Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain.
J Phys Chem B. 2011 Nov 24;115(46):13771-80. doi: 10.1021/jp208562b. Epub 2011 Oct 31.
Protoglobin is the first globin found in Archaea. Its biological role is still unknown, although this protein can bind O(2), CO, and NO reversibly in vitro. The X-ray structure of Methanosarcina acetivorans protoglobin (MaPgb) has shown that access of ligands to the heme, which is completely buried within the protein matrix, can be granted by two apolar tunnels, which are mainly defined by helices G and B (tunnel 1), and helices B and E (tunnel 2). Here we analyze the structural and dynamical behavior of MaPgb through molecular dynamics and computational techniques aimed at shedding light on distinctive features of ligand migration through the tunnels that may be linked to functionality. While tunnel 2 is found to be accessible to diatomic ligands in both deoxygenated and oxygenated forms of the protein, the accessibility of tunnel 1 is controlled through the synergistic effect of both the protein dimeric state and the presence of the heme-bound ligand. Thus, dimerization mainly affects the spatial arrangement of helix G, which influences the shape of tunnel 1. Ligand accessibility through this tunnel is regulated by Phe(145)G8, which can adopt open and closed conformations. Noteworthy, the ratio between open and closed states is modulated by protein dimerization and more strikingly by ligand binding. In particular, sensing of the ligand is mediated by Phe(93)E11, and the steric hindrance between Phe(93)E11 and the heme-bound ligand alters the structural and dynamical behavior of helices B and E, which facilitates opening of tunnel 1. This functional mechanism provides a basis to understand the finding that ligation favors fast rebinding from ligand binding kinetic to MaPgb. Finally, it also suggests that MaPgb might be physiologically involved in a ligand-controlled bimolecular chemical process.
原球蛋白是古菌中发现的第一种球蛋白。其生物学功能尚不清楚，但该蛋白在体外可以可逆地结合 O(2)、CO 和 NO。甲烷八叠球菌原球蛋白（MaPgb）的 X 射线结构表明，配体进入完全埋藏在蛋白质基质中的血红素可以通过两个非极性隧道实现，这两个隧道主要由 G 螺旋和 B 螺旋（隧道 1）以及 B 螺旋和 E 螺旋（隧道 2）定义。在这里，我们通过分子动力学和计算技术分析 MaPgb 的结构和动力学行为，旨在阐明配体通过隧道迁移的独特特征，这些特征可能与功能有关。虽然在蛋白的脱氧和氧合形式下，隧道 2 都可以容纳双原子配体，但隧道 1 的可及性是通过蛋白二聚体状态和血红素结合配体的协同作用来控制的。因此，二聚化主要影响 G 螺旋的空间排列，从而影响隧道 1 的形状。通过这个隧道的配体可及性受到 Phe(145)G8 的调节，它可以采用开放和关闭构象。值得注意的是，开放和关闭状态的比例受蛋白二聚化的调节，更受配体结合的调节。特别是，配体的感应由 Phe(93)E11 介导，Phe(93)E11 和血红素结合配体之间的空间位阻改变了 B 螺旋和 E 螺旋的结构和动力学行为，从而促进了隧道 1 的打开。这种功能机制为理解配体结合有利于 MaPgb 从配体结合动力学快速重新结合的发现提供了基础。最后，它还表明 MaPgb 可能参与了受配体控制的双分子化学反应。
