XAS Investigations on the Iron-Zinc Center of Purple Acid Phosphatase from Red Kidney Beans

Comprehensive characterization of ambient nanoparticles collected near an industrial science park: particle size distributions and relationships with environmental factors

We investigated the characteristics of ambient particles and their relationships with various environmental factors, including gaseous pollutants (CH4, non-methane hydrocarbons (NMHC), total hydrocarbons (THC), NOx, CO, SO2), meteorological parameters (humidity, temperature), and time (day/night, workday/weekend). We used an electrical low-pressure cascade impactor to measure the number and size distributions of ambient particles (0.007-10 tm) that were collected approximately 1 km northwest of Hsinchu Science Park in Taiwan between February and May 2007. The number concentrations of particles were enhanced through photochemical reactions during the day. In addition, high traffic flow during workdays increased the formation of particulates. Except for SO2, all of the gaseous pollutants we studied (CH4, NMHC, THC, NOx, CO) correlated positively with the total number concentrations of ambient particles during daytime, indicating that they might contribute to the particulate burden. The poorer relationship between the SO2 level and the total number concentration of particles suggests that SO2 might participate indirectly in the nucleation process during particle formation, The high enrichment factors for Zn, Pb, Cu, and Mn, which mostly comprised the ultrafine particles (diameter: < 0.1 microm) and fine particles (diameter: 0.1-1 microm), presumably arose from emissions from traffic and high technology factories. Heterogeneous reactions on solid particles might play a role in the removal of SOx and NOx from the atmosphere. Sulfides and nitrides can further react with these local pollutants, forming specific Cu-containing compounds: CuO (39%), CuSO4 (34%), and Cu(NO3)2 (27%), within the ambient particles in this industrial area.

Sulfur K-edge extended X-ray absorption fine structure spectroscopy of homoleptic thiolato complexes with Zn(II) and Cd(II)

The sulfur K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy is applied to homoleptic thiolato complexes with Zn(II) and Cd(II), (Et(4)N)[Zn(SAd)(3)] (1), (Et(4)N)(2)[{Zn(ScHex)(2)}(2)(mu-ScHex)(2)] (2), (Et(4)N)(2)[{Cd(ScHex)(2)}(2)(mu-ScHex)(2)] (3), (Et(4)N)(2)[{Cd(ScHex)}(4)(mu-ScHex)(6)] (4), [Zn(mu-SAd)(2)](n) (5), and [Cd(mu-SAd)(2)](n) (6) (HSAd=1-adamantanethiol, HScHex=cyclohexanethiol). The EXAFS results are consistent with the X-ray crystal data of 1-4. The structures of 5 and 6, which have not been determined by X-ray crystallography, are proposed to be polynuclear structures on the basis of the sulfur K-edge EXAFS, far-IR spectra, and elemental analysis. Clear evidences of the S...S interactions (between bridging atoms or neighboring sulfur atoms) and the S...C(far) interactions (in which C(far) atom is next to carbon atom directly bonded to sulfur atom) were observed in the EXAFS data for all complexes and thus lead to the reliable determination of the structures of 5 and 6 in combination with conventional zinc K-edge EXAFS analysis for 5. This new methodology, sulfur K-edge EXAFS, could be applied for the structural determination of in vivo metalloproteins as well as inorganic compounds.

Calcineurin: form and function

Calcineurin is a eukaryotic Ca(2+)- and calmodulin-dependent serine/threonine protein phosphatase. It is a heterodimeric protein consisting of a catalytic subunit calcineurin A, which contains an active site dinuclear metal center, and a tightly associated, myristoylated, Ca(2+)-binding subunit, calcineurin B. The primary sequence of both subunits and heterodimeric quaternary structure is highly conserved from yeast to mammals. As a serine/threonine protein phosphatase, calcineurin participates in a number of cellular processes and Ca(2+)-dependent signal transduction pathways. Calcineurin is potently inhibited by immunosuppressant drugs, cyclosporin A and FK506, in the presence of their respective cytoplasmic immunophilin proteins, cyclophilin and FK506-binding protein. Many studies have used these immunosuppressant drugs and/or modern genetic techniques to disrupt calcineurin in model organisms such as yeast, filamentous fungi, plants, vertebrates, and mammals to explore its biological function. Recent advances regarding calcineurin structure include the determination of its three-dimensional structure. In addition, biochemical and spectroscopic studies are beginning to unravel aspects of the mechanism of phosphate ester hydrolysis including the importance of the dinuclear metal ion cofactor and metal ion redox chemistry, studies which may lead to new calcineurin inhibitors. This review provides a comprehensive examination of the biological roles of calcineurin and reviews aspects related to its structure and catalytic mechanism.

Speciation of elements in NIST particulate matter SRMs 1648 and 1650

X-ray absorption fine structure (XAFS) spectra for S, Cl, V, Cr, Mn, Cu, Zn, As, Br, Cd and Pb and Mossbauer spectra for Fe have been obtained for two National Institute of Standards and Technology (NIST) particulate matter (PM) standard reference materials (SRMs): urban PM (SRM 1648) and diesel PM (SRM 1650). The spectral data, complemented by information on elemental concentrations from proton-induced X-ray-emission (PIXE) spectroscopy, were used to interpret the speciation of these elements in these complex materials. It appears that all the metallic elements investigated occur in oxidized forms, principally as sulfates in the diesel PM SRM and as sulfates, oxides, and possibly other forms (e.g. clays?) in the urban PM. A minor fraction of the sulfur and major fractions of the halogens, Cl and Br, occur as organosulfide (thiophene) and organohalide occurrences, respectively, that must be associated with the abundant carbonaceous matter that constitutes the major component of the two PM SRMs. Most of the sulfur, however, occurs as sulfate in the urban PM and as bisulfate in the diesel PM. In addition, elemental oxidation states have been determined directly by the spectroscopic techniques. Such information is often the key parameter in determining the toxicity and solubility of specific elements in PM, both of which are important in understanding the threat that such elements may pose to human health. For the two HAP elements, Cr and As, for which the toxicity depends greatly on oxidation state, the XAFS data showed that both elements are present in both SRMs predominantly in the less toxic oxidation states, Cr(III) and As(V). The potential of the XAFS spectra for use as source apportionment signatures is illustrated by reference to chromium, which exists in these two PM SRMs in very different forms.

Cloning and comparative protein modeling of two purple acid phosphatase isozymes from sweet potatoes (Ipomoea batatas)

The sequence of cDNA fragments of two isozymes of the purple acid phosphatase from sweet potato (spPAP1 and spPAP2) has been determined by 5' and 3' rapid amplification of cDNA ends protocols using oligonucleotide primers based on amino acid information. The encoded amino acid sequences of these two isozymes show an equidistance of 72-77% not only to each other, but also to the primary structure of the purple acid phosphatase from red kidney bean (kbPAP). A three-dimensional model of the active site has been constructed for spPAP2 on the basis of the kbPAP crystallographic structure that helps to explain the reported differences in the visible and EPR spectra of spPAP2 and kbPAP.

Biochemical and spectroscopic characterization of catechol oxidase from sweet potatoes (Ipomoea batatas) containing a type-3 dicopper center

Two catechol oxidases have been isolated from sweet potatoes (Ipomoea batatas) and purified to homogeneity. The two isozymes have been characterized by EXAFS, EPR-, UV/Vis-spectroscopy, isoelectric focusing, and MALDI-MS and have been shown to contain a dinuclear copper center. Both are monomers with a molecular mass of 39 kDa and 40 kDa, respectively. Substrate specificity and NH2-terminal sequences have been determined. EXAFS data for the 39 kDa enzyme reveal a coordination number of four for each Cu in the resting form and suggest a Cu(II)-Cu(II) distance of 2.9 A for the native met form and 3.8 A for the oxy form.

Structural and Functional Models for the Dinuclear Copper Active Site in Catechol Oxidases: Syntheses, X-ray Crystal Structures, Magnetic and Spectral Properties, and X-ray Absorption Spectroscopic Studies in Solid State and in Solution

Two novel tridentate dinucleating ligands containing benzimidazole were prepared, 1,3-bis(2-benzimidazolyl)-2-propanol (Hbbp, 1) and 1,5-bis(2-benzimidazolyl)-3-pentanol (Hbbpen, 2). Their complexing properties toward copper were studied in order to obtain structural and functional models for catechol oxidases. Syntheses and crystal structures of dinuclear Cu(II) complexes derived from these ligands are reported. [Cu(2)bbp(2)](ClO(4))(2).2MeOH, 3, crystallizes in the triclinic space group P&onemacr; with the following unit cell parameters: a = 7.702(3) Å, b = 10.973(6) Å, c = 12.396(6) Å, alpha = 100.59(4) degrees, beta = 99.02(4) degrees, gamma = 98.90(4) degrees, V = 998.7(8) Å(3), and Z = 1. [Cu(2)bbpen(2)](ClO(4))(2).3MeOH, 4, crystallizes in the orthorhombic space group Pccn, with the following unit cell parameters: a = 17.478(9) Å, b = 18.795(8) Å, c = 13.888(6) Å, V = 4562.2(4) Å(3), and Z = 4. Magnetic susceptibility measurements in the temperature ranges 4.6-459 K (3) and 4.6-425 K (4) indicate an antiferromagnetic coupling between the Cu(II) centers of both complexes. In order to determine the structures of the complexes in solution, XAS spectra (EXAFS and XANES) were recorded in the solid state and in solution. The interpretation of these data, including multiple scattering calculations, together with UV-vis titrations, shows that the complexes have the same structure in the crystalline state as well as in methanolic solution. Complex 4 is able to oxidize 3,5-di-tert-butylcatechol (3,5-DTBC) to the quinone (catecholase activity). This reaction was also studied by XAS and UV-vis spectroscopy. These measurements reveal the reduction of Cu(II) to Cu(I) accompanied by a decrease of the coordination number.

Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site

Kidney bean purple acid phosphatase (KBPAP) is an Fe(III)-Zn(II) metalloenzyme resembling the mammalian Fe(III)-Fe(II) purple acid phosphatases. The structure of the homodimeric 111-kilodalton KBPAP was determined at a resolution of 2.9 angstroms. The enzyme contains two domains in each subunit. The active site is located in the carboxyl-terminal domain at the carboxy end of two sandwiched beta alpha beta alpha beta motifs. The two metal ions are 3.1 angstroms apart and bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active-site structure is consistent with previous proposals regarding the mechanism of phosphate ester hydrolysis involving nucleophilic attack on the phosphate group by an Fe(III)-coordinated hydroxide ion.