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Updated: Jun 6, 2025

Visualizing the Conformational Dynamics of Membrane Receptors Using Single-Molecule FRET

Visualizing the Conformational Dynamics of Membrane Receptors Using Single-Molecule FRET

Published on: August 17, 2022

单分子FRET实验中的快速与缓慢交换的会计计算揭示了隐藏的合规状态

Justin J Miller¹, Upasana L Mallimadugula², Maxwell I Zimmerman²

¹Departments of Biochemistry & Biophysics and Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.

Journal of chemical theory and computation

|November 26, 2024

概括

这项研究引入了一种新方法,以改善单分子福斯特共振能量转移 (smFRET) 实验和蛋白质结构组合的分子动力学模拟之间的一致性. 这种方法可以解释实验时间的平均值,使蛋白质动态和功能的原子模型更准确.

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功能至关重要,但蛋白质组合的详细原子模型很难创建.
单分子福斯特共振能量转移 (smFRET) 和分子动力学 (MD) 模拟是强大的工具,但它们的整合因缺乏协议而受到限制.
在原子层面了解蛋白质动态对于破译序列结构功能关系至关重要.

研究的目的:

开发和验证一种方法,以改善smFRET实验和MD对蛋白质结构组合的模拟之间的协议.
考虑smFRET测量中的实验时间平均值,以更好地解释模拟数据.
为了使蛋白质动态的准确,实验性接地,全原子模型的创建.

主要方法:

利用来自蛋白质动态的马尔科夫状态模型 (MSM) 的动态信息来解释smFRET实验中的时间平均值.
通过一种新的算法将smFRET实验数据与MD模拟集成在一起.
评估不同的分子力场,以获得模拟准确度.

主要成果:

开发的方法显著提高了MD模拟和smFRET实验之间的一致性,这些实验涉及具有不同动态的蛋白质,从有序 (T4溶酶) 到无序 (ApoE,Aβ40).
鉴定的"隐藏"蛋白质状态由于时间平均而在smFRET中没有直接观察到,类似于NMR中的快速交换状态.
证明剩余的差异可以指导进一步的模拟,以建立以前未计入的状态的模型.

结论:

这种新方法有效地弥合了计算模拟和实验smFRET数据之间的差距,为研究蛋白质动态提供了一个强大的框架.
这种方法可以为灵活,无序或非晶状的蛋白质状态生成准确的原子模型.
这些发现为深入了解蛋白质序列,结构,动态和功能之间的联系铺平了道路.

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Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox

Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox

Published on: July 5, 2021

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

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