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During the conference, I was pleased to have the opportunity to recognise Professor Larry Que for his outstanding service to the Society as I JBIC i Chief Editor. SBIC, its members, and the broader biological inorganic chemistry community owe Larry a huge debt of gratitude for his stewardship of the journal and his leadership through this time. Next year, we will celebrate a quarter of a century of our journal, I JBIC i , and for 20 of the 24 years to date, Larry has been our Chief Editor. [Extracted from the article]

Iron-sulfur clusters are evolutionarily conserved biological structures which play an important role as cofactor for multiple enzymes in eukaryotic cells. The biosynthesis pathways of the iron-sulfur clusters are located in the mitochondria and in the cytosol. The mitochondrial iron-sulfur cluster biosynthesis pathway (ISC) can be divided into at least twenty enzymatic steps. Since the description of frataxin deficiency as the cause of Friedreich’s ataxia, multiple other deficiencies in ISC biosynthesis pathway have been reported. In this paper, an overview is given of the clinical, biochemical and genetic aspects reported in humans affected by a defect in iron-sulfur cluster biosynthesis. [ABSTRACT FROM AUTHOR]

Information about the academic papers and research discussed at the 13th International Conference on Biological Inorganic Chemistry that was held July 15 through July 20, 2007 in Vienna, Austria is presented. A listing of organizational committees involved with the conference is also included. An overview of the conference is provided.

In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe-4S] cluster-containing homologue of the archetypal O sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O, and also NO, availability. Here we show that FnrP undergoes O-driven [4Fe-4S] to [2Fe-2S] cluster conversion that involves up to 2 O per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O concentrations. The rate of the cluster reaction was found to be ~sixfold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer-dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe-4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers. [ABSTRACT FROM AUTHOR]

The article presents abstracts on biochemistry topics including the development of visualization probes with tunable chemical switches for biological applications, in vitro and in vivo application of fluorescent zinc sensors and research on zinc, lysosomes and autophagy.

The article presents abstracts on biochemistry topics including the putative role of the maturases HydE and HydG and FeFe-hydrogenase active site synthesis and assembly, electrons from hydrogen and organometallic biomimetics of hydrogenase enzymes active sites.

The article presents abstracts on biochemistry topics including capillary electrophoresis of nanobiomaterial particles, control of the coordination structure of palladium complexes in an apo-Fr cage and hetero protein assemblies providing a bio-nanocup as a chemical reaction space.

The article presents abstracts on biochemistry topics including the low temperature photolysis study, multi-step electron tunneling in a transmembrane protein and a research on hydrogen bond network around the non-heme iron in photosystem II.

Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S–S-CoB. MCR harbors the nickel porphyrinoid coenzyme F430 as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCRred1 (red for reduced Ni) have been identified. Here, we report a detailed characterization of MCRred1m (“m” for methyl-coenzyme M), which is the complex of MCRred1a (“a” for absence of substrate) with CH3-S-CoM. Using continuous-wave and pulse electron paramagnetic resonance spectroscopy in combination with selective isotope labeling (13C and 2H) of CH3-S-CoM, it is shown that CH3-S-CoM binds in the active site of MCR such that its thioether sulfur is weakly coordinated to the Ni(I) of F430. The complex is stable until the addition of the second substrate, HS-CoB. Results from EPR spectroscopy, along with quantum mechanical calculations, are used to characterize the electronic and geometric structure of this complex, which can be regarded as the first intermediate in the catalytic mechanism. [ABSTRACT FROM AUTHOR]

Metalloenzymes control enzymatic activity by changing the characteristics of the metal centers where catalysis takes place. The conversion between inactive and active states can be tuned by altering the coordination number of the metal site, and in some cases by an associated conformational change. These processes will be illustrated using heme proteins (cytochrome c nitrite reductase, cytochrome c peroxidase and cytochrome cd 1 nitrite reductase), non-heme proteins (superoxide reductase and [NiFe]-hydrogenase), and copper proteins (nitrite and nitrous oxide reductases) as examples. These examples catalyze electron transfer reactions that include atom transfer, abstraction and insertion. [ABSTRACT FROM AUTHOR]

To better understand the biological significance of Ca2+, we report a comprehensive statistical analysis of calcium-binding proteins from the Protein Data Bank to identify structural parameters associated with EF-hand and non-EF-hand Ca2+-binding sites. Comparatively, non-EF-hand sites utilize lower coordination numbers (6 ± 2 vs. 7 ± 1), fewer protein ligands (4 ± 2 vs. 6 ± 1), and more water ligands (2 ± 2 vs. 1 ± 0) than EF-hand sites. The orders of ligand preference for non-EF-hand and EF-hand sites, respectively, were H2O (33.1%) > side-chain Asp (24.5%) > main-chain carbonyl (23.9%) > side-chain Glu (10.4%), and side-chain Asp (29.7%) > side-chain Glu (26.6%) > main-chain carbonyl (21.4%) > H2O (13.3%). Less formal negative charge was observed in the non-EF-hand than in the EF-hand binding sites (1 ± 1 vs. 3 ± 1). Additionally, over 20% of non-EF-hand sites had formal charge values of zero due to increased utilization of water and carbonyl oxygen ligands. Moreover, the EF-hand sites presented a narrower range of ligand distances and bond angles than non-EF-hand sites, possibly owing to the highly conserved helix–loop–helix motif. Significant differences between ligand types (carbonyl, side chain, bidentate) demonstrated that angles associated with each type must be classified separately, and the EF-hand side-chain Ca–O–C angles exhibited an unusual bimodal quality consistent with an Asp distribution that differed from the Gaussian model observed for non-EF-hand proteins. The results of this survey more accurately describe differences between EF-hand and non-EF-hand proteins and provide new parameters for the prediction and design of different classes of Ca2+-binding proteins. [ABSTRACT FROM AUTHOR]

Frataxin is an iron binding mitochondrial matrix protein that has been shown to mediate iron delivery during iron–sulfur cluster and heme biosynthesis. There is a high degree of structural homology for frataxin proteins from diverse sources, and all possess an anionic surface defined by acidic residues. In the human protein these residues principally lie on a surface defined by the α1 helix and β1 sheet and the impact of multiple substitutions of these carboxylate residues on iron binding is described. Full-length human frataxin has previously been shown to undergo self-cleavage to produce a truncated form both in vitro and in vivo. This truncated protein has been shown to bind approximately seven iron centers that are presumably associated with the acidic patch. Relative to this native protein, the stoichiometry decreases according to the number and sites of mutations. Nevertheless, the iron-dependent binding affinity of each frataxin derivative to the iron–sulfur cluster scaffold protein ISU is found to be similar to that of native frataxin, as defined by isothermal titration calorimetry experiments, requiring only one iron center to promote nanomolar binding. While frataxins from various cell types appear to bind differing numbers of iron centers, the physiologically relevant number of bound irons appears to be small, with significantly higher binding affinity following complex formation with partner proteins (micromolar compared with nanomolar binding). By contrast, in reconstitution assays for frataxin-promoted [2Fe–2S]2+ cluster assembly on ISU, one derivative does display a modestly lower reconstitution rate. The overall consensus from these data is to consider a pool of potential sites that can stably bind an iron center when bridged to a variety of physiological targets. [ABSTRACT FROM AUTHOR]

After environmental contamination, U accumulates in the kidneys and in bones, where it causes visible damage. Recent in vitro data prove that the occurrence of citrate increases U bioavailability without changing its speciation. Two hypotheses can explain the role of citrate: it either modifies the U intracellular metabolization pathway, or it acts on the transport of U through cell membrane. To understand which mechanisms lead to increased bioavailability, we studied the speciation of U after accumulation in NRK-52E kidney cells. U speciation was first identified in various exposure media, containing citrate or not, in which U was supplied as U carbonate. The influence of serum proteins was analyzed in order to detect the formation of macromolecular complexes of U. Transmission electron microscopy (TEM) was employed to follow the evolution of the U species distribution among precipitated and soluble forms. Finally, extended X-ray absorption fine structure spectroscopy (EXAFS) enabled the precipitates observed to be identified as U-phosphate. It also demonstrated that the intracellular soluble form of U is U carbonate. These results suggest that citrate does not change U metabolization but rather plays a role in the intracellular accumulation pathway. U speciation inside cells was directly and clearly identified for the first time. These results elucidate the role of U speciation in terms of its bioavailability and consequent health effects. [ABSTRACT FROM AUTHOR]

The interactions with protein targets of the ruthenium(III) complex imidazolium trans-[tetrachloro(dimethyl sulfoxide)(imidazole)ruthenate(III)], NAMI-A, an effective anticancer and antimetastatic agent now in clinical trials, deserve great attention as they are believed to be at the basis of the mechanism of action of this innovative molecule. Here, we report on the reactions of NAMI-A with two well-known model proteins, namely, hen egg white lysozyme and horse heart cytochrome c; these reactions were investigated by a variety of physicochemical methods, including optical spectroscopy, 1H NMR and electrospray ionization mass spectrometry. The combined use of the analytical techniques mentioned resulted in a rather exhaustive description of the NAMI-A–protein interactions; in particular, the formation of fairly stable metal–protein adducts was clearly documented and the nature of the resulting protein-bound metallic fragments ascertained in most cases. Notably, greatly different patterns of interaction were found to be operative for NAMI-A toward these two proteins. The biological implications of the present findings are discussed. [ABSTRACT FROM AUTHOR]

The article presents abstracts of biochemistry research, particularly pertaining to metal sensors in biology. They include "Mimicking nature's signal cascades for amplified detection of biomolecular targets," "Solid Phase Synthesis and Biological Application of Metal-PNA Bioconjugates," and "Organometallic Complexes as Sensors for Biologically Interesting Analytes."

The article presents abstracts of biochemistry research, particularly pertaining to electrontransfer and radicals. They include "The Mechanism of Oxidative Halophenol Dehalogenation by Heme-Containing Peroxidases," "Generation, Spectroscopy, and Reactivity of Highly Oxidized Diiron Species," and "Tryptophan radicals as catalytic intermediates in heme peroxidases."

The article presents abstracts of biochemistry research, particularly pertaining to metal-based environmental chemistry. They include "Vanadium detoxification: Chemical and biochemical aspects," "Characterizing alkane-oxidation mechanisms from a number of environmentally-important metalloenzymes," and "Inhibition effect of Tb(III) on horseradish peroxidase activity."

The article presents abstracts of biochemistry research, particularly pertaining to metalloproteins. They include "Electrocatalytic hydrogen cycling by hydrogenases in the presence of O2: Functional challenges for technology," "Towards the Mechanism of N2 Reduction by Nitrogenase," and "Copper Prion Interactions. Specificity from mammalians to Fishes."

The article presents abstracts of biochemistry research, particularly pertaining to bioinspired coordination chemistry. They include "Dioxygen Binding and Activation Chemistry at Mononuclear Copper Ion Centers," "Nitric Oxide and Hemes, From Toxic Gas to NRVS," and "Weak interactions and reactivities of amino acid side chain groups around the metal center."

The article presents abstracts of biochemistry research, particularly pertaining to metals in medicine. They include "The mitochondrial cell death pathway as a target for gold and other metal-based antitumour compounds," "Transplatinum Compounds as Anticancer Agents. A Real Possibility?," and "The Distribution and Biotransformation of Metal Based Anti-Cancer Agents in Cancer Cells and Tumour Models."

The article presents abstracts of biochemistry research, particularly pertaining to metal trafficking. They include "Copper homeostasis in insects by complex interplay of import, storage and behavioral avoidance," "Malleable proteins and hard metals: the case of nickel sensors and nickel-chaperones," and "Interaction of Vanadium and other transition metal compounds with lipid interfaces."

Frataxin is an iron-binding mitochondrial matrix protein that has been shown to mediate iron delivery during iron–sulfur cluster and heme biosynthesis. Mitochondrial processing peptidase (MPP) yields a form of human frataxin corresponding to residues 56–210. However, structural and functional studies have focused on a core structure that results from an ill-defined cleavage event at the N-terminus. Herein we show that the N-terminus of MPP-processed frataxin shows a unique high-affinity iron site and that this iron center appears to mediate a self-cleavage reaction. Moreover, the N-terminus appears to block previously defined iron-binding sites located on the carboxylate-rich surface defined by the helix (α1) and the β-sheet (β1), most likely through electrostatic contact with the carboxylate-rich surface on the core protein, as well as inhibiting iron-promoted binding of the iron–sulfur cluster assembly scaffold partner protein, ISU. The physiological significance of iron-mediated release of the N-terminal residues from this anionic surface is discussed. [ABSTRACT FROM AUTHOR]

The pH dependence of redox properties, spectroscopic features and CO binding kinetics for the chelated protohemin-6(7)- l-histidine methyl ester (heme-H) and the chelated protohemin-6(7)-glycyl- l-histidine methyl ester (heme-GH) systems has been investigated between pH 2.0 and 12.0. The two heme systems appear to be modulated by four protonating groups, tentatively identified as coordinated H2O, one of heme’s propionates, N ε of the coordinating imidazole, and the carboxylate of the histidine residue upon hydrolysis of the methyl ester group (in acid medium). The p K a values are different for the two hemes, thus reflecting structural differences. In particular, the different strain at the Fe–N ε bond, related to the different length of the coordinating arm, results in a dramatic alteration of the bond strength, which is much smaller in heme-H than in heme-GH. It leads to a variation in the variation of the p K a for the protonation of the N ε of the axial imidazole as well as in the proton-linked behavior of the other protonating groups, envisaging a cross-talk communication mechanism among different groups of the heme, which can be operative and relevant also in the presence of the protein matrix. [ABSTRACT FROM AUTHOR]

Infrared (IR) spectra in combination with chemical analyses have recently shown that the active Ni–Fe site of the soluble NAD+-reducing [NiFe]-hydrogenase from Ralstonia eutropha contains four cyanide groups and one carbon monoxide as ligands. Experiments presented here confirm this result, but show that a variable percentage of enzyme molecules loses one or two of the cyanide ligands from the active site during routine purification. For this reason the redox conditions during the purification have been optimized yielding hexameric enzyme preparations (HoxFUYHI2) with aerobic specific H2–NAD+ activities of 150–185 μmol/min/mg of protein (up to 200% of the highest activity previously reported in the literature). The preparations were highly homogeneous in terms of the active site composition and showed superior IR spectra. IR spectro-electrochemical studies were consistent with the hypothesis that only reoxidation of the reduced enzyme with dioxygen leads to the inactive state, where it is believed that a peroxide group is bound to nickel. Electron paramagnetic resonance experiments showed that the radical signal from the NADH-reduced enzyme derives from the semiquinone form of the flavin (FMN-a) in the hydrogenase module (HoxYH dimer), but not of the flavin (FMN-b) in the NADH-dehydrogenase module (HoxFU dimer). It is further demonstrated that the hexameric enzyme remains active in the presence of NADPH and air, whereas NADH and air lead to rapid destruction of enzyme activity. It is proposed that the presence of NADPH in cells keeps the enzyme in the active state. [ABSTRACT FROM AUTHOR]

The bulky, asymmetric analog of the antitumor drug cisplatin, [PtCl2(tmen)] (tmen = N,N,N′ -trimethylethylenediamine), was used to produce crosslinks with the dinucleotide d(GpG), modeling the most frequent lesions that cisplatin and its analogs cause to DNA. The ligand tmen was chosen because it is expected to constrain the guanine cis to the NMe2 group in the adduct [Pt(tmen){d(GpG)}]+ to an orientation perpendicular to the coordination plane and to stabilize the other guanine in an oblique orientation, thus maintaining a head-to-head geometry typical of cisplatin–d(GpG) crosslinks within single- and double-stranded DNA. Of the four possible combinations of tmen chirality ( R or S symmetry of the coordinated NHMe group) and crosslink direction (5′-G bound cis to the secondary or the tertiary amino group of tmen), two isomers were preponderantly formed, [Pt( R-tmen){d(GpG)}]+ with 5′-G bound cis to NMe2 and [Pt( S-tmen){d(GpG)}]+ with 5′-G bound cis to NHMe. The former was shown to have a right-handed R2 orientation of guanines similar to that found in duplex DNA, whereas the latter had a left-handed L1 orientation that modeled cisplatin–d(GpG) adducts within single-stranded DNA. The R2 rotamer was found to be in an equilibrium (as observed using EXSY spectroscopy) with a minor fraction (≤4%) of a Δ-HT rotamer related to R2 by rotation of the 3′-G about the Pt–N7 bond. The major rotamers R2 and L1 were isolated using reverse-phase HPLC, and their NMR and CD signatures were compared to those of the corresponding rotamers of the less hindered adduct [Pt(dmen)(GpG)]+ (dmen = N,N-dimethylethylenediamine). From this and other comparisons with previously reported platinum dinucleotide complexes, and from molecular modeling, it could be concluded that both steric repulsion between guanine and substituents of the cis amino group and N–H···O6 hydrogen bonding are significant effects favoring the oblique orientation of one guanine base typical of the HH rotamers of [Pt(diamine){d(GpG)}]+ and [Pt(diamine)(GpG)]+ complexes. [ABSTRACT FROM AUTHOR]

Mixed-ligand ruthenium(II) complexes of three photoactive ligands, viz., ( E)-1-[2-(4-methyl-2-pyridyl)-4-pyridyl]-2-(1-naphthyl)-1-ethene (mppne), ( E)-1-(9-anthryl)-2-[2-(4-methyl-2-pyridyl)-4-pyridyl]-1-ethene (mppae) and ( E)-1-[2-(4-methyl-2-pyridyl)-4-pyridyl]-2-(1-pyrenyl)-1-ethene (mpppe), in which a 2,2′-bipyridyl unit is linked via an ethylinic linkage to either a naphthalene, an anthracene or a pyrene chromophore and three electroactive ligands, viz., 4-(4-pyridyl)-1,2-benzenediol (catpy), 5,6-dihydroxy-1,10-phenanthroline (catphen) and 1,2-benzenediol (cat), were synthesized in good to moderate yields. Complexes [Ru(bpy)2(mppne)]2+ (bpy is 2, 2′–bipyridyl), [Ru(bpy)2(mppae)]2+, [Ru(bpy)2(mpppe)]2+, [Ru(bpy)2(sq-py)]+, [Ru(bpy)2(sq-phen)]+ and [Ru(phen)2(bsq)]+ (phen is 1,10-phenanthroline) were fully characterized by elemental analysis, IR, 1H NMR, fast-atom bombardment or electron-impact mass, UV–vis and cyclic voltammetric methods. In the latter three complexes, the ligands catpy, catphen and cat are actually bound to the metal center as the corresponding semiquinone species, viz., 4-(4-pyridyl)-1,2-benzenedioleto(+I) (sq-py), 1,10-phenanthroline-5,6-dioleto(+I) (sq-phen) and 1,2-benzenedioleto(+I) (bsq), thus making the overall charge of the complexes formally equal to + 1 in each case. These three complexes are electron paramagnetic resonance active and exhibit an intense absorption band between 941 and 958 nm owing to metal-to-ligand charge transfer (MLCT, d Ru→ π*sq) transitions. The other three ruthenium(II) complexes containing three photoactive ligands, mppne, mppae and mpppe, exhibit MLCT ( d Ru→ π*bpy ) bands in the 454–461-nm region and are diamagnetic. These can be characterized by the 1H NMR method. [Ru(bpy)2(mppne)]2+, [Ru(bpy)2(mppae)]2+ and [Ru(bpy)2(mpppe)]2+ exhibit redox waves corresponding to the RuIII/RuII couple along with the expected ligand (bpy and substituted bpy) based ones in their cyclic and differential pulse voltammograms (CH3CN, 0.1 M tetrabutylammonium hexafluorophosphate)—corresponding voltammograms of [Ru(bpy)2(sq-py)]+, [Ru(bpy)2(sq-phen)]+ and [Ru(phen)2(bsq)]+ are mainly characterized by waves corresponding to the quinone/semiquinone (q/sq) and semiquinone/1,2-diol (sq/cat) redox processes. The results of absorption and fluorescence titration as well as thermal denaturation studies reveal that [Ru(bpy)2(mppne)]2+ and [Ru(bpy)2(mppae)]2+ are moderate-to-strong binders of calf thymus DNA with binding constants ranging from 105 to 106 M−1. Under the identical conditions of drug and light dose, the DNA (supercoiled pBR 322) photocleavage activities of these two complexes follow the order:[Ru(bpy)2(mppne)]2+>[Ru(bpy)2(mppae)]2+, although the emission quantum yields follow the reverse order. The other ruthenium(II) complexes containing the semiquinone-based ligands are found to be nonluminescent and inefficient photocleavage agents of DNA. However, experiments shows that [Ru(bpy)2(sq)]+-based complexes oxidize the sugar unit and could be used as mild oxidants for the sugar moiety of DNA. Possible explanations for these observations are presented. [ABSTRACT FROM AUTHOR]

Conserved glycines, Gly139 and Gly143, in the distal helix of human heme oxygenase-1 (HO-1) provide the flexibility required for the opening and closing of the heme active site for substrate binding and product dissociation during HO-1 catalysis. Earlier mutagenesis work on human HO-1 showed that replacement of either Gly139 or Gly143 suppresses heme oxygenase activity and, in the case of the Gly139 mutants, increases peroxidase activity (Liu et al. inJ. Biol. Chem.275:34501, 2000). To further investigate the role of the conserved distal helix glycines, we have determined the crystal structures of the human HO-1 G139A mutant, the G139A mutant in a complex with NO, and the G143H mutant at 1.88, 2.18 and 2.08 Å, respectively. The results confirm that fine tuning of the previously noted active-site hydrogen-bonding network is critical in determining whether heme oxygenase or peroxidase activity is observed. [ABSTRACT FROM AUTHOR]

The brown algaLaminaria digitatafeatures a distinct vanadium-dependent iodoperoxidase (vIPO) activity, which has been purified to electrophoretic homogeneity. Steady-state analyses at pH 6.2 are reported for vIPO (K=2.5 mM;k=462 s-1) and for the previously characterised vanadium-dependent bromoperoxidase inL. digitata(K=18.1 mM;k=38 s-1). Although the vIPO enzyme specifically oxidises iodide, competition experiments with halides indicate that bromide is a competitive inhibitor with respect to the fixation of iodide. A full-length complementary ANA (cDNA) was cloned and shown to be actively transcribed inL. digitataand to encode the vIPO enzyme. Mass spectrometry analyses of tryptic digests of vIPO indicated the presence of at least two very similar proteins, in agreement with Southern analyses showing that vIPOs are encoded by a multigenic family inL. digitata. Phylogenetic analyses indicated that vIPO shares a close common ancestor with brown algal vanadium-dependent bromoperoxidases. Based on a three-dimensional structure model of the vIPO active site and on comparisons with those of other vanadium-dependent haloperoxidases, we propose a hypothesis to explain the evolution of strict specificity for iodide inL. digitatavIPO. [ABSTRACT FROM AUTHOR]

The axial ligand effect on reactivity of heme enzymes is explored by means of density functional theoretical calculations of the oxidation reactions of propene by a model compound I species of horseradish peroxidase (HRP). The results are assessed vis-à-vis those of cytochrome P450 compound I. It is shown that the two enzymatic species perform C=C epoxidation and C-H hydroxylation in a multistate reactivity scenario with FeIII and FeIV electromeric situations and two different spin states, doublet and quartet. However, while the HRP species preferentially keeps the iron in a low oxidation state (FeIII), the cytochrome P450 species prefers the higher oxidation state (FeIV). It is found that HRP compound I has somewhat lower barriers than those obtained by the cytochrome P450 species. Furthermore, in agreement with experimental observations and studies on model systems, HRP prefers C=C epoxidation, whereas cytochrome P450 prefers C-H hydroxylation. Thus, had the compound I species of HRP been by itself, it would have been an epoxidizing agent, and at least as reactive as cytochrome P450. In the enzyme, HRP is much less reactive than cytochrome P450, presumably because HRP reactivity is limited by the access of the substrate to compound I. [ABSTRACT FROM AUTHOR]

Cysteine-rich Zn(II)-binding sites in proteins serve two distinct functions: to template or stabilize specific protein folds, and to facilitate chemical reactions such as alkyl transfers. We are interested how the protein environment controls metal site properties, specifically, how naturally occurring tetrahedral Zn(II) sites are affected by the surrounding protein. We have studied the Co(II)- and Zn(II)-binding of a series of derivatives of L36, a small zinc ribbon protein containing a (Cys)3His metal coordination site. UV-vis spectroscopy was used to monitor metal binding by peptides at pH 6.0. For all derivatives, the following trends were observed: (1) Zn(II) binds tighter than Co(II), with an averageK/Kof 2.8(±2.0)×103; (2) mutation of the metal-binding ligand His32 to Cys decreases the affinity of L36 derivatives for both metals; (3) a Tyr24 to Trp mutation in theß-sheet hydrophobic cluster increasesKandK; (4) mutation in theß-hairpin turn, His20 to Asn generating an Asn-Gly turn, also increasesKandK; (5) the combination of His20 to Asn and Tyr24 to Trp mutations also increasesKandK, but the increments versus C3H are less than those of the single mutations. Furthermore, circular dichroism, size-exclusion chromatography, and 1D and 2D1H NMR experiments show that the mutations do not change the overall fold or association state of the proteins. L36, displaying Co(II)- and Zn(II)-binding sensitivity to various sequence mutations without undergoing a change in protein structure, can therefore serve as a useful model system for future structure/reactivity studies. [ABSTRACT FROM AUTHOR]

Proteins of the Rieske and Rieske-type family contain a [2Fe-2S] cluster with mixed ligation by two histidines and two cysteines, and play important roles in various biological electron transfer reactions. We report here the comparative orientation-selected ESEEM and HYSCORE studies of the reduced clusters from two hyperthermophilic Rieske-type proteins; a high-potential, archaeal Rieske protein called sulredoxin (SDX) fromSulfolobus tokodaiiwith weak homology to the cytochromebc-associated Rieske proteins, and a low-potential, archaeal homolog of an oxygenase-associated Rieske-type ferredoxin (ARF) fromSulfolobus solfataricus.14N ESEEM and HYSCORE spectra of SDX and ARF show well-defined variations, which are primarily determined by changes of quadrupole couplings (up to 50% depending on the selected orientation) of the two coordinated nitrogens. These are due to variations in coordination geometry of the histidine imidazole ligands rather than to variations of hyperfine couplings of these nitrogens, which do not exceed 8-10%. The measured quadrupole couplings and their differences in the two proteins are consistent with those calculated using the reported crystal structures of high- and low-potential Rieske proteins. These results suggest that exploration of quadrupole tensors might provide a more accurate method for characterization of the histidine coordination in different proteins and mutants than hyperfine tensors, and might have potential applications in a wider range of biological systems. [ABSTRACT FROM AUTHOR]

The membrane-bound [NiFe]-hydrogenase fromAllochromatium vinosumcan occur in several inactive or active states. This study presents the first systematic infrared characterisation of theA. vinosumenzyme, with emphasis on the spectro-electrochemical properties of the inactive/active transition. This transition involves an energy barrier, which can be overcome at elevated temperatures. The reduced Ready enzyme can exist in two different inactive states, which are in an apparent acid-base equilibrium. It is proposed that a hydroxyl ligand in a bridging position in the Ni-Fe site is protonated and that the formed water molecule is subsequently removed. This enables the active site to bind hydrogen in a bridging position, allowing the formation of the fully active state of the enzyme. It is further shown that the active site in enzyme reduced by 1 bar H2 can occur in three different electron paramagnetic resonance (EPR)-silent states with a different degree of protonation. [ABSTRACT FROM AUTHOR]

The interaction of a series of phosphate diesters and triesters (1=diphenyl phosphate,2=dimethyl phosphate,3=bis(2-ethylhexyl) phosphate,4=trimethyl phosphate,5=methyldiphenyl phosphate,6=triphenyl phosphate) with [Mg(15-crown-5)]2+ (15-crown-5=1,4,7,10,13-pentaoxocyclopentadecane) was studied as a simplified model for the interaction of aqueous Mg2+ ion with phosphate-containing biomolecules such as RNA. Using electrospray mass spectrometry, we confirm the formation of 1:1 adducts in the gas phase. Proton and31P NMR titration data were used to construct binding isotherms, and a 1:1 binding equilibrium was fit to the isotherms at room temperature to estimate the binding affinities. The binding affinity data are consistent with ditopic coordination of neutral dialkyl phosphate ligands to the [Mg(15-crown-5)]2+ unit. This involves inner-sphere coordination to the Mg2+ via an oxygen atom, which is complemented by a weak hydrogen-bonding interaction with the crown ether ligand. Ditopic interaction is consistent with low-temperature NMR spectra showing four different configurations for1coordinated to [Mg(15-crown-5)]2+, which are interpreted in terms of hindered rotation around the Mg-Ophos bond. Thermochemical analysis of the binding affinity data suggests that the second-shell interaction contributes only about 1 kcal/mol to the binding free energy, so additional factors, such as steric constraints, must be operative to give a preferred phosphate orientation in this system. However, the experimental data do suggest that second-shell interactions contribute as much as 40% of the total binding energy, consistent with the pronounced ability of aqueous Mg2+ to form salt-bridges linking secondary and tertiary elements of RNA structure. [ABSTRACT FROM AUTHOR]

The considerable recent advances in copper-dioxygen coordination chemistry demonstrate the existence of a variety of dioxygen-derived Cu n-O2 complexes, forming a basis for discussion of alternate oxidant types in copper chemistry and biochemistry. Peroxo complexes may react as nucleophilic reagents, and several types of electrophilic mono- or dicopper (hydro)peroxides exist. Side-on peroxo-dicopper(II) species effect aromatic hydroxylations, including phenolic substrates, in model systems and in the enzyme tyrosinase. Bis-µ-oxo-dicopper(III) entities are capable of hydrogen-atom abstraction reactions, or atom transfer to phosphines and sulfides. The scope and mechanisms of mononuclear Cu(II) superoxides or peroxides are yet to be established, but may be relevant to monooxygenases like peptidylglycine a-hydroxylating monooxygenase. [ABSTRACT FROM AUTHOR]

The article presents abstracts of biochemistry research, particularly pertaining to biomineralization. They include "Polyamine-Silica Interactions: A Biomimetic Model System for the Biomineralization in Diatoms," "Peptides from a Combinational Library Regulate Ferritin Iron," and "Insight into Iron trafficking within the dinuclear iron site of Escherichia coli bacterioferritin."

The article presents abstracts of biochemistry research, particularly pertaining to bioinorganic clusters and nanoparticles. They include "A New Aspect of Fe/S-Cluster Synthesis--Relevance to the Active Site of Nitrogenase and Hydrogenase," "Iron and copper carboxylate clusters as biological active substances," and "Nano-sized silica-polymer complexes: A possible form of intracellular silica transport particles."

The article presents abstracts of biochemistry research, particularly pertaining to bioinorganic prebiotic chemistry. They include "Chemical Evolution towards the Origin of Life," "Polymerization on the rocks. Aluminosilicate surfaces as promoters for the peptide bond formation," and "Interactions between amino acid-containing ternary Pt(II) complexes and aromatic molecules."