Oxygen Entry through Multiple Pathways in T-State Human Hemoglobin

Chloride Ions Stabilize Human Adult Hemoglobin in the T-State, Competing with Allosteric Interaction of Oxygen Molecules

In the context of a molecular-level understanding of the allostery mechanisms, human adult hemoglobin (HbA) has been extensively studied for over half a century. Chloride ions (Cl^-) have been known as one of HbA allosteric effectors, which stabilizes the T-state preferable to release oxygen molecules. The functional mechanisms were individually proposed by Ueno and Perutz several decades ago. Ueno considered that the site-specific Cl^- binding is essential, while Perutz proposed the non-site-specific interaction between HbA and Cl^-. Each speculation explains the mechanism plausibly since each was tightly associated with its reasonable experimental observation. However, both mechanisms themselves still seem to make their speculations controversial. In the present study, we have theoretically reconsidered these apart from their approaches. Our atomistic molecular dynamics simulations then showed that the increase of Cl^- concentration suppresses the conformational conversion from the T-state. Interestingly, chloride ions loosely interact with the amino acid residues inside the HbA central cavity, suggesting that both Perutz's and Ueno's speculations are involved in understanding the microscopic roles of Cl^-. In conclusion, we theoretically certified that the effect of Cl^- competes against that of solvated O₂, i.e., the destabilization of T-state through the non-site-specific interaction, implying the concerted regulation of HbA under physiological conditions.

Structural Basis of Human KCNQ1 Modulation and Gating

KCNQ1, also known as Kv7.1, is a voltage-dependent K⁺ channel that regulates gastric acid secretion, salt and glucose homeostasis, and heart rhythm. Its functional properties are regulated in a tissue-specific manner through co-assembly with beta subunits KCNE1-5. In non-excitable cells, KCNQ1 forms a complex with KCNE3, which suppresses channel closure at negative membrane voltages that otherwise would close it. Pore opening is regulated by the signaling lipid PIP2. Using cryoelectron microscopy (cryo-EM), we show that KCNE3 tucks its single-membrane-spanning helix against KCNQ1, at a location that appears to lock the voltage sensor in its depolarized conformation. Without PIP2, the pore remains closed. Upon addition, PIP2 occupies a site on KCNQ1 within the inner membrane leaflet, which triggers a large conformational change that leads to dilation of the pore's gate. It is likely that this mechanism of PIP2 activation is conserved among Kv7 channels.

Thermodynamic Scaling of Interfering Hemoglobin Strain Field Waves

Hemoglobin (Hgb) forms tetramers (dimerized α-β dimers), which enhance its globular stability and may also facilitate small gas molecule transport, as shown by recent all-atom Newtonian solvated simulations. Hydropathic bioinformatic thermodynamic scaling enables close comparisons of hemoglobin dimers with myoglobin and neuroglobin, and reveals many nonlocal wave-like features of strained Hgb structures at the coarse-grained amino acid level. The thermodynamic analysis employs two hydropathic scales, one describing abrupt first-order unfolding transitions, the other continuous second-order transitions. Small molecule exchange at hemes is a first-order process. Wave-like collective tetrameric features appropriate to ligand absorption and release, seen in optical experiments (short times), are identified thermodynamically at long times. Strain fields localized near hemes interfere with extended strain fields associated with dimer interfacial misfit, resulting in novel wavelength dependent dimer correlation function Fano antiresonances.

O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7

Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the release of O2 to the solvent via a transient E7 channel. To reveal the O2 escape routes controlled by HisE7 and to evaluate its role in gating heme access, we compare simulations of O2 diffusion from the distal heme pockets of the T and R states of HbA performed with HisE7 in its open (protonated) and closed (neutral) conformations. Irrespective of HisE7's conformation, we observe the same four or five escape routes leading directly from the α- or β-distal heme pockets to the solvent. Only 21-53% of O2 escapes occur via these routes, with the remainder escaping through routes that encompass multiple internal cavities in HbA. The conformation of the distal HisE7 controls the escape of O2 from the heme by altering the distal pocket architecture in a pH-dependent manner, not by gating the E7 channel. Removal of the HisE7 side chain in the GlyE7 variant exposes the distal pockets to the solvent, and the percentage of O2 escapes to the solvent directly from the α- or β-distal pockets of the mutant increases to 70-88%. In contrast to O2, the dominant water route from the bulk solvent is gated by HisE7 because protonation and opening of this residue dramatically increase the rate of influx of water into the empty distal heme pockets. The occupancy of the distal heme site by a water molecule, which functions as an additional nonprotein barrier to binding of the ligand to the heme, is also controlled by HisE7. Overall, analysis of gas and water diffusion routes in the subunits of HbA and its GlyE7 variant sheds light on the contribution of distal HisE7 in controlling polar and nonpolar ligand movement between the solvent and the hemes.

Non-site-specific allosteric effect of oxygen on human hemoglobin under high oxygen partial pressure

Protein allostery is essential for vital activities. Allosteric regulation of human hemoglobin (HbA) with two quaternary states T and R has been a paradigm of allosteric structural regulation of proteins. It is widely accepted that oxygen molecules (O₂) act as a “site-specific” homotropic effector, or the successive O₂ binding to the heme brings about the quaternary regulation. However, here we show that the site-specific allosteric effect is not necessarily only a unique mechanism of O₂ allostery. Our simulation results revealed that the solution environment of high O₂ partial pressure enhances the quaternary change from T to R without binding to the heme, suggesting an additional “non-site-specific” allosteric effect of O₂. The latter effect should play a complementary role in the quaternary change by affecting the intersubunit contacts. This analysis must become a milestone in comprehensive understanding of the allosteric regulation of HbA from the molecular point of view.