Journal of Physical Chemistry B, Vol.117, No.20, 6082-6091, 2013
Oxygen Entry through Multiple Pathways in T-State Human Hemoglobin
The heme oxygen (O-2) binding site of human hemoglobin (HbA) is buried in the interior of the protein, and there is a debate over the O-2 entry pathways from solvent to the binding site. As a first step to understand HbA O-2 binding process at the atomic level, we detected all significant multiple O-2 entry pathways from solvent to the binding site in the alpha and beta subunits of the T-state tetramer HbA by utilizing ensemble molecular dynamics (MD) simulation. By executing 128 independent 8 ns MD trajectories in O-2-rich aqueous solvent, we simulated the O-2 entry processes and obtained 141 and 425 O-2 entry events in the alpha and beta 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 O-2 entry estimated from the MD simulations correspond to the experimentally observed values, suggesting that O-2 ligands enter the binding site through multiple pathways. The obtained multiple pathway map can be utilized for future detailed analysis of HbA O-2 binding process.