Crystal structures of unligated and CN‐ligated <i>Glycera dibranchiata</i> monomer ferric hemoglobin components III and IV

Park, HaJeung; Yang, Cheng; Treff, Nathan R.; Satterlee, James D.; Kang, ChulHee

doi:10.1002/prot.10199

Cited by 10 publications

(8 citation statements)

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“…The distal pocket of GMH3 is essentially devoid of amino acids whose side chains provide H-bonding groups, so the appearance of this signal likely indicates that the heme pocket incorporates a water molecule in this state and that this provides a stabilizing H-bond. Neither ferro-GMH3 nor cyanoferri-GMH3 contain heme-pocket water molecules, and the 1 H ENDOR data for the “daughter” [FeO 2 ] sup 7 show that the dioxygen moiety of the “parent” [FeO 2 ] 6 oxy-ferro-GMH3 does not experience a stabilizing H-bond. Thus, it would appear that a water molecule enters the heme pocket during annealing.…”

Section: Resultsmentioning

confidence: 99%

“…Five percent of the population was subjected to random taxonomic classification to confirm the species homogeneity of the specimen sample. The three monomer hemoglobin components (II, III, and IV) were isolated in the Fe(III) forms, using a combination of size exclusion chromatography and ion exchange chromatography, as previously described. , Component III monomer hemoglobin was concentrated in 0.1 M potassium phosphate buffer, pH 6.8, using Amicon pressure ultrafiltration cells, and then frozen in bulk and stored at −80 °C.…”

Section: Methodsmentioning

confidence: 99%

“…In all of these superoxo centers, the unpaired-spin density resides primarily (or exclusively) in a π* orbital on the dioxygen moiety; as a result, the g tensor is characterized by the principal values, g 1 ≫ g 2 ≳ g 3 ≈ g e . Indeed, Symons suggested, without corroboration from 17 O hyperfine couplings or 1 H/ 14 N ENDOR data, that such a species may be formed upon cryoreduction of monomeric oxy-Hb (oxy-GMH3) from Glycera dibranchiata , which differs from mammalian Hb and Mb in having a leucine in place of the distal histidine. , …”

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A Superoxo-Ferrous State in a Reduced Oxy-Ferrous Hemoprotein and Model Compounds

et al. 2003

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Cryoreduction of the [FeO2]6 (n = 6 is the number of electrons in 3d orbitals on Fe and pi* orbitals on O2) dioxygen-bound ferroheme through irradiation at 77 K generates an [FeO2]7 reduced oxy-heme. Numerous investigations have examined [FeO2]7 centers that have been characterized as peroxo-ferric centers, denoted [FeO2]per7, in which a ferriheme binds a dianionic peroxo-ligand. The generation of such an intermediate can be understood heuristically if the [FeO2]6 parent is viewed as a superoxo-ferric center and the injected electron localizes on the O-O moiety. We here report EPR/ENDOR experiments which show quite different properties for the [FeO2]7 centers produced by cryoreduction of monomeric oxy-hemoglobin (oxy-GMH3) from Glycera dibranchiata, which is unlike mammalian "globins" in having a leucine in place of the distal histidine; of frozen aprotic solutions of oxy-ferrous octaethyl porphyrin; and of the oxy-ferrous complex of the heme model, cyclidene. These [FeO2]7 centers are characterized as "superoxo-ferrous" centers ([FeO2]sup7), with nearly unit spin density localized on a superoxo moiety which is end-on coordinated to a low-spin ferrous ion. This assignment is based on their g tensors and 17O hyperfine couplings, which are characteristic of the superoxide ion coordinated to a diamagnetic metal ion, and on the absence of detectable ENDOR signals either from the in-plane 14N ligands or from an exchangeable H-bond proton. Such a center would arise if the electron that adds to the [FeO2]6 superoxo-ferric parent localizes on the Fe ion, to make a superoxo-ferrous moiety. Upon annealing to T > 150 K, the [FeO2]sup7 species converts to peroxo/hydroperoxo-ferric ([FeO2H]7) intermediates. These experiments suggest that the primary reduction product is [FeO2]sup7 and that the internal redox transition to [FeO2]per7/[FeO2H]7 states is driven at least in part by H-bonding/proton donation by the environment.

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Section: Resultsmentioning

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Section: Methodsmentioning

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A Superoxo-Ferrous State in a Reduced Oxy-Ferrous Hemoprotein and Model Compounds

et al. 2003

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“…The complete absence of amino acids having a polar or hydrogen-bonding acceptor/donor side chain contributes to the strong hydrophobicity of the distal heme pocket, which is an adverse factor for HCN ionization. In the case of G. dibranchiata hemoglobin, the absence of the histidine at the distal position was also proposed to explain the anomalous cyanide binding [58] because the replacement of histidine (E7) by hydrophobic residues considerably slowed the binding on-rate. This proposal does not hold for Ngb since the E7 position is occupied by the conserved His64 and an alternative mechanism must be invoked.…”

Section: Discussionmentioning

confidence: 99%

Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin

et al. 2012

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Neuroglobin (Ngb) is a globin present in the brain and retina of mammals. This hexacoordinated hemoprotein binds small diatomic molecules, albeit with lower affinity compared with other globins. Another distinctive feature of most mammalian Ngb is their ability to form an internal disulfide bridge that increases ligand affinity. As often seen for prosthetic heme b containing proteins, human Ngb exhibits heme heterogeneity with two alternative heme orientations within the heme pocket. To date, no details are available on the impact of heme orientation on the binding properties of human Ngb and its interplay with the cysteine oxidation state. In this work, we used 1H NMR spectroscopy to probe the cyanide binding properties of different Ngb species in solution, including wild-type Ngb and the single (C120S) and triple (C46G/C55S/C120S) mutants. We demonstrate that in the disulfide-containing wild-type protein cyanide ligation is fivefold faster for one of the two heme orientations (the A isomer) compared with the other isomer, which is attributed to the lower stability of the distal His64–iron bond and reduced steric hindrance at the bottom of the cavity for heme sliding in the A conformer. We also attribute the slower cyanide reactivity in the absence of a disulfide bridge to the tighter histidine–iron bond. More generally, enhanced internal mobility in the CD loop bearing the disulfide bridge hinders access of the ligand to heme iron by stabilizing the histidine–iron bond. The functional impact of heme disorder and cysteine oxidation state on the properties of the Ngb ligand is discussed.

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“…The different stability of heme-Fe(III)-cyanide complexes is primarily determined by the rate of ligand dissociation (the values of the first-order dissociation rate constant range between 1 × 10 -2 and 1 × 10 -6 s -1 ). On the other hand, values of the second-order rate constant for cyanide binding to ferric Mbs and Hbs (i.e., k on ) usually range between 1 × 10 2 and 1 × 10 3 M -1 s -1 ( − ).…”

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Cyanide Binding to Truncated Hemoglobins: A Crystallographic and Kinetic Study^,

et al. 2004

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Cyanide is one of the few diatomic ligands able to interact with the ferric and ferrous heme-Fe atom. Here, the X-ray crystal structure of the cyanide derivative of ferric Mycobacterium tuberculosis truncated hemoglobin-N (M. tuberculosis trHbN) has been determined at 2.0 A (R-general = 17.8% and R-free = 23.5%), and analyzed in parallel with those of M. tuberculosis truncated hemoglobin-O (M. tuberculosis trHbO), Chlamydomonas eugametos truncated hemoglobin (C. eugametos trHb), and sperm whale myoglobin, generally taken as a molecular model. Cyanide binding to M. tuberculosis trHbN is stabilized directly by residue TyrB10(33), which may assist the deprotonation of the incoming ligand and the protonation of the outcoming cyanide. In M. tuberculosis trHbO and in C. eugametos trHb the ligand is stabilized by the distal pocket residues TyrCD1(36) and TrpG8(88), and by the TyrB10(20) - GlnE7(41) - GlnE11(45) triad, respectively. Moreover, kinetics for cyanide binding to ferric M. tuberculosis trHbN and trHbO and C. eugametos trHb, for ligand dissociation from the ferrous trHbs, and for the reduction of the heme-Fe(III)-cyanide complex have been determined, at pH 7.0 and 20.0 degrees C. Despite the different heme distal site structures and ligand interactions, values of the rate constant for cyanide binding to ferric (non)vertebrate heme proteins are similar, being influenced mainly by the presence in the heme pocket of proton acceptor group(s), whose function is to assist the deprotonation of the incoming ligand (i.e., HCN). On the other hand, values of the rate constant for the reduction of the heme-Fe(III)-cyanide (non)vertebrate globins span over several orders of magnitude, reflecting the different ability of the heme proteins considered to give productive complex(es) with dithionite or its reducing species SO(2)(-). Furthermore, values of the rate constant for ligand dissociation from heme-Fe(II)-cyanide (non)vertebrate heme proteins are very different, reflecting the different nature and geometry of the heme distal residue(s) hydrogen-bonded to the heme-bound cyanide.

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Crystal structures of unligated and CN‐ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV

Cited by 10 publications

References 55 publications

A Superoxo-Ferrous State in a Reduced Oxy-Ferrous Hemoprotein and Model Compounds

A Superoxo-Ferrous State in a Reduced Oxy-Ferrous Hemoprotein and Model Compounds

Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin

Cyanide Binding to Truncated Hemoglobins: A Crystallographic and Kinetic Study^,

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Crystal structures of unligated and CN‐ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV

Cited by 10 publications

References 55 publications

A Superoxo-Ferrous State in a Reduced Oxy-Ferrous Hemoprotein and Model Compounds

A Superoxo-Ferrous State in a Reduced Oxy-Ferrous Hemoprotein and Model Compounds

Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin

Cyanide Binding to Truncated Hemoglobins: A Crystallographic and Kinetic Study,

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Cyanide Binding to Truncated Hemoglobins: A Crystallographic and Kinetic Study^,