Haemoglobin: The structural changes related to ligand binding and its allosteric mechanism

Abstract

The structural changes that occur on ligand binding to haemoglobin have been studied by comparison of the atomic co-ordinates of human deoxy, horse met and human carbonmonoxy haemoglobin, using computer graphics and least-squares fitting methods. The changes that occur on going from deoxy to either of the liganded forms are very similar. These include tertiary structure changes within the α 1 β 1 dimer and a quaternary structure change in which the packing of α 1 β 1 against α 2 β 2 alters. On going from deoxy to liganded haemoglobin, no significant structural change occurs in the central regions of the α 1 β 1 dimer, including the α 1 β 1 interface and nearby helices B, C, G and H in both subunits. Movements occur in the outer parts of the dimer, where the haems, F helices and FG corners of both subunits move towards the centre of the molecule. The two haems and the two FG corners come ~2 Å closer together. One important effect of the changes in both subunits is to translate the F helix across the face of the haem by ~1 Å. This moves the haem-linked histidine F8 from a position that is asymmetric with respect to the porphyrin nitrogens in deoxy to a more symmetric position in liganded haemoglobin. The motion of the β haem removes the ligand-binding site from the vicinity of ValβE11, which hinders ligand binding in deoxy. The changes in tertiary structure are linked to the quaternary change through the motion of the FG corners. The C helices and FG corners of α 1 β 1 are in contact with the FG corners and C helices of α 2 β 2 in both quaternary structures. In the quaternary change the contacts between α 1FG and β 2C and between α 2FG and β 1C act as “flexible joints” allowing small relative motions. The same side-chains are involved in the contacts in both structures. The contacts between α 1C and β 2FG and between α 2C and β 1FG act as “switch” regions, having two different stable positions with different side-chains in contact. The change between the two positions involves a relative movement of ~6 Å. The quaternary structure change to liganded haemoglobin destroys the contacts made by the C-terminal residues of each subunit in deoxy haemoglobin, and these residues rotate freely in the liganded form. These structural results, together with other work, particularly the calculations of Gelin & Karplus and of Warshel, support a description of the haemoglobin mechanism in which (1) the binding of ligand to the deoxy form is accompanied by steric strain, originating from the particular position of the F helix and of His F8 relative to the haem. (2) The strain leads to decreased stability of the deoxy quaternary structure relative to the liganded quaternary structure, so that the proportion of molecules in the high-affinity form increases as successive ligands bind. (3) The quaternary structure change to the high-affinity form induces tertiary structure changes that reposition the F helix and HisF8 relative to the haem and there is then no strain on ligand binding. In the absence of ligand the deoxy structure is favoured by the greater surface area buried between α 1 β 1 and α 2 β 2 in this quaternary structure. Further implications of the structural results are discussed.