Transient 2D IR spectroscopy of ubiquitin unfolding dynamics
Transient 2D IR spectroscopy of ubiquitin unfolding dynamics
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DOI：
10.1073/pnas.0700959104
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发表时间：
2007-09-04
影响因子：
11.1
通讯作者：
Tokmakoff, Andrei
中科院分区：
文献类型：
--
作者：
Chung, Hoi Sung;Ganim, Ziad;Tokmakoff, Andrei
瞬态二维红外（2D IR）光谱被用作探针的蛋白质展开动力学的快速展开实验与分子动力学模拟的直接比较。在实验中，泛素的展开是由激光温度跳变启动的，并且使用酰胺I 2D IR光谱探测从纳秒到毫秒的蛋白质结构演变。温度跳跃准备一个子系综附近的展开过渡态，导致准无势垒展开（“突发阶段”）之前的毫秒激活展开动力学。泛素的猝发相展开的特征在于β-折叠的振动之间的耦合的损失，该过程在2D IR光谱中表现为折叠的两个IR活性模式的对角峰和交叉峰的频率蓝移和强度降低。随着片层展开，β-片层酰胺基团的波动和溶剂暴露的增加也以均匀线宽的增加为特征。实验光谱进行了比较与二维红外光谱计算的时间演变的结构在分子动力学模拟泛素展开。解折叠被描述为泛素β-折叠中链的顺序解折叠，使用该折叠的两个集合坐标：（i）相邻A-链I和II之间的天然链间接触和（ii）该折叠内剩余的β-链接触。所使用的方法说明了二维红外光谱可用于实验和模拟的详细动态比较的一般原则。
Transient two-dimensional infrared (2D IR) spectroscopy is used as a probe of protein unfolding dynamics in a direct comparison of fast unfolding experiments with molecular dynamics simulations. In the experiments, the unfolding of ubiquitin is initiated by a laser temperature jump, and protein structural evolution from nanoseconds to milliseconds is probed using amide I 2D IR spectroscopy. The temperature jump prepares a subensemble near the unfolding transition state, leading to quasi-barrierless unfolding (the "burst phase") before the millisecond activated unfolding kinetics. The burst phase unfolding of ubiquitin is characterized by a loss of the coupling between vibrations of the beta-sheet, a process that manifests itself in the 2D IR spectrum as a frequency blue-shift and intensity decrease of the diagonal and cross-peaks of the sheet's two IR active modes. As the sheet unfolds, increased fluctuations and solvent exposure of the beta-sheet amide groups are also characterized by increases in homogeneous linewidth. Experimental spectra are compared with 2D IR spectra calculated from the time-evolving structures in a molecular dynamics simulation of ubiquitin unfolding. Unfolding is described as a sequential unfolding of strands in ubiquitin's beta-sheet, using two collective coordinates of the sheet: (i) the native interstrand contacts between adjacent A-strands I and II and (ii) the remaining beta-strand contacts within the sheet. The methods used illustrate the general principles by which 2D IR spectroscopy can be used for detailed dynamical comparisons of experiment and simulation.