Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-Ku, Sapporo 001-0020, Japan.
Weizmann Institute of Science, Rehovot 76100, Israel.
J Chem Phys. 2018 Mar 28;148(12):123325. doi: 10.1063/1.5016487.
Hierarchical features of the energy landscape of the folding/unfolding behavior of adenylate kinase, including its dependence on denaturant concentration, are elucidated in terms of single-molecule fluorescence resonance energy transfer (smFRET) measurements in which the proteins are encapsulated in a lipid vesicle. The core in constructing the energy landscape from single-molecule time-series across different denaturant concentrations is the application of rate-distortion theory (RDT), which naturally considers the effects of measurement noise and sampling error, in combination with change-point detection and the quantification of the FRET efficiency-dependent photobleaching behavior. Energy landscapes are constructed as a function of observation time scale, revealing multiple partially folded conformations at small time scales that are situated in a superbasin. As the time scale increases, these denatured states merge into a single basin, demonstrating the coarse-graining of the energy landscape as observation time increases. Because the photobleaching time scale is dependent on the conformational state of the protein, possible nonequilibrium features are discussed, and a statistical test for violation of the detailed balance condition is developed based on the state sequences arising from the RDT framework.
本文采用单分子荧光共振能量转移（smFRET）技术，在脂质囊泡中对腺嘌呤激酶的折叠/去折叠行为的能量景观进行了研究，包括其对变性剂浓度的依赖性。在构建来自不同变性剂浓度的单分子时间序列的能量景观时，核心是应用率失真理论（RDT），该理论自然考虑了测量噪声和采样误差的影响，同时结合了突变点检测和 FRET 效率相关的光漂白行为的量化。能量景观是作为观察时间尺度的函数构建的，揭示了在小时间尺度下处于超盆地中的多个部分折叠构象。随着时间尺度的增加，这些变性状态合并成一个单一的盆地，表明随着观察时间的增加，能量景观的粗粒化。由于光漂白时间尺度取决于蛋白质的构象状态，因此讨论了可能的非平衡特征，并基于 RDT 框架中产生的状态序列，开发了一个违反详细平衡条件的统计检验。
