Tomita Ayana, Sato Tokushi, Ichiyanagi Kouhei, Nozawa Shunsuke, Ichikawa Hirohiko, Chollet Matthieu, Kawai Fumihiro, Park Sam-Yong, Tsuduki Takayuki, Yamato Takahisa, Koshihara Shin-Ya, Adachi Shin-Ichi
Department of Materials Science, Tokyo Institute of Technology, Meguro, Tokyo 152-8551, Japan.
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2612-6. doi: 10.1073/pnas.0807774106. Epub 2009 Feb 9.
Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.
蛋白质含有一些体积相对较小的腔。尽管这些堆积缺陷与蛋白质的热力学不稳定性有关，但这些腔在控制蛋白质功能（如配体迁移和结合）方面也发挥着特定作用。这个问题已经在一种著名的蛋白质——肌红蛋白（Mb）中得到了广泛研究。Mb在埋于蛋白质基质中的血红素位点可逆地结合气体配体，并且拥有几个配体分子可以驻留的内部腔。至于配体如何在内部腔之间找到其迁移途径，这仍然是一个悬而未决的问题。在此，我们报道了Mb中配体迁移过程中内部腔的动态和连续结构变形。我们的方法，即在低温下用脉冲激光连续照射天然一氧化碳肌红蛋白晶体，揭示了CO分子迁移到每个腔中会诱导腔周围氨基酸残基的结构变化，这导致腔通过一种呼吸运动而扩张。配体和腔的连续运动表明了一种由诱导契合产生的配体迁移通道的自开放机制，这通过德劳内三角剖分法的计算几何分析得到了进一步支持。这一结果表明内部腔的呼吸运动作为蛋白质基质中配体迁移的一种普遍机制具有关键作用。
