III. Institute of Physics-Biophysics, Georg August University, 37077 Göttingen, Germany.
Biochemistry Department, Oxford University, South Parks Rd, Oxford OX1 3QU, United Kingdom.
Phys Rev E. 2019 Nov;100(5-1):052405. doi: 10.1103/PhysRevE.100.052405.
The conformational flexibility and dynamics of unfolded peptide chains is of major interest in the context of protein folding and protein functioning. The rate with which amino acids at different positions along the peptide chain meet sets an upper speed limit for protein folding. By using single-molecule photo-induced energy transfer spectroscopy, we have systematically measured end-to-end and end-to-internal site contact formation rates for several intrinsically disordered protein fragments (IDPs) (11 to 41 amino acids) and have also determined their hydrodynamic radius using dual-focus fluorescence correlation spectroscopy. For interpreting the measured values, we have developed a Brownian dynamics model (based on bead-rod chain dynamics in a thermal bath including hydrodynamic interactions) which quantitatively reproduces all measured data surprisingly well while requiring only two fit parameters. The model provides a complete picture of the peptides' dynamics and allows us to translate the experimental rates and radii into molecular properties of the peptides: We find a persistence length of l_{P}=5.2±1.9Å, a hydrodynamic radius of a=3.5±0.7Å per amino acid, and that excluded volume effects play an important role in the dynamics of IDPs.
未折叠肽链的构象灵活性和动力学是蛋白质折叠和功能的主要研究内容。肽链上不同位置的氨基酸相遇的速度为蛋白质折叠设定了上限。通过使用单分子光诱导能量转移光谱法，我们系统地测量了几个固有无序蛋白片段 (IDP)（11 到 41 个氨基酸）的端到端和端到内部位点接触形成速率，并使用双焦点荧光相关光谱法确定了它们的流体力学半径。为了解释测量值，我们开发了一个布朗动力学模型（基于热浴中的珠-棒链动力学，包括流体动力学相互作用），该模型令人惊讶地很好地重现了所有测量数据，而仅需要两个拟合参数。该模型提供了肽动力学的完整描述，并使我们能够将实验速率和半径转换为肽的分子特性：我们发现，持久长度 l_{P}=5.2±1.9Å，每个氨基酸的流体力学半径 a=3.5±0.7Å，并且排斥体积效应在 IDP 的动力学中起着重要作用。
