A theoretical study on the reaction pathways of peroxynitrite formation and decay at nonheme iron centers

A computational study based on density functional theory was undertaken to identify possible reaction pathways for the formation and decomposition of peroxynitrite at models of the active sites of the nonheme superoxide scavenging enzymes superoxide reductase (SOR) and iron superoxide dismutase (FeSOD). Two peroxynitrite isomers and their possible protonated states were investigated, namely Fe? OONO^?, Fe? N(O)OO^?, Fe? OONOH, and Fe? N(O)OOH. Peroxynitrite formation at the active sites was assumed by either the interaction of a peroxynitrite cis/trans anion with the pentacoordinated iron active site or the interaction between a nitric oxide bound adduct and superoxide; both scenarios were found to be facile for all models investigated. The ferrous adducts of the Fe? OONO^?isomer were found to undergo instant heterolytic cleavage of the O? ONO bond to yield nitrite, whereas for the ferric adducts, the homolytic cleavage of the O? ONO bond to yield nitrogen dioxide was found to be energetically facile. For the Fe? N(O)OO^? isomer, the active site models of FeSOD and SOR were only able to accommodate the cis isomer of peroxynitrite. Ferric adducts of the cis Fe? OONO^? isomer were found to be energetically more stable than their trans counterparts and were also more stable than the cis adducts of the Fe? N(O)OO^? isomer; conversely, the protonated forms of all adducts of the Fe? OONOH isomer were found to be lower in energy than their equivalent Fe? N(O)OOH adducts. Multiple reaction pathways for the decomposition of the formed peroxynitrite adducts (whether the anions or the protonated forms) were proposed and explored. The energy requirements for the decomposition processes ranged from exothermic to highly demanding depending on the peroxynitrite isomer, the type of model (whether an SOR or FeSOD active site), and the oxidation state of iron. © 2014 Wiley Periodicals, Inc.     

Synthesis and structural characterization of an anti-inflammatory principle purified from Lindera aggregata

Linderaggrine A (1) was characterized from the roots of Lindera aggregata and its chemical structure was established by the spectral analysis and chemical transformation. The chemical preparation of 1 and its isomer 2 provide unambiguous evidences for the structural determination of the naturally isolated compound. In addition, the inhibition of superoxide anion generation and elastase release by human neutrophils in response to FMLP/cytochalasin B of these synthetic products had been examined and among the tested compounds, linderaggrine A (1) displayed significant potential against the superoxide anion generation.     

Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters

The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn‐superoxide dismutase (SOD) has been inferred from high‐resolution X‐ray crystallography. Long‐duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second‐generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn‐SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short‐duration MD simulations of 296 waters solvating Cu/Zn‐SOD. Six representative geometries are selected and energy‐minimized. Single‐point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest‐energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments (2.7–3.0 Debye), equal and larger than the one computed by SIBFA in ice‐like arrangements (2.7 D).     

Fabrication of Superoxide Dismutase (SOD) Imprinted Poly(ionic liquid)s via eATRP and its Application in Electrochemical Sensor

Superoxide dismutase (SOD) plays an important role in nearly all living cells. In this study, SOD imprinted poly(ionic liquid)s (SIPILs) were prepared on the surface of the bare Au electrode modified with nano‐palladium and nano‐gold (Au/nPd/nAu/SIPILs). SIPILs was synthesized with 1‐vinyl‐3‐propyl imidazole sulfonate ionic liquids as functional monomers via electrochemically mediated atom transfer radical polymerization (eATRP) catalyzed by SOD. The Au/nPd/nAu/SIPILs was examined by cyclic voltammetry (CV), scanning electron microscope (SEM), energy‐dispersive spectrometer (EDS) and X‐ray photoelectron spectroscopy (XPS). The Au/nPd/nAu/SIPILs was also used as an electrochemical sensor to determine SOD by differential pulse voltammetry (DPV). Under the optimal conditions, the detection range of SOD was from 1.0×10^?8 to 1.0×10² mg L^?1 with a limit of detection of 8.90×10^?9 mg L^?1 (S/N=3). Compared with other methods, the sensor based on SIPILs had the broader linear range and lower detection limit.     

Effect of hydrostatic pressure on the fluorescence of indole derivatives

Effects of hydrostatic pressure on the fluorescence emission of L-tryptophan, N-acetyl-L-trytophanamide and indole were investigated. An increase in pressure ranging from 1 bar to 2.4 kbar results in reversible red-shifts of the emission of the three fluorophores. The pressure-induced redshift amounts to about 170 cm^–1 at 2.4 kbar, and appears related to changes in Stokes shift of the fluorophores caused by pressure effects on the dielectric constant and/or refractive index of the medium. As the pressure range investigated here is the range commonly used in studies of protein subunit association and/or folding, these observations raise the need for caution in interpreting pressure-induced spectral shifts. The significance of these observations to pressure studies of proteins is illustrated by investigation of pressure effects on human Cu,Zn Superoxide dismutase (SOD) and azurin fromPseudomonas aeruginosa. A reversible 170 cm^–1 red-shift of the emission of SOD was observed upon pressurization to 2.4 kbar. This might be interpreted as pressure-induced conformational changes of the protein. However, further studies using SOD that had been fully unfolded by guanidine hydrochloride, and fluorescence anisotropy measurements indicated that the observed red-shift was likely due to a direct effect of pressure on the fluorescence of the single tryptophan residue of SOD. Similar pressure-induced red-shifts were also observed for the buried tryptophan residue of azurin or for azurin that had been previously denatured by guanidine hydrochloride. These observations further suggest that the effective dielectric constant of the protein matrix is affected by pressure similarly to water.     

Sonochemistry of cytochrome c. Evidence for superoxide formation by ultrasound in argon-saturated aqueous solution

Formation of superoxide anion radicals (O₂^·−) induced by 50 kHz ultrasound in argon (Ar)-saturated aqueous solution was studied. Although EPR-spin trapping study with 5,5-dimethyl-1-pyrroline N-oxide (DMPO;100 mM) revealed the formation of DMPO-adducts of hydroxyl radicals (^·OH) and hydroperoxy radicals (HO₂^·; acid form of O2^·−) in O₂-saturated solution after sonication, no evidence of HO₂^· was found in Ar-saturated solution. When ferricytochrome c (cytochrome c) in Ar-saturated aqueous solution was sonicated, the reduced form of cytochrome c was observed and 80% of its formation was inhibited by the addition of superoxide dismutase (SOD). Sodium formate enhanced the production of the reduced form of cytochrome c. The % inhibition by SOD for the reduction increased in the order of Xe > Ar > He in accord with the higher temperatures of the cavitation bubbles. These results indicate that the O₂^·− is formed by directly by the sonolysis of water in the absence of O₂ when the temperature of cavitation bubble collapse is sufficiently high.     

稳定直线型硝酮-O_2~(-·)加合物的构型因素解析

对生命体系中的氧自由基,Spin trapping-ESR方法是公认的特征分析手段[1].然而,对超氧阴离子自由基(O2-·)而言,其自由基加合物稳定性差.对此,人们通过改变硝酮的取代基团,设计出更为有效的O2-·捕获探针[2,3].另外,Zweier研究组[4,5]还应用密度泛函理论研究了影响五元环状硝酮     

无花果叶超氧化物歧化酶的分离、纯化及性质研究

以我国山东无花果树(Brunswike, 原产法国Ficus carica)树叶为原料, 采用缓冲液抽提、硫酸铵分级、DEAE-Sepharose Fast Flow阴离子交换层析和Sephacryl S-100 HR分子筛层析分离纯化得到电泳纯CuZn-SOD, 并对其酶学性质进行研究.     

巯基乙胺修饰电极法测定植物体内超氧阴离子自由基

盐酸羟胺与超氧阴离子自由基反应生成NO2-,通过检测NO2-的生成量,可间接测定超氧阴离子自由基。基于上述原理,建立了一种用巯基乙胺自组装修饰金电极测定生物体系中超氧阴离子自由基的新方法。实验结果表明,在pH4.8的HAc-NaAc缓冲溶液中,修饰电极对NO2-的氧化具有良好的电催化作用,差分脉冲溶出伏安法测定其氧化峰电流与NO2-的浓度在5.0×10-8~1.0×10-4mol/L范围内呈线性关系,其线性回归方程为ipa(μA)=3.726C(μmol/L) 0.0257,相关系数为0.9983;检出限为1.0×10-8mol/L。该法用于玉米幼苗和叶片中超氧阴离子自由基产生速率的测定,结果令人满意。     

New briaranes from the octocorals Briareum excavatum (Briareidae) and Junceella fragilis (Ellisellidae)

Six 12-hydroxybriaranes, including four new diterpenoids, briaexcavatins I-L (1-4), and two known metabolites, excavatolides C (5) and E (6), have been isolated from the cultured scleraxonia Briareum excavatum. In addition, the gorgonian coral Junceella fragilis yielded a new chlorinated briarane, fragilide C (10). The structures of above compounds were determined by spectroscopic methods and the structures of 5 and 6 were further confirmed by X-ray data analysis for the first time. The absolute configuration of 6 was elucidated by chemical conversion. Some of these briaranes have displayed inhibitory effects on superoxide anion generation by human neutrophils.