单分子FRET实验中快速与缓慢交换的计算揭示了隐藏的构造状态
Justin J Miller1,2, Upasana L Mallimadugula2, Maxwell I Zimmerman2
1Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States.
bioRxiv : the preprint server for biology
|June 19, 2024
概括
这项研究通过计算模拟中的实验时间平均值来改进蛋白质建模. 这种方法增强了单分子Förster共振能量转移 (smFRET) 和分子动力学之间的协议,揭示了隐藏的蛋白质状态.
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:
- 蛋白质结构和动力学对于功能至关重要,但很难创建蛋白质组合的详细原子模型.
- 单分子弗斯特共振能量转移 (smFRET) 实验和分子动力学模拟之间经常存在差异.
研究的目的:
- 调查实验时间平均计算是否解释了smFRET和模拟之间的差异.
- 开发一种改进的计算方法,用于构建精确的蛋白质结构组合模型.
主要方法:
- 利用马尔科夫状态模型中的动力信息来解释smFRET测量中的时间平均值.
- 对具有不同动态的蛋白质进行模拟和实验数据的比较 (T4溶酶,ApoE,Aβ40).
- 评估不同的分子动力学力场.
主要成果:
- 开发的方法显著改善了模拟和smFRET实验在各种蛋白质之间的一致性.
- 在蛋白质动态中确定了"隐藏状态",由于时间平均化,smFRET中无法直接观察.
- 证明剩余的差异可以指导进一步的模拟来发现以前未计入的状态.
结论:
- 计算实验时间平均值对于协调smFRET和分子动力学模拟至关重要.
- 这种综合方法可以构建更准确的蛋白质结构模型.
- 有助于更深入地了解蛋白质中的序列结构功能关系.
相关概念视频
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
829
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
829
Protein Dynamics in Living Cells
2.1K
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...
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...
2.1K


