Kikuchi H, Wako H, Yura K, Go M, Mimuro M
Department of Physics, Nippon Medical School, Kawasaki 211-0063, Japan.
Biophys J. 2000 Sep;79(3):1587-600. doi: 10.1016/S0006-3495(00)76409-5.
Phycobiliproteins are basic building blocks of phycobilisomes, a supra-molecular assembly for the light-capturing function of photosynthesis in cyanobacteria and red algae. One functional form of phycobiliproteins is a trimeric form consisting of three identical units having C(3) symmetry, with each unit composed of two kinds of subunits, the alpha-subunit and beta-subunit. These subunits have similar chain folds and can be divided into either globin-like or X-Y helices domains. We studied the significance of this two-domain structure for their assembled structures and biological function (light-absorption) using a normal mode analysis to investigate dynamic aspects of their three-dimensional structures. We used C-phycocyanin (C-PC) as an example, and focused on the interactions between the two domains. The normal mode analysis was carried out for the following two cases: 1) the whole subunit, including the two domains; and 2) the globin-like domain alone. By comparing the dynamic properties, such as correlative movements between residues and the fluctuations of individual residues, we found that the X-Y helices domain plays an important role not only in the C(3) symmetry assemblies of the subunits in phycobiliproteins, but also in stabilizing the light absorption property by suppressing the fluctuation of the specific Asp residues near the chromophore. Interestingly, the conformation of the X-Y helices domain corresponds to that of a module in pyruvate phosphate dikinase (PPDK). The module in PPDK is involved in the interactions of two domains, just as the X-Y helices domain is involved in the interactions of two subunits. Finally, we discuss the mechanical construction of the C-PC subunits based on the normal mode analysis.
藻胆蛋白是藻胆体的基本组成部分，藻胆体是一种超分子组装体，用于蓝细菌和红藻光合作用的光捕获功能。藻胆蛋白的一种功能形式是三聚体形式，由具有C(3)对称性的三个相同单元组成，每个单元由两种亚基组成，即α亚基和β亚基。这些亚基具有相似的链折叠结构，可分为类球蛋白结构域或X-Y螺旋结构域。我们使用正常模式分析来研究其三维结构的动态方面，以探讨这种双结构域结构对其组装结构和生物学功能（光吸收）的意义。我们以C-藻蓝蛋白（C-PC）为例，重点研究了两个结构域之间的相互作用。对以下两种情况进行了正常模式分析：1）包括两个结构域的整个亚基；2）单独的类球蛋白结构域。通过比较动态特性，如残基之间的相关运动和单个残基的波动，我们发现X-Y螺旋结构域不仅在藻胆蛋白亚基的C(3)对称组装中起重要作用，而且通过抑制发色团附近特定天冬氨酸残基的波动来稳定光吸收特性。有趣的是，X-Y螺旋结构域的构象与磷酸丙酮酸二激酶（PPDK）中的一个模块的构象相对应。PPDK中的这个模块参与两个结构域的相互作用，就像X-Y螺旋结构域参与两个亚基的相互作用一样。最后，我们基于正常模式分析讨论了C-PC亚基的机械结构。
