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相关概念视频

Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

4.6K
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 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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Multi-pass Transmembrane Proteins and β-barrels01:09

Multi-pass Transmembrane Proteins and β-barrels

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In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
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相关实验视频

Updated: Sep 19, 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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MSBack:使用受约束扩散的高粗粒度蛋白质的多尺度后映射.

Curt Waltmann1, Yihang Wang1, Chengxi Yang

  • 1Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.

Journal of chemical theory and computation
|June 2, 2025
PubMed
概括
此摘要是机器生成的。

我们开发了MSBack,这是一种新的扩散模型方法,可以从粗粒度模型中重建全原子蛋白质结构. 这促进了生物分子模拟和对病毒等复杂物体的结构分析.

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Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT
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Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT

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Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
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相关实验视频

Last Updated: Sep 19, 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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Mapping Molecular Diffusion in the Plasma Membrane by Multiple-Target Tracing MTT
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Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
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科学领域:

  • 生物物理学的生物物理.
  • 计算生物学 计算生物学
  • 结构生物学 结构生物学

背景情况:

  • 粗粒度 (CG) 分子动力学模拟生物分子行为,但失去结构细节.
  • 将CG模型逆向映射到全原子分辨率是具有挑战性的,特别是在低分辨率 (每残留物少于一个位点) 时.
  • 低分辨率的CG模型对于模拟像病毒 (例如,SARS-CoV-2,HIV-1) 这样的大型复合体至关重要.

研究的目的:

  • 开发一种方法,从高度粗粒的蛋白质结构中准确地重建所有原子.
  • 为了应对在每个残留点下一个位置的分辨率下对蛋白质进行逆向映射的尚未解决的挑战.
  • 为了能够对大型生物分子复合体进行详细的结构分析.

主要方法:

  • 提出MSBack,这是一个扩散模型的方法,用于向后映射.
  • 限制了扩散过程,使所有原子坐标与CG坐标相匹配.
  • 在没有再培训的情况下利用现有的全原子结构的扰动.
  • 基于物理的综合方法,用于细粒度的后映射.

主要成果:

  • MSBack 随机生成与CG坐标相匹配的α-碳痕迹.
  • 成功地证明了成熟的HIV-1囊体的完整逆向映射.
  • 实现了对背映射的HIV-1囊体结构的1 Å分辨率.
  • 该方法适用于以大型复合体所需的分辨率模拟的蛋白质.

结论:

  • MSBack有效地从低分辨率的CG模型中重建全原子蛋白质结构.
  • 这种方法克服了当前后映射技术的局限性.
  • 能够对大型生物分子系统及其相互作用进行详细的结构洞察.