Venture Business Laboratory, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
J Phys Chem B. 2013 May 23;117(20):6082-91. doi: 10.1021/jp401459b. Epub 2013 May 9.
The heme oxygen (O2) binding site of human hemoglobin (HbA) is buried in the interior of the protein, and there is a debate over the O2 entry pathways from solvent to the binding site. As a first step to understand HbA O2 binding process at the atomic level, we detected all significant multiple O2 entry pathways from solvent to the binding site in the α and β subunits of the T-state tetramer HbA by utilizing ensemble molecular dynamics (MD) simulation. By executing 128 independent 8 ns MD trajectories in O2-rich aqueous solvent, we simulated the O2 entry processes and obtained 141 and 425 O2 entry events in the α and β subunits of HbA, respectively. We developed the intrinsic pathway identification by clustering method to achieve a persuasive visualization of the multiple entry pathways including both the shapes and relative importance of each pathway. The rate constants of O2 entry estimated from the MD simulations correspond to the experimentally observed values, suggesting that O2 ligands enter the binding site through multiple pathways. The obtained multiple pathway map can be utilized for future detailed analysis of HbA O2 binding process.
人血红蛋白 (HbA) 的血红素 (O2) 结合位点埋藏在蛋白质内部，关于 O2 从溶剂进入结合位点的途径存在争议。为了在原子水平上理解 HbA O2 结合过程，我们通过使用集合分子动力学 (MD) 模拟，检测了 T 态四聚体 HbA 的α和β亚基中所有重要的 O2 进入结合位点的多条途径。通过在富含 O2 的水溶液中执行 128 个独立的 8 ns MD 轨迹，我们模拟了 O2 进入过程，并在 HbA 的α和β亚基中分别获得了 141 和 425 个 O2 进入事件。我们开发了通过聚类方法识别固有途径的方法，实现了对多条进入途径的有力可视化，包括每条途径的形状和相对重要性。从 MD 模拟中估计的 O2 进入速率常数与实验观察到的值相对应，表明 O2 配体通过多条途径进入结合位点。获得的多途径图谱可用于未来对 HbA O2 结合过程的详细分析。
