水化合物结合.
  • 这些发现强调了蛋白质-碳水化合物相互作用在细胞功能中的重要作用,并为进一步研究开辟了道路.