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相关概念视频

Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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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.
The primary structure of a protein is its amino acid sequence....
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Ligand Binding Sites02:40

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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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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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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相关实验视频

Updated: Jun 17, 2025

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

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结构告知蛋白质语言模型是变异效应的强有力的预测器.

Yuanfei Sun1, Yang Shen2,3,4

  • 1Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, Texas, USA.

Human genetics
|August 8, 2024
PubMed
概括
此摘要是机器生成的。

结构信息化的蛋白质语言模型 (pLMs) 通过结合结构上下文来改善变异效应预测. 这种方法提高了健身景观的捕捉性,超过了更大,仅序列模型的性能.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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相关实验视频

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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A Protocol for Computer-Based Protein Structure and Function Prediction
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科学领域:

  • 计算生物学 计算生物学
  • 蛋白质工程是指蛋白质工程.
  • 生物信息学是一种生物信息学.

背景情况:

  • 蛋白质语言模型 (pLMs) 学习进化序列分布以预测变异效应.
  • 只有序列的plm可能无法完全捕捉受蛋白质结构影响的变异效应.
  • 需要将结构上下文整合到pLM中以提高准确性.

研究的目的:

  • 评估结构背景对仅序列的plm对变异效应预测的影响.
  • 开发一个框架,将蛋白质结构信息纳入pLMs.
  • 为了提高蛋白质健身景观的预测.

主要方法:

  • 引入了基于结构的pLMs (SI-pLMs),使用顺序和结构的交叉模式表示.
  • 扩展的掩饰序列 denoising 从序列和结构数据共同学习.
  • 训练并评估SI-pLMs在深度突变发生检测扫描基准上.

主要成果:

  • SI-pLM在变异效应预测基准上取得了最佳表现,表现优于竞争方法.
  • 基于结构的模型比仅使用序列的大型模型或在更多数据上训练的模型更有效.
  • 案例研究表明,健身景观的分离性得到改善,关键残留物得到保护.

结论:

  • 将结构上下文集成到pLM中,比简单地增加模型大小或数据更有效地捕捉健身景观.
  • SI-pLMs提供了一种强大的方法,通过利用蛋白质结构来增强变异效应预测.
  • SI-pLM框架可以应用于现有的pLM,而无需在预测过程中使用结构数据.