Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins

Recent crystallographic studies have revealed the structures of some invertebrate extracellular giant hemoglobins of 3,600 kDa or 400 kDa and their common quaternary structure of dodecameric subassembly composed of four kinds of globin subunits (A1, A2, B1, and B2). These results have provided insight into the mechanisms of their unique functional properties of oxygen binding and sulfide binding. All of these structures were solved with oxygenated or CO-liganded forms at low or moderate resolutions. We have determined the crystal structure of 400 kDa Hb from a polychaete Oligobrachia mashikoi at 1.95 A resolution. The electron densities at higher resolution confirm the existence of an isoform of the B1 subunit because of the inconsistency with the model that was built from the formerly known amino acid sequence. The brownish color of the crystals used in this study and the absorption spectrum from the dissolved crystals strongly indicated that the obtained structure was a ferric met state, whereas complete absence of electron density around the distal heme pockets were observed at the A2, B1, and B2 subunits. We concluded that the obtained structure was in unliganded met forms at three of four globin subunits in the 24mer assembly and in oxygenated forms at the remaining A1 subunits. The partially unliganded structure showed remarkable structural changes at the AB loop regions causing quaternary rearrangements of the EF-dimer structure. In contrast, few changes occurred at the interface regions composed of the E and F helices. These results suggest that the ligand-induced structural changes of Oligobrachia Hb are quite different from those of the well-studied mollusk Hb having the same EF-dimer structure. The structural rearrangements make the dodecameric subassembly form a tighter conformation than those of fully oxygenated or CO-liganded dodecamer structure.     

6-Halogenopyridin-2-olato complexes with the diruthenium(2+) core: Equilibria between head-to-head and head-to-tail structures

The dinuclear bis(6-X-pyridin-2-olato) ruthenium complexes [Ru₂(μ-XpyO)₂(CO)₄(PPh₃)₂] (X = Cl (4B) and Br (5B)), [Ru₂(μ-XpyO)₂(CO)₄(CH₃CN)₂] (X = Cl (6B), Br (7B) and F (8B)) and [Ru₂(μ-ClpyO)₂(CO)₄(PhCN)₂] (9B) were prepared from the corresponding tetranuclear coordination dimers [Ru₂(μ-XpyO)₂(CO)₄]₂ (1: X = Cl; 2: X = Br) and [Ru₂(μ-FpyO)₂(CO)₆]₂ (3) by treatment with an excess of triphenylphosphane, acetonitrile and benzonitrile, respectively. In the solid state, complexes 4B-9B all have a head-to-tail arrangement of the two pyridonate ligands, as evidenced by X-ray crystal structure analyses of 4B, 6B and 9B, in contrast to the head-to-head arrangement in the precursors 1-3. A temperature- and solvent-dependent equilibrium between the yellow head-to-tail complexes and the red head-to-head complexes 4A-7A and 9A, bearing an axial ligand only at the O,O-substituted ruthenium atom, exists in solution and was studied by NMR spectroscopy. Full ¹H and ¹³C NMR assignments were made in each case. Treatment of 1 and 2 with the N-heterocyclic carbene (NHC) 1-butyl-3-methylimidazolin-2-ylidene provided the complexes [Ru₂(μ-XpyO)₂(CO)₄(NHC)], X = Cl (11A) or Br (12A). An XRD analysis revealed the head-to-head arrangement of the pyridonate ligands and axial coordination of the carbene ligand at the O,O-substituted ruthenium atom. The conversion of 11A and 12A into the corresponding head-to-tail complexes was not possible.     

A thermodynamic and crystallographic study of complexes of the highly preorganized ligand 8-hydroxyquinoline-2-carboxylic acid

The metal ion complexing properties of the ligand HQC (8-hydroxyquinoline-2-carboxylic acid) are reported. The structures of [Zn(HQCH)₂] · 3H₂O (1) and [Cd(HQCH)₂] · 3H₂O (2) were determined (HQCH = HQC with phenol protonated). Both 1 and 2 are triclinic, space group , with Z = 2. For 1 a = 7.152(3), b = 9.227(4), c = 15.629(7) Å,  = 103.978(7)°, β = 94.896(7)°, γ = 108.033(8)°, R = 0.0499. For 2 a = 7.0897(5), b = 9.1674(7), c = 16.0672(11) Å,  = 105.0240(10)°, β = 93.9910(10)°, γ = 107.1270(10)°, R = 0.0330. In 1 the Zn has a distorted octahedral coordination geometry, with Zn–N of 2.00 and 2.15 Å, and Zn–O to the protonated phenolic oxygens of 2.431 and 2.220 Å. The structure of 2 is similar, with Cd–N bonds of 2.220 and 2.228 Å, with Cd–O bonds to the protonated phenolate oxygens of 2.334 and 2.463 Å. The structures of 1 and 2, and isomorphous Ni(II) and Co(II) HQC complexes reported in the literature, show very interesting short (<2.5 Å) O–O distances in H-bonds involving the protons on the coordinated phenolates and lattice water molecules. These are discussed in relation to the possible role of short low-energy H-bonds in alcohol dehydrogenase in mediating the transfer of the hydroxyl proton of the alcohol to an adjacent serine oxygen.

The formation constants for HQC are determined by UV–Visible spectroscopy at 25 °C in 0.1 M NaClO₄ with Mg(II), Ca(II), Sr(II), Ba(II), La(III), Gd(III), Zn(II), Cd(II), Ni(II), Cu(II), and Pb(II). These show greatest stabilization with metal ions with an ionic radius above 1.0 Å. This is as would be expected from the fact that HQC forms two five-membered chelate rings on complex-formation, which favors larger metal ions. The ligand design concept of using rigid aromatic backbones in ligands to achieve high levels of preorganization, and hence the high log K values (for a tridentate ligand) and strong metal ion selectivities observed for HQC, is discussed.     

Multinuclear magnetic resonance study of Pt(II) compounds with sulfoxide ligands and crystal structures of complexes of the types [Pt(R2SO)X3] and Pt(R2SO)2Cl2

Pt(II) complexes of the types K[Pt(R₂SO)X₃], NR₄[Pt(R₂SO)X₃] and Pt(R₂SO)₂Cl₂ (where X = Cl or Br) were characterized by multinuclear magnetic resonance spectroscopy (¹⁹⁵Pt, ¹H and ¹³C). In ¹⁹⁵Pt NMR, the chloro ionic compounds have shown signals between −2979 and −3106 ppm, while the cis disubstituted complexes were observed at higher fields, between −3450 and −3546 ppm. The signal of the compound trans-Pt(DPrSO)₂Cl₂ was found at higher field (−3666 ppm) than its cis analogue (−3517 ppm), since π-back-donation is considerably less effective in the trans geometry. In ¹H NMR, a single signal was observed for the sulfoxide in [Pt(DMSO)Cl₃]⁻, but for the other more sterically hindered ligands, two series of resonances were observed for the protons in α and β positions. The coupling constant ³J(¹⁹⁵Pt-¹H) are between 15 and 33 Hz. The ¹³C NMR results were interpreted in relation to the concept of inversed polarization of the π sulfoxide bond. The ²J(¹⁹⁵Pt-¹³C) values vary between 35 and 66 Hz, while a few ³J(¹⁹⁵Pt-¹³C) couplings were observed (13-26 Hz). The crystal structures of five monosubstituted ionic compounds N(n-Bu)₄[Pt(TMSO)Cl₃], N(Me)₄[Pt(DPrSO)Cl₃], K[Pt(EMSO)Cl₃], K[Pt(TMSO)Br₃] · H₂O and N(Et)₄[Pt(DPrSO)Br₃] and one disubstituted complex cis-Pt(DBuSO)₂Cl₂ were determined. The trans influence of the different ligands is discussed.     

Comparison of Structurally-Related Alkoxide, Amine, and Thiolate-Ligated M (M= Fe, Co) Complexes: the Influence of Thiolates on the Properties of Biologically Relevant Metal Complexes

Mechanistic pathways of metalloenzymes are controlled by the metal ion’s electronic and magnetic properties, which are tuned by the coordinated ligands. The functional advantage gained by incorporating cysteinates into the active site of non-heme iron enzymes such as superoxide reductase (SOR) is not entirely understood. Herein, we compare the structural and redox properties of a series of structurally-related thiolate, alkoxide, and amine-ligated Fe(II) complexes in order to determine how the thiolate influences properties critical to function. Thiolates are shown to reduce metal ion Lewis acidity relative to alkoxides and amines, and have a strong trans influence thereby helping to maintain an open coordination site. Comparison of the redox potentials of the structurally analogous compounds described herein shows that alkoxide ligands favor the higher-valent Fe³⁺ oxidation state, amine ligands favor the reduced Fe²⁺ oxidation state, and thiolates fall somewhere in between. These properties provide a functional advantage for substrate reducing enzymes in that they provide a site at the metal ion for substrate to bind, and a moderate potential that facilitates both substrate reduction and regeneration of the catalytically active reduced state. Redox potentials for structurally-related Co(II) complexes are shown to be cathodically-shifted relative to their Fe(II) analogues, making them ineffective reducing agents for substrates such as superoxide.