A DFT study on the relative affinity for oxygen of the alpha and beta subunits of hemoglobin

Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study

There is no doubt that electric fields of a specific frequency and intensity could excite certain vibrational modes of a macromolecule, which alters its mode coupling and conformation. Motivated by recent experiments and theories, we study the mode coupling between the Fe-CO mode and CO-stretch mode and vibration energy transfer among the active site and proteins in carboxyhemoglobin (HbCO) under different electric fields using the quasi-static two-dimensional infrared spectra. This study uses iron-porphyrin-imidazole-CO and two distal histidines in HbCO as the subsystem. The potential energy and dipole moment surfaces of the subsystem are calculated using an all-electron ab initio (B3LYP-D3(BJ)) method with the basis set Lanl2dz for the Fe atom and 6-31G(d,p) for C, H, O, and N atoms. Although the subsystem is reduced dimensionally, the anharmonic frequency and anharmonicity of the CO-stretch mode show excellent agreement with experimental values. We use the revealing noncovalent interaction method to confirm the hydrogen bond between the H_ε atom of the His63 and the CO molecule. Our study confirms that the mode coupling between the Fe-CO mode and CO-stretch mode does not exist when the subsystem is free of electric field perturbation, which is coupled when the electric field is -0.5142 V/nm. In addition, with the increases of distance between the active site and the His92, there is no vibrational energy transfer between them when the electric field is 1.028 V/nm. We believe that our work could provide new ideas for increasing the dissociation efficiency of the Fe-CO bond and theoretical references for experimental research.

Dissimilar flexibility of α and β subunits of human adult hemoglobin influences the protein dynamics and its alteration induced by allosteric effectors

The general question by what mechanism an "effector" molecule and the hemes of hemoglobin interact over widely separated intramolecular distances to change the oxygen affinity has been extensively investigated, and still has remained of central interest. In the present work we were interested in clarifying the general role of the protein matrix and its dynamics in the regulation of human adult hemoglobin (HbA). We used a spectroscopy approach that yields the compressibility (κ) of the protein matrix around the hemes of the subunits in HbA and studied how the binding of heterotropic allosteric effectors modify this parameter. κ is directly related to the variance of volume fluctuation, therefore it characterizes the molecular dynamics of the protein structure. For the experiments the heme groups either in the α or in the β subunits of HbA were replaced by fluorescent Zn-protoporphyrinIX, and series of fluorescence line narrowed spectra were measured at varied pressures. The evaluation of the spectra yielded the compressibility that showed significant dynamic asymmetry between the subunits: κ of the α subunit was 0.17±0.05/GPa, while for the β subunit it was much higher, 0.36±0.07/GPa. The heterotropic effectors, chloride ions, inositol hexaphosphate and bezafibrate did not cause significant changes in κ of the α subunits, while in the β subunits the effectors lead to a significant reduction down to 0.15±0.04/GPa. We relate our results to structural data, to results of recent functional studies and to those of molecular dynamics simulations, and find good agreements. The observed asymmetry in the flexibility suggests a distinct role of the subunits in the regulation of Hb that results in the observed changes of the oxygen binding capability.

Ultrafast Dynamics of Carboxy-Hemoglobin: Two-Dimensional Infrared Spectroscopy Experiments and Simulations

This Letter presents a comparison between experimental and simulated 2D mid-infrared spectra of carboxy-hemoglobin in the spectral region of the carbon monoxide stretching mode. The simulations rely on a fluctuating potential energy surface that includes both the effect of heme and the protein surroundings computed from molecular dynamics simulations. A very good agreement between theory and experiment is obtained with no adjustable parameters. The simulations show that the effect of the distal histidine through the hydrogen bond is strong and is directly responsible for the slow decay of the frequency-frequency correlation function on a 10 ps time scale. This study confirms that fluctuations in carboxy-hemoglobin are more inhomogeneous than those in the more frequently studied carboxy-myoglobin. The comparison between simulations and experiments brings valuable information on the complex relation between protein structure and spectral diffusion.

Vibrational ladder climbing in carboxy-hemoglobin: effects of the protein environment

We present simulations on vibrational ladder climbing in carboxy-hemoglobin. Motivated by recent experiments, we study the influence of different realistic pump probe parameters. To allow for a direct comparison with experimental results, transient absorption spectra obtained by a weak probe pulse following the strong, shaped pump pulse are calculated. The influence of the protein fluctuations is taken into account using a recently developed microscopic model. This model consists of a quantum Hamiltonian describing the CO vibration in carboxy-hemoglobin, together with a fluctuating potential, which is obtained by electronic structure calculation based on a large number of protein configurations. Using realistic pulse parameters, vibrational excitations to very high-lying states are possible, in qualitative agreement with experimental observations.

A model for the flexibility of the distal histidine in dehaloperoxidase-hemoglobin A based on X-ray crystal structures of the carbon monoxide adduct

Dehaloperoxidase hemoglobin A (DHP A) is a multifunctional hemoglobin that appears to have evolved oxidative pathways for the degradation of xenobiotics as a protective function that complements the oxygen transport function. DHP A possesses at least two internal binding sites, one for substrates and one for inhibitors, which include various halogenated phenols and indoles. Herein, we report the X-ray crystallographic structure of the carbonmonoxy complex (DHPCO). Unlike other DHP structures with 6-coordinated heme, the conformation of the distal histidine (H55) in DHPCO is primarily external or solvent exposed, despite the fact that the heme Fe is 6-coordinated. As observed generally in globins, DHP exhibits two distal histidine conformations (one internal and one external). In previous structural studies, we have shown that the distribution of H55 conformations is weighted strongly toward the external position when the DHP heme Fe is 5-coordinated. The large population of the external conformation of the distal histidine observed in DHPCO crystals at pH 6.0 indicates that some structural factor in DHP must account for the difference from other globins, which exhibit a significant external conformation only when pH < 4.5. While the original hypothesis suggested that interaction with a heme-Fe-bound ligand was the determinant of H55 conformation, the current study forces a refinement of that hypothesis. The external or open conformation of H55 is observed to have interactions with two propionate groups in heme, at distances of 3.82 and 2.73 Å, respectively. A relatively weak hydrogen bonding interaction between H55 and CO, combined with strong interactions with heme propionate (position 6), is hypothesized to strengthen the external conformation of H55. Density function theory (DFT) calculations were conducted to test whether there is a weaker hydrogen bond interaction between H55 and heme bonded CO or O₂. Molecular dynamics simulations were conducted to examine how the tautomeric forms of H55 affect the dynamic motions of the distal histidine that govern the switching between open and closed conformations. The calculations support the modified hypothesis suggesting a competition between the strength of interactions with heme ligand and the heme propionates as the factors that determine the conformation of the distal histidine.

Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors

Hydroxyurea is the only FDA approved treatment of sickle cell disease. It is believed that the primary mechanism of action is associated with the pharmacological elevation of nitric oxide in the blood; however, the exact details of this are still unclear. In the current work, we investigate the atomic level details of this process using a combination of flexible-ligand/flexible-receptor virtual screening coupled with energetic analysis that decomposes interaction energies. Utilizing these methods, we were able to elucidate the previously unknown substrate binding modes of a series of hydroxyurea analogs to hemoglobin and the concomitant structural changes of the enzyme. We identify a backbone carbonyl that forms a hydrogen bond with bound substrates. Our results are consistent with kinetic and electron paramagnetic resonance (EPR) measurements of hydroxyurea-hemoglobin reactions, and a full mechanism is proposed that offers new insights into possibly improving substrate binding and/or reactivity.

Haemoglobin polymorphisms affect the oxygen-binding properties in Atlantic cod populations

A major challenge in evolutionary biology is to identify the genes underlying adaptation. The oxygen-transporting haemoglobins directly link external conditions with metabolic needs and therefore represent a unique system for studying environmental effects on molecular evolution. We have discovered two haemoglobin polymorphisms in Atlantic cod populations inhabiting varying temperature and oxygen regimes in the North Atlantic. Three-dimensional modelling of the tetrameric haemoglobin structure demonstrated that the two amino acid replacements Met55beta1Val and Lys62beta1Ala are located at crucial positions of the alpha1beta1 subunit interface and haem pocket, respectively. The replacements are proposed to affect the oxygen-binding properties by modifying the haemoglobin quaternary structure and electrostatic feature. Intriguingly, the same molecular mechanism for facilitating oxygen binding is found in avian species adapted to high altitudes, illustrating convergent evolution in water- and air-breathing vertebrates to reduction in environmental oxygen availability. Cod populations inhabiting the cold Arctic waters and the low-oxygen Baltic Sea seem well adapted to these conditions by possessing the high oxygen affinity Val55-Ala62 haplotype, while the temperature-insensitive Met55-Lys62 haplotype predominates in the southern populations. The distinct distributions of the functionally different haemoglobin variants indicate that the present biogeography of this ecologically and economically important species might be seriously affected by global warming.