局部分子运动编码蛋白质的时间分辨红外光谱
Local molecular motions encode time-resolved infrared spectra of proteins
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中文总结 AI 辅助
研究人员结合瞬态红外光谱与非平衡分子动力学模拟，建立实验弛豫时间与局部结构运动的关联，应用于PDZ3、PDZ2蛋白，揭示蛋白质分级弛豫机制，搭建光谱与动力学分子机制的连接框架。
中文摘要 AI 辅助
时间分辨红外光谱探测蛋白质动力学的时间尺度跨度超过十个数量级，但观测到的动力学信号背后的分子运动仍不明确。本文将瞬态红外光谱与非平衡分子动力学模拟相结合，建立实验弛豫时间与局部结构运动的直接关联。研究单结构域别构蛋白时发现，残基间接触距离是最能忠实再现实验动力学的结构表征；相关性分析识别出介导二级结构元件间通信的局部协同接触网络，这些接触网络的特征时间尺度与实验观测的弛豫过程定量匹配，使每个动力学步骤可对应到特定分子运动。将该框架应用于PDZ3的别构信号传播和PDZ2的光诱导配体解离，该框架提供了原子层面的蛋白质分级弛豫图像，建立了连接瞬态红外光谱与蛋白质动力学分子机制的通用框架。
英文摘要
Time-resolved infrared spectroscopy probes protein dynamics over timescales spanning more than ten orders of magnitude, yet the molecular motions underlying the observed kinetic signatures have remained elusive. Here we combine transient infrared spectroscopy with nonequilibrium molecular dynamics simulations to establish a direct connection between experimental relaxation times and local structural motions. Studying single-domain allosteric proteins, we find that inter-residue contact distances provide the structural representation that most faithfully reproduces the experimental dynamics. Correlation analysis identifies localized networks of coordinated contacts that mediate communication between secondary-structure elements. The characteristic timescales of these contact networks quantitatively match the experimentally observed relaxation processes, enabling each kinetic step to be assigned to a specific molecular motion. Applied to allosteric signal propagation in PDZ3 and photoinduced ligand unbinding in PDZ2, this framework provides an atomistic picture of hierarchical protein relaxation and establishes a general framework for connecting transient infrared spectroscopy with the molecular mechanisms of protein dynamics.
