Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

Jochen S Hub, Marcus B Kubitzki and Bert L de Groot

PLOS Computational Biology, 2010, vol. 6, issue 5, 1-11

Abstract: We present molecular dynamics simulations of unliganded human hemoglobin (Hb) A under physiological conditions, starting from the R, R2, and T state. The simulations were carried out with protonated and deprotonated HC3 histidines His(β)146, and they sum up to a total length of 5.6µs. We observe spontaneous and reproducible T→R quaternary transitions of the Hb tetramer and tertiary transitions of the α and β subunits, as detected from principal component projections, from an RMSD measure, and from rigid body rotation analysis. The simulations reveal a marked asymmetry between the α and β subunits. Using the mutual information as correlation measure, we find that the β subunits are substantially more strongly linked to the quaternary transition than the α subunits. In addition, the tertiary populations of the α and β subunits differ substantially, with the β subunits showing a tendency towards R, and the α subunits showing a tendency towards T. Based on the simulation results, we present a transition pathway for coupled quaternary and tertiary transitions between the R and T conformations of Hb.Author Summary: As the prototypic allosteric protein, human hemoglobin (Hb) has drawn extensive scientific efforts for many decades. Human Hb exists in two quaternary conformations, the low-affinity (or deoxy) T state, and the high-affinity (or oxy) R state, and the transition between the T and the R state is mainly characterized by a 15° rotation of the α1β1 dimer with respect to the α1β2 dimer. Subsequent binding of molecular oxygen to the four heme groups drives the Hb tetramer from the deoxy T to the oxy R state, rendering the T→R transitions the molecular process that underlies the well-known cooperativity of ligand binding. Despite the wealth of structural information available for Hb, the mechanistic coupling between the quaternary transition and the tertiary transitions in the individual subunits remains poorly understood. We report spontaneous and reproducible T-R transitions of Hb in molecular dynamics simulations, allowing us to study the mechanism underlying the transitions in atomistic detail. We pay special attention to the interplay between the tertiary and quaternary transitions of Hb, as well as to the tertiary t/r populations of the subunits in a particular (T or R) quaternary state. Interestingly, we observe a pronounced asymmetry between the α and β subunits with the β subunits being more strongly linked to the quaternary transitions than the α subunits. The simulations allow us to propose a pathway for coupled quaternary and tertiary transitions between the R and T conformations of Hb.

Date: 2010
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1000774

DOI: 10.1371/journal.pcbi.1000774

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