论文标题
分析蛋白质NMR松弛数据的明确运动模型
Explicit models of motions to analyze NMR relaxation data in proteins
论文作者
论文摘要
核磁共振(NMR)是表征分子运动的首选工具。在生物大分子中,尤其可以通过核自旋松弛速率探测到纳米秒的动作,这取决于自旋相互作用框架方向的时间波动。在过去的40年中,使用无模型(MF)方法成功分析了放松率,该方法对动议的性质和报告的有效振幅和时间尺度没有任何假设。但是,除非与分子动力学(MD)模拟相辅相成,否则从这种类型的分析中获得动作的机理图片充其量很难。尽管精度有限,但可以使用此类模拟来获取构建旨在分析NMR松弛数据的明确模型的信息。在这里,我们介绍了如何构建此类模型,特别适合描述含有甲基蛋白质的副链链的运动,并将其与MF方法进行比较。我们在合成数据上表明,在旋转型跳跃的存在下,明确的运动模型更强大,这在蛋白质侧链的甲基甲基中占主导地位。我们希望这项工作激励使用明确的运动模型来分析MD和NMR数据。
Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nano-second motions, in particular, can be probed by nuclear spin relaxation rates which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model Free (MF) approach which makes no assumption on the nature of motions and reports on the effective amplitude and time-scale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methyl-bearing protein side-chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side-chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data.