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相关概念视频

Nuclear Overhauser Enhancement (NOE)01:07

Nuclear Overhauser Enhancement (NOE)

646
Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling.  This phenomenon, called the Nuclear Overhauser Enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring...
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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
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Molecular Models02:00

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
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Additional Subnuclear Structures02:10

Additional Subnuclear Structures

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The eukaryotic nucleus is a double membrane-bound organelle that contains nearly all of the cell’s genetic material in the form of chromosomes. It is rightly called the “brain” of the cell as it shoulders the responsibility of responding to various physiological processes, stress, altered metabolic conditions, and other cellular signals. 
The nucleus contains many membrane-less subnuclear organelles or nuclear bodies, such as nucleoli, Cajal bodies, speckles,...
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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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相关实验视频

Updated: Jun 16, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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OpenNucleome用于高分辨率的核结构和动态建模.

Zhuohan Lao1, Kartik D Kamat1, Zhongling Jiang1

  • 1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.

eLife
|August 15, 2024
PubMed
概括

OpenNucleome是一个新的开源软件,用于模拟人类核. 它有助于揭示基因组区域如何定于核体,支持基因组功能的核区分模型.

科学领域:

  • 细胞生物学 细胞生物学
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • 人类核的结构对于细胞功能和基因调节至关重要.
  • 先进的实验方法提供了洞察力,但解释需要计算建模工具.
  • 对于核组织研究,缺乏标准化的建模软件.

研究的目的:

  • 介绍OpenNucleome,这是一个开源软件,用于人类核的GPU加速分子动力学模拟.
  • 启用基于高分辨率的染色体 (100KB分辨率),核膜,核细胞和斑点的粒子建模.
  • 促进核架构,冷凝物形成和非平衡效应的动态模拟.

主要方法:

  • 开发了OpenNucleome,这是一个利用GPU加速分子动态的开源软件.
  • 实现了基于染色体,核膜,核细胞和斑点的基于粒子的表示.
  • 应用软件来研究核组织中"固定点"的形成.

主要成果:

  • OpenNucleome提供了核架构的精确结构模型.
  • 模拟揭示了"固定点" (基因组位置定) 出现背后的机制.
  • "固定点"的定能够抵御染色体位置和核形状的波动.
关键词:
3D基因组是什么 3D基因组染色体折叠的发生染色体是一种染色体.基因表达的基因表达方式人类 人类 人类 人类 人类 人类 人类分子生物物理学分子生物物理学核部位是核部位的组成部分.结构生物学结构生物学

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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相关实验视频

Last Updated: Jun 16, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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结论:

  • 这些发现支持核区划模型解释基因组功能.
  • OpenNucleome 作为一个有价值的工具,用于核生物学中的机械探索.
  • 该软件增强了核组织研究中的实验数据的解释.