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相关概念视频

Protein Folding01:25

Protein Folding

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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...
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Protein Organization01:13

Protein Organization

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Overview
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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Amyloid Fibrils03:03

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Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
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Within a biological system, the DNA encodes the RNA, and the nucleotide sequence in the RNA further defines the amino acid sequence in the protein. This is referred to as “The Central Dogma of Molecular Biology” - a term coined by Francis Crick.  Central dogma is a firm principle in biology that defines the flow of genetic information within any life form. The two fundamental steps in central dogma are - transcription and translation.
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Microfluidic Mixers for Studying Protein Folding
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Microfluidic Mixers for Studying Protein Folding

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通过折叠扩散生成蛋白质结构.

Kevin E Wu1,2,3, Kevin K Yang4, Rianne van den Berg5

  • 1Department of Computer Science, Stanford University, Stanford, CA, USA.

Nature communications
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此摘要是机器生成的。

这项研究引入了一种新的扩散模型,用于生成新型蛋白质结构. 该模型模仿了天然的蛋白质折叠,在计算上创建了现实的和多样化的3D蛋白质骨干.

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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物学是结构生物学.
  • 生物物理学的生物物理.

背景情况:

  • 通过计算产生新的,物理可折叠的蛋白质结构对于生物发现和治疗开发至关重要.
  • 当前的神经网络方法难以直接产生多样化和新型蛋白质结构.
  • 了解蛋白质折叠机制是设计新蛋白质的关键.

研究的目的:

  • 开发一种基于扩散的生成模型,用于创建新的蛋白质骨干结构.
  • 在计算生成过程中利用自然蛋白质折叠的原理.
  • 克服现有的神经网络模型在生成多样化的蛋白质结构方面的局限性.

主要方法:

  • 代表蛋白质骨干作为描述原子取向的角度的序列.
  • 在这种表示上训练使用一个否定扩散概率模型 (DDPM).
  • 在DDPM中使用简单的变压器架构.
  • 通过从随机状态到稳定的形状去化来生成结构.

主要成果:

  • 该模型无条件生成高度现实的蛋白质结构.
  • 生成的结构表现出与自然存在的蛋白质相似的复杂性和模式.
  • 基于角度的表示通过避免复杂的等价变量网络来简化模型.

结论:

  • 扩散模型为新的蛋白质结构生成提供了一个有希望的方法.
  • 开发的方法成功地产生了多样化和现实的蛋白质骨干.
  • 开源版本促进了对计算蛋白质设计的进一步研究.