Reverse Engineering the Cooperative Machinery of Human Hemoglobin

Abstract

Hemoglobin transports molecular oxygen from the lungs to all human tissues for cellular respiration. Its α2β2 tetrameric assembly undergoes cooperative binding and releasing of oxygen for superior efficiency and responsiveness. Over past decades, hundreds of hemoglobin structures were determined under a wide range of conditions for investigation of molecular mechanism of cooperativity. Based on a joint analysis of hemoglobin structures in the Protein Data Bank (Ren, companion article), here I present a reverse engineering approach to elucidate how two subunits within each dimer reciprocate identical motions that achieves intradimer cooperativity, how ligand-induced structural signals from two subunits are integrated to drive quaternary rotation, and how the structural environment at the oxygen binding sites alter their binding affinity. This mechanical model reveals the intricate design that achieves the cooperative mechanism and has previously been masked by inconsistent structural fluctuations. A number of competing theories on hemoglobin cooperativity and broader protein allostery are reconciled and unified.

Reaction Trajectory Revealed by a Joint Analysis of Protein Data Bank

“…The main differences between t and r are localized at FGs and the C-termini of both subunits as seen from the second decomposed lower triangles ( Figure S7a, d ). These observations lead to the findings in the companion article that depicts the structural mechanism of intradimer cooperativity and quaternary rotation [ 5 ].…”

“…Figure 2 implies that each snapshot of Hb structure in PDB carries an order within a large collection, which is a source of dynamic information. The companion article takes advantages of this information implied by the order along a reaction trajectory to support the mechanism of Fe-Ni hybrid Hb and allosteric effectors [ 5 ].…”

“…Here the novel use of distance geometry presents a computational means to reveal plausible structures that may only transiently occur during allosteric transition. The more fundamental reason why these structures spanning the allosteric taboo gap have never been captured by crystallographic experiments is presented in the companion article [ 5 ], which is a direct outcome of the mechanism of quaternary transition crossing the wide taboo gap.…”

“…A flowchart ( Figure 1 ) summarizes key steps in the analytical loop developed here. The companion article [ 5 ] provides a brief introduction to the structure and function relationship of human hemoglobin (Hb), and describes a reverse engineering approach to a mechanical model that depicts the inner workings of a cooperative machinery based on evidences collected from this meta-analysis of hundreds Hb structures. See Materials and Methods (MM) for a description of the structural collection and a list of notations used in both articles.…”

Ultrafast Structural Changes Decomposed from Serial Crystallographic Data

“…S3) that are closely related to structural responses in the globin. Similar in-plane sliding is even more significant in tetrameric hemoglobins (Baldwin and Chothia, 1979), which is the origin of the cooperative oxygen affinity (Ren, 2013b). However, the functional role of the heme in-plane sliding in Mb is not yet clear and this discussion branches away from the topic here on ultrafast structural changes.…”