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相关概念视频

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Conservation of Protein Domains02:26

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Translation in Prokaryotes

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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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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.
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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.
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Insertion of Single-pass Transmembrane Proteins in the RER01:26

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Integral membrane proteins are proteins adhered to the lipid bilayer of a cell organelle or membrane. They can be of two types: transmembrane integral proteins that span the lipid bilayer and monotopic proteins that are attached to either side of the membrane but do not pass through it.
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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
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使用域到域翻译生成相互作用的蛋白序列.

Barthelemy Meynard-Piganeau1,2, Caterina Fabbri2, Martin Weigt1

  • 1Computational and Quantitative Biology, LCQB UMR 7238, Institut de Biologie Paris Seine, CNRS, Sorbonne Université, Paris 75005, France.

Bioinformatics (Oxford, England)
|July 3, 2023
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概括

这项研究引入了一种用于设计与特定合作伙伴相互作用的蛋白质序列的新方法,从而推进了蛋白质工程. 这种方法使用一个翻译框架来生成依赖于它们相互作用者的人工蛋白质域.

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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:

  • 设计具有特定功能的新型蛋白质对于生物和生物医学应用至关重要.
  • 当前的生成模型往往侧重于单个蛋白序列,缺乏功能特异性或上下文相互作用.
  • 自然语言处理 (NLP) 技术越来越多地适用于氨基酸序列设计.

研究的目的:

  • 开发一种用于生成旨在与特定合作伙伴蛋白质域相互作用的蛋白质域序列的方法.
  • 将计算式蛋白质设计扩展到单个序列之外的功能互动.
  • 为了适应序列生成的蛋白质间域相互作用.

主要方法:

  • 将蛋白质域相互作用设计作为一个序列对序列翻译问题.
  • 训练一个模型以生成基于给定的交互器域序列的条件的人工合作伙伴序列.
  • 利用来自自然多域蛋白质的数据来指导翻译过程.
  • 探索大型语言模型的微调,并使用AlphaFold 2进行质量评估.

主要成果:

  • 开发的方法优于现有的浅 autoregressive 策略,用于生成相互作用的蛋白质序列.
  • 这种方法成功地产生了人工蛋白质域序列,这些序列取决于它们的相互作用器.
  • 该方法适用于不同蛋白质之间的相互作用,证明了其多功能性.
  • AlphaFold 2可以用来评估生成的蛋白质序列的质量.

结论:

  • 拟议的基于翻译的方法为设计功能性蛋白质-蛋白质相互作用提供了一个强大的新策略.
  • 这项工作通过结合相互作用特异性来推进生成性蛋白质设计领域.
  • 代码和数据的可用性促进了蛋白质工程领域的进一步研究和应用.