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相关概念视频

Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

4.3K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Protein Folding01:22

Protein Folding

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Overview
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Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

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Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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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

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....
6.3K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.8K
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...
10.8K

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相关实验视频

Updated: Jun 11, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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通过蛋白质结构扩散精确的形状采样.

Jiahao Fan1,2, Ziyao Li2,3, Eric Alcaide2,4

  • 1School of Physics, Peking University, Beijing 100871, China.

Journal of chemical information and modeling
|September 28, 2024
PubMed
概括
此摘要是机器生成的。

UFConf使用一种新的扩散模型方法准确地采样各种蛋白质构造,优于现有方法. 这一进步有助于药物发现和生物研究,通过更有效地预测蛋白质结构.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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相关实验视频

Last Updated: Jun 11, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
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科学领域:

  • 计算生物学 计算生物学
  • 结构生物学 结构生物学
  • 药物发现 药物发现 药物发现

背景情况:

  • 精确的蛋白质构成采样对于生物和医学进步至关重要.
  • 深度学习已经改善了蛋白质结构预测,但预测各种稳定构造仍然具有挑战性.
  • 现有的方法往往会从训练数据中显示出构造偏差.

研究的目的:

  • 开发一种新的方法,UFConf,用于从氨基酸序列中稳定地采样各种蛋白质构造.
  • 为了提高蛋白质结构预测的准确性和结构有效性.
  • 为了证明UFConf在药物发现应用中的实用性,特别是蛋白质-连接体对接.

主要方法:

  • 通过实施基于构造的扩散过程,将AlphaFold2转化为扩散模型.
  • 调整模型架构以有效处理分散的输入.
  • 开发了一种使用结构聚类来缓解构成偏差的等级重量调整协议.

主要成果:

  • 与现有方法相比,UFConf在成功采样和结构有效性方面表现出卓越的表现.
  • 在分子动力学模拟中,UFConf成功克服了能量障碍,使得采样更有效.
  • 在药物发现的盲目测试中,UFConf准确地预测了一种新型的蛋白质连接体复合体.

结论:

  • UFConf提供了一种强大的新方法,用于采样各种蛋白质构造.
  • 该方法显示了加速药物发现和推进生物研究的巨大潜力.
  • UFConf提供了多功能采样功能,包括部分采样和结构性插值.