Effects of mutations on the molecular dynamics of oxygen escape from the dimeric hemoglobin of Scapharca inaequivalvis

Abstract

Like many hemoglobins, the structure of the dimeric hemoglobin from the clam Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the structure would seem to make that pathway less likely. Locally enhanced sampling molecular dynamics are used here to suggest alternative pathways in the wild-type and six mutant proteins. In most cases the point mutations change the selection of exit routes observed in the simulations. Exit via the histidine gate is rarely seem although oxygen molecules do occasionally cross over the interface from one subunit to the other. The results suggest that changes in flexibility and, in some cases, creation of new cavities can explain the effects of the mutations on ligand exit paths.

Ligand and interfacial dynamics in a homodimeric hemoglobin

“… 51 These simulations investigated O 2 diffusion in WT and a number of HbI mutants and found the following ligand-escape routes: between the B and G helices (5 cases, also observed here), between the E and F helices (4), between the B and E helices (2), and between the C and G helices (1, also observed here). However, in these locally enhanced sampling simulations, the histidine gate was not found to be an important ligand escape route, 51 at variance with previous spectroscopic work. 21 Coupling: The present simulations support coupling of ligand- and protein-motion as suggested by recent NMR experiments.…”

“…The histidine gate, which was found to allow water entrance in the present work, has been proposed to be the major ligand exit route from the previous spectroscopic work 21 but was not found to be operative in simulations of O 2 diffusion in 14 different HbI variants and in the present work. 51 Concerning the time scale of ligand escape, the present study finds such a process on the 100 ns time scale which is about an order of magnitude longer than escape times from biased simulations such as locally enhanced sampling. 51 …”

“… 51 Concerning the time scale of ligand escape, the present study finds such a process on the 100 ns time scale which is about an order of magnitude longer than escape times from biased simulations such as locally enhanced sampling. 51 …”