层次摩擦记忆导致快速折叠蛋白质的亚扩散配置动态
Anton Klimek1, Benjamin A Dalton1, Lucas Tepper1
1Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany.
概括
蛋白质动态显示由于摩擦记忆效应而导致的亚扩散,而不是自由能量景观. 这些记忆效应对于准确建模蛋白质折叠和构造变化至关重要.
科学领域:
- 生物物理学的生物物理.
- 计算生物学 计算生物学
- 化学物理 化学物理
背景情况:
- 蛋白质表现出复杂的配置动态,通常以亚扩散为特征.
- 蛋白质动态中这种亚扩散的根本原因仍然不完全理解.
- 研究这些动态是理解蛋白质折叠和功能的关键.
研究的目的:
- 调查非马科夫摩擦和自由能量景观对快速折叠蛋白质动态的影响.
- 分析折叠反应坐标的平均平方位移 (MSD) 和平均第一次通道时间 (MFPT).
- 确定蛋白质结构动态中亚扩散的主要驱动因素.
主要方法:
- 利用分子动力学模拟来提取摩擦内存内核.
- 通过使用等级式多次指数函数来描述摩擦内存内核.
- 在MSD和MFPT中分析了亚扩散,考虑了摩擦和自由能量景观效应.
主要成果:
- 摩擦记忆效应会在较短的时间范围内导致MSD的亚扩散.
- 自由能源的景观有助于在更长的时间尺度下分发.
- 在快速折叠的蛋白质中,摩擦记忆效应主导了MSD缩放行为,而不是自由能量景观效应.
结论:
- 非马科维摩擦是快速折叠蛋白质动态中亚扩散的主要驱动因素.
- 马科维模型不足以准确地捕捉蛋白质折叠动态.
- 记忆效应,而不是自由能量景观或坐标依赖摩擦,是次扩散的主要来源.
相关概念视频
Protein Folding
127.9K
Overview
127.9K
Protein Folding
11.5K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
11.5K
Molecular Chaperones and Protein Folding
19.9K
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...
19.9K
Molecular Chaperones and Protein Folding
15.1K
15.1K
Electron Configuration of Multielectron Atoms
65.2K
The alkali metal sodium (atomic number 11) has one more electron than the neon atom. This electron must go into the lowest-energy subshell available, the 3s orbital, giving a 1s22s22p63s1 configuration. The electrons occupying the outermost shell orbital(s) (highest value of n) are called valence electrons, and those occupying the inner shell orbitals are called core electrons. Since the core electron shells correspond to noble gas electron configurations, we can abbreviate electron...
65.2K
Protein Folding Quality Check in the RER
5.3K
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...
5.3K


