Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin
Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin
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DOI：
10.1073/pnas.1603539113
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发表时间：
2016-09-20
影响因子：
11.1
通讯作者：
Hub, Jochen S.
中科院分区：
文献类型：
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作者：
Brinkmann, Levin U. L.;Hub, Jochen S.
“蛋白质震动”指的是蛋白质中多余能量的耗散，这是对局部扰动的响应，例如化学键的断裂或光子的吸收。飞秒时间分辨小角和广角X射线散射（TR-SWAXS）能够跟踪这种超快蛋白质动力学。然而，由于实验的结构解释是复杂的，蛋白质地震的分子图像仍然难以捉摸。此外，最近的TR-SWAXS数据产生了新的问题，这些数据被解释为整个蛋白质的欠阻尼振荡，从而挑战了长期存在的过阻尼全局蛋白质动力学概念。基于分子动力学模拟，我们提出了一个详细的一氧化碳（CO）的光解离后，在肌红蛋白的蛋白质震动的分子电影。模拟表明，蛋白质震动的特征是单个压力峰，该压力峰在500 fs内各向异性传播穿过蛋白质并进一步进入溶剂。通过从模拟中计算TR-SWAXS模式，我们可以将倒空间SWAXS信号中的特征解释为特定的真实空间动力学，例如CO位移和压力波传播。值得注意的是，我们发现，小角度的数据主要检测调制的溶剂密度，但不是裸蛋白质的振荡，从而调和最近的TR-SWAXS实验的概念过阻尼的全球蛋白质动力学。
"Protein quake" denotes the dissipation of excess energy across a protein, in response to a local perturbation such as the breaking of a chemical bond or the absorption of a photon. Femtosecond time-resolved small-and wide-angle X-ray scattering (TR-SWAXS) is capable of tracking such ultrafast protein dynamics. However, because the structural interpretation of the experiments is complicated, a molecular picture of protein quakes has remained elusive. In addition, new questions arose from recent TR-SWAXS data that were interpreted as underdamped oscillations of an entire protein, thus challenging the long-standing concept of overdamped global protein dynamics. Based on molecular-dynamics simulations, we present a detailed molecular movie of the protein quake after carbon monoxide (CO) photodissociation in myoglobin. The simulations suggest that the protein quake is characterized by a single pressure peak that propagates anisotropically within 500 fs across the protein and further into the solvent. By computing TR-SWAXS patterns from the simulations, we could interpret features in the reciprocal-space SWAXS signals as specific real-space dynamics, such as CO displacement and pressure wave propagation. Remarkably, we found that the small-angle data primarily detect modulations of the solvent density but not oscillations of the bare protein, thereby reconciling recent TR-SWAXS experiments with the notion of overdamped global protein dynamics.