The Nitrite Anion Binds to Human Hemoglobin via the Uncommon <i>O</i>-Nitrito Mode

The nitrite anion is known to oxidize and degrade hemoglobin (Hb). Recent literature reports suggest a nitrite reductase activity for Hb, converting nitrite into nitric oxide. Surprisingly, no structural information about Hb−nitrite interactions has been reported. We have determined the crystal structure of the ferric Hb−nitrite complex at 1.80 Å resolution. The nitrite ligand adopts the uncommon O-nitrito binding mode. In addition, the nitrito conformations in the α and β subunits are different, reflecting subtle effects of the distal His in orienting the nitrite ligand in the O-nitrito binding mode

DataSheet1_3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins.zip

The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms. Importantly, the constellation of interactions between residue sidechains and their environments can be recorded as three-dimensional maps that, in turn, can be clustered. The clustered average map sets compose a library of interaction profiles encoding interaction strengths, interaction types and the optimal 3D position for the interacting partners. This library is backbone angle-dependent and suggests solvent and lipid accessibility for each unique interaction profile. In this work, in addition to analysis of soluble proteins, a large set of membrane proteins that contained optimized artificial lipids were evaluated by parsing the structures into three distinct components: soluble extramembrane domain, lipid facing transmembrane domain, core transmembrane domain. The aliphatic residues were extracted from each of these sets and passed through our calculation protocol. Notable observations include: the roles of aliphatic residues in soluble proteins and in the membrane protein’s soluble domains are nearly identical, although the latter are slightly more solvent accessible; by comparing maps calculated with sidechain-lipid interactions to maps ignoring those interactions, the potential extent of residue-lipid and residue-interactions can be assessed and likely exploited in structure prediction and modeling; amongst these residue types, the levels of lipid engagement show isoleucine as the most engaged, while the other residues are largely interacting with neighboring helical residues.</p

DataSheet_1_Pyridoxamine Supplementation Effectively Reverses the Abnormal Phenotypes of Zebrafish Larvae With PNPO Deficiency.pdf

Neonatal epileptic encephalopathy (NEE), as a result of pyridoxine 5′-phosphate oxidase (PNPO) deficiency, is a rare neural disorder characterized by intractable seizures and usually leads to early infant death. The clinical phenotypes do not respond to antiepileptic drugs but are alleviated in most cases by giving large doses of pyridoxal 5′-phosphate (PLP). PLP is the active form of vitamin B6 participating in more than 100 enzymatic pathways. One of the causes of NEE is pathogenic mutations in the gene for human PNPO (hPNPO). PNPO is a key enzyme in converting pyridoxine (PN), the common dietary form of vitamin B6, and some other B6 vitamers to PLP. More than 25 different mutations in hPNPO, which result in reduced catalytic activity, have been described for PNPO-deficiency NEE. To date, no animal model is available to test new therapeutic strategies. In this report, we describe using zebrafish with reduced activity of Pnpo as an animal model. Knocking down zPnpo resulted in developmental anomalies including brain malformation and impaired locomotor activity, similar to the clinical features of PNPO-deficiency NEE. Other anomalies include a defective circulation system. These anomalies were significantly alleviated by co-injecting either zpnpo or hPNPO mRNAs. As expected from clinical observations in humans, supplementing with PLP improved the morphological and behavioral anomalies. PN only showed marginal positive effects, and only in a few anomalies. Remarkably, pyridoxamine (PM), another dietary form of vitamin B6, showed rescue effects even at a lower concentration than PLP, presenting a possible new therapeutic treatment for PNPO-deficiency NEE. Finally, GABA, a neurotransmitter whose biosynthesis depends on a PLP-dependent enzyme, showed some positive rescue effect. These results suggest zebrafish to be a promising PNPO-deficiency model for studying PLP homeostasis and drug therapy in vivo.</p

Comparison of 4PUS with other truncated N^1-165 domain M1 structures (in ribbon diagrams).

<p>Unless noted otherwise, monomers A and B are colored grey and orange, respectively. <b>A</b>. Superposition of monomers A of 4PUS (grey), 1AA7 (yellow), and 1EA3 (red). <b>B</b>. Dimeric structure of 1AA7 showing face-to-face interaction between the two monomers. <b>C</b>. Relative positions of the non-superposed monomers B of 4PUS (grey), 1AA7 (yellow) and 3MD2 (red) after superposition of the corresponding monomers A. For clarity, only parts of the non-superposed monomers B are shown. <b>D</b>. Two monomers of 1EA3 interacting in a face-to-back fashion with the positively charged residues facing the negatively charged residues. For clarity not all positive or negative residues at the monomer faces are shown.</p

Models of the Cytochromes. Axial Ligand Orientation and Complex Stability in Iron(II) Porphyrinates: The Case of the Noninteracting d_π Orbitals

The synthesis and characterization of seven bis-pyridine and bis-imidazole complexes of iron(II) tetramesitylporphyrinate are reported. X-ray crystal structures of three of the complexes, [Fe(TMP)(4-CNPy)2], [Fe(TMP)(3-CNPy)2], and [Fe(TMP)(4-MePy)2], have been solved and all show parallel axial ligand orientations with nearly planar porphyrinato cores. The Mössbauer spectra of six of the complexes, having pyridine ligands with pKa(PyH+) ranging from ∼1.1 (4-CNPy) to 9.7 (4-NMe2Py), have been determined. The Mössbauer isomer shifts at 120 K are in the range of 0.36−0.45 mm/s, and the quadrupole splittings (ΔEQ) are in the range of 1.11−1.27 mm/s. Thus, unlike the corresponding Fe(III) complexes, the X-ray structures and Mössbauer spectroscopic parameters of these (tetramesitylporphyrinato)iron(II)−bis(pyridine) complexes are shown to be essentially independent of the basicity and π donor/acceptor properties of the axial pyridine ligands. These solid-state structural and spectroscopic properties are compared to the thermodynamic properties of the same series of complexes in solution (Nesset, M. J. M.; Shokhirev, N. V.; Enemark, P. D.; Jacobson, S. E.; Walker, F. A. Inorg. Chem. 1996, 35, 5188):  The equilibrium constants, β2II, for binding two ligands to [FeII(TMP)(DMF)] are also nearly independent of the basicity of the axial pyridine ligand, although the FeIII/FeII reduction potentials vary strongly with ligand basicity due to the large variation in β2III, the equilibrium constant for binding two ligands to the Fe(III) complex. Hence, it appears that low-spin d6 metalloporphyrins have a marked preference for parallel orientation of planar axial ligands, and that the charge asymmetry at the iron nucleus (deduced from Mössbauer quadrupole splittings) and the thermodynamics of ligand binding are unaffected by the electronic properties of the axial ligand. The major reason for the marked preference for parallel ligand orientation for iron(II) porphyrinates appears to be lack of a means of energy stabilization of the ruffled core of the perpendicular orientation

Data collection and refinement statistics of Safo-4PUS-pH4.7.

a<p>R_mege = Σ_hklΣ_i/I_hkli–hkli>/Σ_hklΣ_ihkli>.</p>b<p>R_free was calculated with 5% excluded reflection from the refinement.</p><p>Data collection and refinement statistics of Safo-4PUS-pH4.7.</p

<i>Psiadia punctulata</i> major flavonoids alleviate exaggerated vasoconstriction produced by advanced glycation end products - Fig 5

Effect of different concentrations of PPT, bioactive fraction (Fr. I), and isolated compounds 1–4 on the formation of fluorescent dityrosine (A) and N`-formylkynurenine (NFK), (B) when BSA is incubated with MG for one hour. AG was used as standard anti AGEs drug. Results are expressed as mean ± SEM (n = 3). # p < 0.05 when compared to control group, * p < 0.05 when compared to MG group; by Two Way ANOVA and Bonferroni post hoc test.</p

Structure of truncated N^1-165 domain of M1 (PDB code 4PUS) at pH 4.7.

<p>A. Monomer A of 4PUS. The N-terminal and C-terminal domains are shown in grey ribbons. Shown in yellow sticks are the basic NLS motif residues (Arg101, Lys102, Lys104, Arg105), Lys95 and Lys98 located on the right face of the molecules; the negatively charged residues Glu8, Glu23, Glu29, Asp30, Asp38, and Glu44 located on the left face of the molecule; and representative hydrophobic core residues on H1 and H4 buried between the N-terminal and C-terminal domains. For clarity not all residues of interest are shown. The nine helices are labelled <b>B</b>. Dimeric structure showing the positively charged residues including the NLS (yellow sticks) on the surface of the molecule. Monomers A and B are colored in grey and orange, respectively. Note the disorder in the N-terminal domain of monomer B. <b>C</b>. Same as figure B, but rotated by ∼90°. <b>D and E</b>. Final refined 2Fo-Fc electron density maps (contoured at 0.9α) of analogous regions (residues 45–50) of monomers A and B, respectively. The region in monomer B is clearly disordered.</p

Schematic representation of the proposed multiple conformational transitions in M1 structures.

<p><b>A</b>. Cartoon diagrams illustrating the oligomeric state of the M1 crystal structures, including 4PUS (grey), 1AA7 (blue), 3MD2 (red), 1EA3 (magenta) and 2Z16 (yellowish-green). Structures at neutral pH (top) are monomeric and arranged face-to-back; those at acidic pH (bottom) are dimeric and arranged face-to-face. Disorder in the Safo (4PUS) structure is indicated by a light-colored region bounded by a dashed line. <b>B</b>. Cartoon illustrating the interfacial regions of 4PUS (grey), 1AA7 (blue), 3MD2 (red), 1EA3 (magenta) and 2Z16 (yellowish-green). Individual M1 chains (consisting of two four-helix bundles separated by a linker) are represented as rectangles. Each crystal structure is represented by an ‘A’ chain (leftmost rectangle; grey border) and a ‘B’ chain (rightmost rectangle). The acidic (red) and basic (blue) residues at the interfacial regions are labeled and may be grouped into five clusters (K21; E8, E29 and D30; R76, R77 and R78; D89, D94, K95, K98, R101 and K104; R134) based on their proximity to one another on the M1 surface. Salt bridges are represented by yellow rectangles joining opposite charges. Note that the salt-bridge interactions depicted in Liu (3MD2) are>3.7 Å. Green transparent boxes within the rectangles represent the relative amount of shared interfacial surface area (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109510#pone-0109510-t002" target="_blank">Table 2</a>).</p

Design, Synthesis, and Biological Evaluation of Allosteric Effectors That Enhance CO Release from Carboxyhemoglobin

Carbon monoxide (CO) poisoning causes between 5,000−6,000 deaths per year in the US alone. The development of small molecule allosteric effectors of CO binding to hemoglobin (Hb) represents an important step toward making effective therapies for CO poisoning. To that end, we have found that the synthetic peptide IRL 2500 enhances CO release from COHb in air, but with concomitant hemolytic activity. We describe herein the design, synthesis, and biological evaluation of analogs of IRL 2500 that enhance the release of CO from COHb without hemolysis. These novel structures show improved aqueous solubility and reduced hemolytic activity and could lead the way to the development of small molecule therapeutics for the treatment of CO poisoning