Multiscale simulation reveals multiple pathways for H2 and O2 transport in a [NiFe]-hydrogenase.
Multiscale simulation reveals multiple pathways for H2 and O2 transport in a [NiFe]-hydrogenase.
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多尺度模拟揭示了 [NiFe]-氢化酶中 H2 和 O2 运输的多种途径。
DOI：
10.1021/ja109712q
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发表时间：
2011
影响因子：
15
通讯作者：
J. Blumberger
中科院分区：
文献类型：
--
作者：
Po;R. Best;J. Blumberger
氢化酶是催化氢分子可逆转化为质子和电子的酶。气体分子到达活性位点的机制对于理解酶的功能是重要的，并且可能在对氢的选择性超过抑制剂分子中起作用。在这里，我们开发了一个通用的多尺度分子模拟方法，用于计算扩散速率和确定底物或抑制剂气体可以到达蛋白质活性位点的途径。结合动力学数据从平衡模拟和增强采样，我们构建了一个主方程描述的气体分子内的酶的运动。我们发现，随时间变化的活性位点的气体人口可以适合相同的现象学速率定律用于解释实验，与相应的扩散速率与实验数据非常吻合。然而，与气体遵循明确定义的疏水隧道的传统图片相反，我们发现存在多种可达路径网络，气体分子可以通过这些路径到达活性位点。先前确定的隧道仅占总流量的60%左右。我们的研究结果表明，涉及残基Val 74的突变扩散速率的急剧下降可能部分是由于紧邻结合位点的通道Val 74-Arg 476变窄，这解释了为什么Leu 122的突变在实验中仅具有可忽略的影响。我们的方法是不是特定的[NiFe]-氢化酶，并应普遍适用于蛋白质中的小分子的运输。
Hydrogenases are enzymes that catalyze the reversible conversion of hydrogen molecules to protons and electrons. The mechanism by which the gas molecules reach the active site is important for understanding the function of the enzyme and may play a role in the selectivity for hydrogen over inhibitor molecules. Here, we develop a general multiscale molecular simulation approach for the calculation of diffusion rates and determination of pathways by which substrate or inhibitor gases can reach the protein active site. Combining kinetic data from both equilibrium simulations and enhanced sampling, we construct a master equation describing the movement of gas molecules within the enzyme. We find that the time-dependent gas population of the active site can be fit to the same phenomenological rate law used to interpret experiments, with corresponding diffusion rates in very good agreement with experimental data. However, in contrast to the conventional picture, in which the gases follow a well-defined hydrophobic tunnel, we find that there is a diverse network of accessible pathways by which the gas molecules can reach the active site. The previously identified tunnel accounts for only about 60% of the total flux. Our results suggest that the dramatic decrease in the diffusion rate for mutations involving the residue Val74 could be in part due to the narrowing of the passage Val74-Arg476, immediately adjacent to the binding site, explaining why mutations of Leu122 had only a negligible effect in experiment. Our method is not specific to the [NiFe]-hydrogenase and should be generally applicable to the transport of small molecules in proteins.