Teixeira Vitor H, Baptista António M, Soares Cláudio M
Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa, Oeiras, Portugal.
Biophys J. 2006 Sep 15;91(6):2035-45. doi: 10.1529/biophysj.106.084376. Epub 2006 May 26.
Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H(2)), but little is known about the diffusion of H(2) toward the active site. Here we analyze pathways for H(2) permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H(2) easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H(2) molecules that reach the active site made their approach from the side of the Ni ion. H(2) is able to reach distances of <4 A from the active site, although after 6 A permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H(2) inside the protein and at lower distances from the active site. This valine can be a control point in the H(2) access to the active center.
氢化酶催化分子氢（H₂）的可逆氧化反应，但对于H₂向活性位点的扩散情况却知之甚少。在此，我们利用显式溶剂中的分子动力学（MD）模拟来分析H₂的渗透途径。进行了各种MD模拟重复实验，以改善对系统状态的采样。在每次模拟中，H₂都能轻易地渗透过氢化酶，并且它优先在通道中移动。所有到达活性位点的H₂分子都是从镍离子一侧靠近的。H₂能够到达距离活性位点小于4埃的位置，不过在6埃之后渗透就变得困难了。在这个区域，我们将缬氨酸-67突变为丙氨酸并进行新的MD模拟。这些模拟结果显示蛋白质内部以及距活性位点较近距离处的H₂有所增加。这种缬氨酸可能是H₂进入活性中心的一个控制点。
