Mechanism of tertiary structural change in hemoglobin.

Abstract

A reaction path is presented by which the effects of oxygen binding in hemoglobin are transmitted from a heme group to the surface of its subunit. Starting from the known deoxy geometry, it is shown by calculations with emirical energy functions and comparisons with available data Iow the change in heme geometry on ligation introduces a perturbation that leads to the tertiary structural alterations essential for cooperativity. It is found that there is little strain on the unliganded heme; instead, the reduced oxygen affinity of hemoglobin results from the strain on the liganded subunit in a tetramer with the deoxy quaternary structure. The cooperative nature of the binding of oxygen by hemoglobin is one of the most intensively studied phenomena in protein chemistry (1). From the classic x-ray work of Perutz and his collaborators (2, 3), supplemented by the physical and chemical studies of others (4, 5), the outlines of the cooperative mechanism have been determined. The essential elements are two quaternary structures (oxy and deoxy) for the hemoglobin tetramer (6), two tertiary structures (liganded and unliganded) for each subunit, and the presence of ionic, van der Waals, and hydrophobic interactions that couple the tertiary structural change of the subunits to the relative stabilities of the quaternary structures. These elements have been incorporated into a statistical mechanical model that describes ligand binding as a-function of solution conditions and accounts for the effects of mutations and chemical modifications (7,8).To complete the description of the cooperative mechanism, the statistical-mechanical model must be supplemented by an understanding of the origin of the important structural changes and their associated energies. It is necessary to know at the atomic level how ligand binding alters the tertiary structure of an individual subunit and how these alterations in subunit geometry affect and can be affected by the quaternary structure of the hemoglobin tetramer. In this paper, we focus on the first of these two problems. From calculations based on empirical energy functions (9) and comparisons with the available data, we are able to determine the properties of the heme group and of the surrounding globin chain that lead to the essential tertiary structural changes. A localized reaction path that involves directly only a relatively small number of globin atoms is found to transmit information concerning ligand binding from the heme group to the surface of the subunit. It is shown that there is little strain on the heme in unliganded hemoglobin, but that the flattening of the heme and shortening of the iron-histidine bond induced by oxygen binding produce steric repulsions between the heme and the globin that alter the subunit geometry. Nonbonded contacts between the asymmetrically positioned His F8(87) and the heme appear to initiate a rotation of the latter. This in turn produces a large displacement of Val FG5(93), which is the key residue in transmitting structural changes to the al...

Evolution of allosteric models for hemoglobin

“…From fitting an improved set of experimental data on the pH dependence of oxygen binding, and allowing the salt bridges to have unequal strength, Karplus and coworkers found that K 5 K R , from which they concluded that there are additional constraints on ligand binding to T in addition to the salt bridges, which is presumably the strain in the allosteric core postulated by Gelin et al (22,53,54).…”

“…We associate the r and t conformations with the different conformations of the allosteric core described by Karplus and coworkers (53,54). Again, for clarity and simplicity, we only consider subunit conformations of the T quaternary structure at alkaline pH where all ionizable salt bridges are broken.…”

“…First, X-ray crystallography of the mutant hemoglobin Kansas showed that the salt bridges do not break in the crystal upon CO binding to the T quaternary structure, in sharp contrast to the prediction of the Perutz mechanism. Second, Karplus and coworkers revisited the Perutz stereochemical mechanism using energy minimization to map out a reaction path from the hemes to the subunit interfaces upon oxygen binding (53,54). From the latter they concluded that the low affinity of subunits in the T quaternary structure is not due to the tension at heme, as proposed by Perutz, but to the strain induced in what they called the 'allosteric core' upon oxygen binding, particularly the steric repulsion between the proximal histidine and the pyrrole nitrogens of the porphyrin ring associated with motion of the iron into the heme plane.…”

In Crystals of Complexes of Streptavidin with Peptide Ligands Containing the HPQ Sequence the pK of the Peptide Histidine Is Less than 3.0

“…Structural Basis for the Large Perturbation of the pK a of the Peptide Histidine-The experimentally determined pK a values of certain noncatalytic residues in naturally occurring proteins are shifted by as much as 2.5 units (46). Larger shifts in the pK a values often occur in functionally important residues, such as those at active sites where buried charged residues often participate in catalysis (47)(48)(49)(50)(51). For example, the pK a of active site Asp 26 in reduced thioredoxin is elevated by more than 5 units (52).…”

SPINACH ON THE CEILING: A Theoretical Chemist's Return to Biology

“…Gelin showed how the effect of undoming of the heme induced by the binding of oxygen was transmitted to the interface between the hemoglobin subunits. The analysis provided an essential element in the cooperative mechanism in its demonstration at an atomic level of detail how communication between the subunits occurred (35). Another application of pre-CHARMM was Dave Case's simulation of ligand escape after photodissociation from myoglobin (16); a study that was followed by the work of Ron Elber (25), which gave rise to the locally enhanced sampling (LES) and multiple copy simultaneous search (MCSS) methods.…”