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相关概念视频

Protein Translocation Machinery on the ER Membrane01:28

Protein Translocation Machinery on the ER Membrane

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The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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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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Insertion of Multi-pass Transmembrane Proteins in the RER01:29

Insertion of Multi-pass Transmembrane Proteins in the RER

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The rough ER membrane synthesizes, assembles, and embeds transmembrane proteins in diverse topologies. These proteins function as transporters or channels and can remain in the ER membrane or are sent to the Golgi complex, lysosome, and cell membrane.
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
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Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

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Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
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相关实验视频

Updated: Jul 7, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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灵活的蛋白质-蛋白质对接与多轨代变压器.

Lee-Shin Chu1, Jeffrey A Ruffolo2, Ameya Harmalkar1

  • 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

Protein science : a publication of the Protein Society
|December 26, 2023
PubMed
概括

GeoDock是一种新的深度学习方法,比传统方法更快地预测蛋白质-蛋白质对接结构. 它允许在结合过程中进行构造变化,提高复杂结构预测和虚拟选的准确性.

关键词:
深度学习是一种深度学习.灵活的蛋白质对接蛋白质与蛋白质的相互作用

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SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy
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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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相关实验视频

Last Updated: Jul 7, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

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SNARE-mediated Fusion of Single Proteoliposomes with Tethered Supported Bilayers in a Microfluidic Flow Cell Monitored by Polarized TIRF Microscopy
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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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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
  • 生物信息学是一种生物信息学.

背景情况:

  • 由于广泛的采样和重新排名,传统的蛋白质-蛋白质对接是缓慢的,限制了基于结构的虚拟选等高通量应用.
  • 现有的蛋白质对接的深度学习方法更快,但往往取得低的成功率,并假定刚性对接,忽视关键的结合诱导的构造变化.

研究的目的:

  • 开发一种新的深度学习方法,GeoDock,用于准确和高效的蛋白质-蛋白质对接,以考虑构造灵活性.
  • 为了使高通量复杂结构预测,并促进应用程序,如虚拟选和研究体机制.

主要方法:

  • GeoDock使用了多轨代变压器网络,只采用蛋白质序列和结构作为输入.
  • 该模型被设计为在残留水平上灵活,预测蛋白质结合时的形状变化.
  • 与其他深度学习模型不同,GeoDock不需要多个序列对齐.

主要成果:

  • 在DIPS测试组中,GeoDock在DIPS测试组中取得了43%的top-1成功率,超过了其他测试方法的表现.
  • 在解决训练集污染后,DIPS的成功率为31%.
  • 在DB5.5和抗体-抗原数据集上,GeoDock超越了其他深度学习模型,但落后于传统方法和AlphaFold-Multimer.

结论:

  • GeoDock为蛋白质-蛋白质对接提供了显著的速度改进,推断时间低于1秒/GPU.
  • 架构为捕捉绑定过程中的骨干灵活性提供了基础,尽管绑定诱导的结构变化仍然是一个挑战.
  • GeoDock的速度使其适用于大规模结构选和虚拟选应用.