论文标题

蛋白质中三级结构元素的运动的速度有多快?

How fast are the motions of tertiary-structure elements in proteins?

论文作者

Haran, Gilad, Mazal, Hisham

论文摘要

蛋白质运动在多个时间和距离上发生。蛋白质三级结构元件(即结构域)的大规模运动特别有趣,因为它们对于许多酶的催化活性以及蛋白质机器和电动机的功能周期至关重要。理论估计值表明,域运动应非常快,发生在纳米秒或微秒的时间尺度上。实际上,域运动的自由能屏障可能涉及盐桥,这可能会在微秒内破裂。可以直接在快速时间尺度上直接探测域运动的实验方法才出现。该观点简要讨论了其中一些技术,包括NMR和单分子荧光光谱。我们介绍了一些最近的研究,这些研究证明了超快域运动,并讨论了它们的潜在作用。特别令人惊讶的是,观察到某些蛋白质机器中功能周期快得多的三级结构元件动力学。这些迅速动议可以逐案合理化。例如,可以利用多基底酶中的快速域闭合来优化相对底物方向。在构象动力学与功能周期的时间尺度上,大的不匹配是蛋白质中的一般设计原理尚待确定。

Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the functional cycles of protein machines and motors. Theoretical estimates suggest that domain motions should be very fast, occurring on the nanosecond or microsecond time scales. Indeed, free-energy barriers for domain motions are likely to involve salt bridges, which can break in microseconds. Experimental methods that can directly probe domain motions on fast time scales have appeared only in recent years. This Perspective discusses briefly some of these techniques, including NMR and single-molecule fluorescence spectroscopies. We introduce a few recent studies that demonstrate ultrafast domain motions, and discuss their potential roles. Particularly surprising is the observation of tertiary-structure element dynamics that are much faster than the functional cycles in some protein machines. These swift motions can be rationalized on a case-by-case basis. For example, fast domain closure in multi-substrate enzymes may be utilized to optimize relative substrate orientation. Whether a large mismatch in time scales of conformational dynamics vs. functional cycles is a general design principle in proteins remains to be determined.

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