在无序蛋白质模拟中,从能量陷中解开折叠
Jeffrey M Lotthammer1,2, Alex S Holehouse1,2
1Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.
Journal of chemical information and modeling
|March 5, 2025
概括
我们开发了一种新的算法,用于在模拟中量化蛋白质结构异质性. 这种方法准确地评估了内在无序蛋白质 (IDP) 的采样,确保了可靠的模拟结果.
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:
- 蛋白质结构异质性对于生物过程至关重要,特别是在缺乏稳定结构的内在无序蛋白质 (IDP) 中.
- 了解蛋白序列与其动态构成组合之间的关系是阐明IDP功能的关键.
- 目前在模拟中评估形状采样的方法,如视觉检查,有风险掩盖采样差的区域.
研究的目的:
- 在蛋白质模拟中开发和介绍一种用于量化局部结构异质性的新型算法.
- 提供一种定量方法,用于评估内在无序蛋白质的模拟中构造性采样的程度.
- 为了能够对内在无序蛋白质的模拟方法和力场进行可靠的比较.
主要方法:
- 开发了一种算法,通过比较骨干二面角分布来量化每余量的局部形状异质性.
- 使用限制性聚合物模型作为广泛的形状异质性的统计参考.
- 从分子模拟与独立的全原子模拟中比较分布.
主要成果:
- 在模拟中,该算法在定量上区分了样本良好,样本差和折叠的蛋白质区域.
- 在各种玩具,合成和生物系统中证明了算法的有效性.
- 建立了一种可靠的方法来评估内在无序蛋白质模拟中的构造性采样.
结论:
- 准确评估局部形状采样对于验证模拟方法和固有无序蛋白质的力场至关重要.
- 这种算法提高了从蛋白质结构异质性的分子模拟中得出的结论的可靠性和稳定性.
- 开发的方法促进了对增强的采样技术和力场性能进行更严格的评估.
更多相关视频
相关概念视频
Protein Folding
117.0K
Overview
117.0K
Molecular Chaperones and Protein Folding
17.6K
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
The...
17.6K
Intrinsically Disordered Proteins
17.7K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
17.7K
Noncovalent Attractions in Biomolecules
47.1K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
47.1K
Protein Folding Quality Check in the RER
3.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.7K
Conservation of Protein Domains Over Different Proteins
10.7K
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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.7K


