The complete folding pathway of a protein from nanoseconds to microseconds
The complete folding pathway of a protein from nanoseconds to microseconds
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DOI：
10.1038/nature01428
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发表时间：
2003-02-20
期刊：
影响因子：
64.8
通讯作者：
Fersht, AR
中科院分区：
文献类型：
--
作者：
Mayor, U;Guydosh, NR;Fersht, AR
结合实验和模拟数据来描述蛋白质折叠所涉及的所有结构和途径是有问题的。过渡态可以通过 phi 值 (1,2) 进行实验映射，但在有利于折叠的条件下，变性态 (3) 很难分析。此外，原子分辨率的计算机模拟目前仅限于大约一微秒或更短。超快折叠蛋白在两种方法均可实现的时间尺度上折叠和展开 (4,5)，因此我们在这里研究三螺旋束蛋白 Engrailed 同源结构域 (6) 的折叠途径。实验上，蛋白质在一微秒内崩溃，产生具有大量天然α螺旋二级结构的中间体，这是在有利于折叠的条件下变性状态的主要组成部分。突变蛋白显示这种状态是紧凑的，并且含有动态的、类似天然的螺旋和非结构化侧链。在这种状态与自然状态之间的过渡状态中，螺旋结构几乎完全形成，并且它们的对接正在进行中，接近经典的扩散碰撞模型。分子动力学模拟给出了与实验高度一致的速率常数和结构细节，从而完成了原子分辨率下折叠的描述。
Combining experimental and simulation data to describe all of the structures and the pathways involved in folding a protein is problematical. Transition states can be mapped experimentally by phi values(1,2), but the denatured state(3) is very difficult to analyse under conditions that favour folding. Also computer simulation at atomic resolution is currently limited to about a microsecond or less. Ultrafast-folding proteins fold and unfold on timescales accessible by both approaches(4,5), so here we study the folding pathway of the three-helix bundle protein Engrailed homeodomain(6). Experimentally, the protein collapses in a microsecond to give an intermediate with much native alpha-helical secondary structure, which is the major component of the denatured state under conditions that favour folding. A mutant protein shows this state to be compact and contain dynamic, native-like helices with unstructured side chains. In the transition state between this and the native state, the structure of the helices is nearly fully formed and their docking is in progress, approximating to a classical diffusion-collision model. Molecular dynamics simulations give rate constants and structural details highly consistent with experiment, thereby completing the description of folding at atomic resolution.