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相关概念视频

Protein Organization01:24

Protein Organization

6.6K
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....
6.6K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.6K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
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Protein Folding01:22

Protein Folding

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Overview
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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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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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构建特定于蛋白质结构的旋体库.

Algirdas Grybauskas1, Saulius Gražulis1

  • 1Sector of Crystallography and Cheminformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, 7 Saulėtekio Ave, Vilnius, LT- 10257, Lithuania.

Bioinformatics (Oxford, England)
|July 13, 2023
PubMed
概括
此摘要是机器生成的。

这项研究引入了一种用于预测蛋白质侧链位置的新方法,生成定制二面角图书馆,以提高蛋白质建模和相互作用预测的准确性. 该rotag软件提供了一个更精确的替代标准rotamer库.

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科学领域:

  • 计算生物学 计算生物学
  • 结构生物信息学 结构生物信息学
  • 蛋白质建模模型

背景情况:

  • 精确的蛋白质侧链定位对于预测蛋白质-配体和蛋白质-蛋白质相互作用至关重要.
  • 使用预定义的旋转体库的现有方法可以过度简化几何形状,并错过罕见的蛋白质结构的形状,从而导致不准确.
  • 这些局限性阻碍了蛋白质建模中精确的侧链原子位置预测.

研究的目的:

  • 开发一种改进的方法来预测蛋白质侧链结构.
  • 为了生成特定于蛋白质的二面角图书馆,以解释当地的原子和分子环境.
  • 为了提高侧链定位的准确性,超出了标准旋转机库的能力.

主要方法:

  • 开发了一种新的计算方法来扫描硬质可访问的侧链形状.
  • 为特定的目标蛋白质量身定制的定制二面角图书馆.
  • 在开源软件包"rotag"中实现了该技术.

主要成果:

  • 提出的方法成功地产生了潜在的旋转器,避免了预定义库的限制.
  • 与广泛使用的旋转机库相比,获得的平均根平均平方偏差 (RMSD) 更接近实验确定的侧链原子位置.
  • 特定于蛋白质的库可以捕获更准确的侧链几何.

结论:

  • 新方法在预测蛋白质建模的侧链形状方面提供了更高的准确性.
  • 定制的二面角图书馆通过考虑独特的结构特征来改善蛋白质相互作用的预测.
  • 开源的"rotag"软件包为研究界提供了一个有价值的工具.