Soranno Andrea, Holla Andrea, Dingfelder Fabian, Nettels Daniel, Makarov Dmitrii E, Schuler Benjamin
Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1833-E1839. doi: 10.1073/pnas.1616672114. Epub 2017 Feb 21.
Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L. We use single-molecule Förster resonance energy transfer (FRET) to measure the global reconfiguration dynamics of the chain, and photoinduced electron transfer (PET), a contact-based method, to quantify the rate of loop formation between two residues. This combination enables us to probe unfolded-state dynamics on different length scales, corresponding to different parts of the intramolecular distance distribution. Both FRET and PET measurements show that internal friction dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarkable agreement with recent large-scale molecular dynamics simulations using a new water model. The simulations indicate that intrachain interactions and dihedral angle rotation correlate with the presence of internal friction, and theoretical models of polymer dynamics provide a framework for interrelating the contribution of internal friction observed in the two types of experiments and in the simulations. The combined results thus provide a coherent and quantitative picture of internal friction in unfolded proteins that could not be attained from the individual techniques.
在蛋白质折叠反应的各个阶段，内摩擦对蛋白质动力学都有着重要贡献。即使在未折叠和内在无序的蛋白质中，内摩擦也有很大影响，这已通过多种实验技术和模拟得到证实。然而，这些方法探究的是内摩擦的不同方面，并且应用于不同的分子系统，这就引发了关于结果兼容性的问题。为了获得一个综合的观点，我们在此将两种互补的实验技术、模拟和理论应用于同一系统：未折叠的蛋白质L。我们使用单分子荧光共振能量转移（FRET）来测量链的整体重排动力学，以及光诱导电子转移（PET），一种基于接触的方法，来量化两个残基之间环形成的速率。这种结合使我们能够在不同长度尺度上探究未折叠态动力学，对应于分子内距离分布的不同部分。FRET和PET测量均表明，在低变性剂浓度下，内摩擦主导未折叠态动力学，并且结果与使用新水模型的近期大规模分子动力学模拟显著一致。模拟表明链内相互作用和二面角旋转与内摩擦的存在相关，聚合物动力学的理论模型为关联在两种类型实验和模拟中观察到的内摩擦贡献提供了一个框架。因此，综合结果提供了未折叠蛋白质内摩擦的连贯且定量的图景，这是单个技术无法实现的。
