Itoh Kazuhito, Sasai Masaki
Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan.
Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14736-41. doi: 10.1073/pnas.0402978101. Epub 2004 Oct 4.
Conformational dynamics in protein functioning covers a wide range of time scales from nanosecond fluctuations around a conformation to the large-amplitude conformational changes of milliseconds or longer. We illustrate a picture of cooperative coupling among such motions of different time scales in a model protein, photoactive yellow protein, by proposing a model that can consistently explain the experimental results on the photocycle of photoactive yellow protein. The model provides a scenario in which the global collective motion induced by the unfolding of the N-terminal domain promotes the loosening of the atomistic packing around the chromophore, which produces the favorable molecular environment for the photoexcited chromophore, thereby stabilizing the partially unfolded intermediate in the photocycle. The proteinquake, the large conformational change triggered by the local structural disturbance, plays a decisive role in controlling the kinetics of functioning.
蛋白质功能中的构象动力学涵盖了广泛的时间尺度，从围绕一种构象的纳秒级波动到毫秒或更长时间的大幅度构象变化。我们通过提出一个能够连贯解释光活性黄色蛋白光循环实验结果的模型，展示了在模型蛋白光活性黄色蛋白中不同时间尺度的此类运动之间协同耦合的图景。该模型提供了一种情形，即由N端结构域展开引发的全局集体运动促进了发色团周围原子堆积的松弛，这为光激发的发色团产生了有利的分子环境，从而稳定了光循环中的部分展开中间体。由局部结构扰动引发的大幅度构象变化——“蛋白质震颤”，在控制功能动力学方面起着决定性作用。
