Oxygen Entry through Multiple Pathways in T‑State Human Hemoglobin

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.