Collective Dynamics Underlying Allosteric Transitions in Hemoglobin

Hemoglobin is the prototypic allosteric protein. Still, its molecular allosteric mechanism is not fully understood. To elucidate the mechanism of cooperativity on an atomistic level, we developed a novel computational technique to analyse the coupling of tertiary and quaternary motions. From Molecular Dynamics simulations showing spontaneous quaternary transitions, we separated the transition trajectories into two orthogonal sets of motions: one consisting of intra-chain motions only (referred to as tertiary-only) and one consisting of global inter-chain motions only (referred to as quaternary-only). The two underlying subspaces are orthogonal by construction and their direct sum is the space of full motions. Using Functional Mode Analysis, we were able to identify a collective coordinate within the tertiary-only subspace that is correlated to the most dominant motion within the quaternary-only motions, hence providing direct insight into the allosteric coupling mechanism between tertiary and quaternary conformation changes. This coupling-motion is substantially different from tertiary structure changes between the crystallographic structures of the T- and R-state. We found that hemoglobin's allosteric mechanism of communication between subunits is equally based on hydrogen bonds and steric interactions. In addition, we were able to affect the T-to-R transition rates by choosing different histidine protonation states, thereby providing a possible atomistic explanation for the Bohr effect.Author Summary: Hemoglobin transports oxygen from our lungs to other tissues. Its effectiveness in binding and unbinding of oxygen is based on a type of regulation called allostery. Thereby, already bound oxygen molecules in either of the four binding sites of hemoglobin increase the likelihood of oxygen binding in the other sites; the sites act cooperatively. It is known that the four protein chains of hemoglobin – each containing one oxygen binding site – need to rearrange globally or the cooperativity is lost. But how do the individual chains communicate with each other in this rearrangement? This is still not resolved on the molecular level. By applying the computational technique of molecular dynamics simulations we were able to simulate the motions of the individual atoms of hemoglobin during such a global rearrangement. We present a novel method that allows to directly analyse the coupling of motions within and between the four protein chains and thereby reveal the allosteric mechanism. That allows us to classify which amino acids are important for the cooperativity and in what way: by either pushing other amino acids away or attracting them. Also, we have observed in simulations how pH differences could affect the cooperativity.