The effects of biofilms on chemical processes in surficial sediments

1. The objectives of the present work were: (a) to evaluate the effects of the development and the presence of a photosynthetically active algal biofilm on chemical fluxes and processes at the sediment–water interface; (b) to measure the effects of the biofilm on chemical concentration gradients in the bulk sediment; and (c) to monitor pH and dissolved oxygen concentration in the biofilm, and through the sediment–water interface using microelectrodes. 2. Two experiments were performed over a period of 8 weeks using a recirculating fluvarium channel containing river sediments with an exposed surface of 0.2 m² and 20 dm³ of overlying solution. The first experiment was in darkness with minimal effects of a photosynthetically active biofilm. The second experiment in natural light produced a complex photosynthetic biofilm involving a succession of diatoms, green algae and cyanobacteria. 3. The solution overlying the biofilm was monitored continuously for dissolved calcium, silicon, phosphorus, alkalinity and oxygen, as well as conductivity, temperature and pH. The surface of the sediment was also monitored for biological and physical changes as the biofilm developed. The overlying solution was analysed over a period of 48 h at 2-h intervals to examine the effects of a well-developed algal biofilm. At the end of the 48 h, pH and oxygen microelectrodes were used to measure gradients above and through the biofilm, and porewaters were analysed from sediments which had been longitudinally sectioned at a maximum depth resolution of 0.5 mm. 4. Biofilm development had a large influence on the composition of the overlying solution and the development of vertical concentration gradients of solutes in the porewater. Once a diatom community was established, the concentration of dissolved silicon was low (< 40 μm ), with all the silicon diffusing from the underlying sediment being consumed in the biofilm (≈ 0.026 μmol m^?2 s^?1 at the end of the experiment). 5. The concentrations of calcium, alkalinity and phosphorus in digested sediment increased near the sediment–water interface. X-ray diffraction analysis showed that calcite was formed at the surface. Estimation of the fluxes of alkalinity and calcium in the overlying solution were consistent with calcite formation during daylight and possible dissolution in darkness. The maximum precipitation flux of calcium was 0.87 μmol m^?2 s^?1 and the maximum net release flux was 0.89 μmol m^?2 s^?1. 6. The net loss of soluble reactive phosphorus from the overlying solution measured over the intensive sampling period of 48 h is consistent with a coprecipitation mechanism and a surface density of phosphorus included in the lattice of calcite of 0.097 μmol m^?2. Processes in the biofilm rather than diffusion from the sediment porewater control chemical fluxes of calcium, alkalinity and phosphorus from the sediment to the overlying water.     

Ecology of the bacteria of the sulphur cycle with special reference to anoxic-oxic interface environments

H2S is produced as a main end-product of anaerobic mineralization in anoxic, sulphate-rich environments by a diverse population of sulphate-reducing bacteria. The sulphate reducers can carry out an almost complete oxidation of detrital organic matter to CO2. The H2S consequently becomes an important electron carrier from the anoxic to the oxic world. Thiobacilli and other colourless sulphur bacteria have the potential to oxidize the H2S at the oxic-anoxic interface in sediments or stratified waters, but their role is still poorly understood. A comparison of sulphide oxidation processes in the chemoclines of the Black Sea, the Solar Lake and in A beggiatoa mat indicated that depth scales and retention times of coexisting O2 and H2S regulate the bacterial involvement in the sulphide oxidation. The H2S specialists, Beggiatoa and Thiovulum, are optimally adapted to compete with the autocatalytic oxidation of H2S by O2. Microelectrode measurements show retention times of O2-H2S in the bacterial mats or veils of less than 1 s. In photic chemoclines of stratified waters or sulfureta, the phototrophic sulphur bacteria or cyanobacteria interact with the sulphide oxidation at the O2-H2S interface. Short cycles between H2S and intermediate oxidation products, So or S2O2 3-, are created. The bacteria of the sulfuretum are highly adapted to the diurnal rhythm of light, O2 and H2S.     

Histidine 332 of the D1 polypeptide modulates the magnetic and redox properties of the manganese cluster and tyrosine Y(Z) in photosystem II

An electron spin-echo envelope modulation study [Tang, X.-S., Diner, B. A., Larsen, B. S., Gilchrist, M. L., Jr., Lorigan, G. A., and Britt, R. D. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 704-708] and a recent Fourier transform infrared study [Noguchi, T., Inoue, Y., and Tang, X.-S. (1999) Biochemistry 38, 10187-10195], both conducted with [(15)N]histidine-labeled photosystem II particles, show that at least one histidine residue coordinates the O(2)-evolving Mn cluster in photosystem II. Evidence obtained from site-directed mutagenesis studies suggests that one of these residues may be His332 of the D1 polypeptide. The mutation D1-H332E is of particular interest because cells of the cyanobacterium Synechocystis sp. PCC 6803 that contain this mutation evolve no O(2) but appear to assemble Mn clusters in nearly all photosystem II reaction centers [Chu, H.-A., Nguyen, A. P. , and Debus, R. J. (1995) Biochemistry 34, 5859-5882]. Photosystem II particles isolated from the Synechocystis D1-H332E mutant are characterized in this study. Intact D1-H332E photosystem II particles exhibit an altered S(2) state multiline EPR signal that has more hyperfine lines and narrower splittings than the S(2) state multiline EPR signal observed in wild-type PSII particles. However, the quantum yield for oxidizing the S(1) state Mn cluster is very low, corresponding to an 8000-fold slowing of the rate of Mn oxidation by Y(Z)(*), and the temperature threshold for forming the S(2) state is approximately 100 K higher than in wild-type PSII preparations. Furthermore, the D1-H332E PSII particles are unable to advance beyond the Y(Z)(*)S(2) state, as shown by the accumulation of a narrow "split" EPR signal under multiple turnover conditions. In Mn-depleted photosystem II particles, charge recombination between Q(A)(*)(-) and Y(Z)(*) in D1-H332E is accelerated in comparison to wild-type, showing that the mutation alters the redox properties of Y(Z) in addition to those of the Mn cluster. These results are consistent with D1-His332 being located near the Mn-Y(Z) complex and perhaps ligating Mn.     

The function of D1-H332 in Photosystem II electron transport studied by thermoluminescence and chlorophyll fluorescence in site-directed mutants of Synechocystis 6803.

The His332 residue of the D1 protein has been identified as the likely ligand of the catalytic Mn ions in the water oxidizing complex (Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J. & Iwata, S. (2004) Science 303, 1831-1838). However, its function has not been fully clarified. Here we used thermoluminescence and flash-induced chlorophyll fluorescence measurements to characterize the effect of the D1-H333E, D1-H332D and D1-H332S mutations on the electron transport of Photosystem II in intact cells of the cyanobacterium Synechocystis 6803. Although the mutants are not photoautotrophic they all show flash-induced thermoluminescence and chlorophyll fluorescence, which originate from the S(2)Q(A) (-) and S(2)Q(B) (-) recombinations demonstrating that charge stabilization takes place in the water oxidizing complex. However, the conversion of S(2) to higher S states is inhibited and the energetic stability of the S(2)Q(A) (-) charge pair is increased by 75, 50 and 7 mV in the D1-H332D, D1-H332E and D1-H332S mutants, respectively. This is most probably caused by a decrease of E(m)(S(2)/S(1)). Concomitantly, the rate of electron donation from Mn to Tyr-Z(b) during the S(1) to S(2) transition is slowed down, relative to the wild type, 350- and 60-fold in the D1-H332E and D1-H332D mutants, respectively, but remains essentially unaffected in D1-H332S. A further effect of the D1-H332E and D1-H332D mutations is the retardation of the Q(A) to Q(B) electron transfer step as an indirect consequence of the donor side modification. Our data show that although the His residue in the D1-332 position can be substituted by other metal binding residues for binding photo-oxidisable Mn it is required for controlling the functional redox energetics of the Mn cluster.     

Evidence for the presence of a component of the Mn complex of the photosystem II reaction centre which is exposed to water in the S(2) state of the water oxidation complex

The interaction of water oxidising photosystem II preparations with the aqueous environment has been investigated using electron spin echo envelope modulation spectroscopy in the presence of 2H(2)O. The spectra show interaction of 2H of 2H(2)O with the preparation in the S(2) state. The component interacting with water decays during 1-4 weeks storage at 77 K. No interaction of water with the classical multiline S(2) Mn signal, which is more stable on storage at 77 K, was detected. The results show that a component of the water oxidation complex, possibly involving the Mn centre, is accessible to water and may be the water binding site for photosynthetic water oxidation.     

Macrophyte induced microchemical changes in the water column of a northern Boreal Lake

Water quality was compared between open water and vegetated regions of the littoral zone of a Boreal lake. Within region variation occurred in vegetated areas and was species dependent. In the water lily versus the open water stations, conductivity and concentrations of B, Ca, Fe, K, Mg, Mn, S and Sr were elevated in the water column while N concentrations were lower. Wild rice areas were characterized by lower S and higher conductivity and Ca and Fe concentrations than open water areas. Variations in water quality in the vegetated regions occurred as a result of chemical exchange with the sediment in the proximity of the vegetation. Elemental concentrations in the sediment appeared to vary as a result of root aeration and nutrient uptake by the plants. Open water stations had elevated sediment levels of N, P and Al while elevated levels of Na were present in both the open water and wild rice plots. Water lily stations exhibited higher pH levels and higher concentrations of Fe, Mn and Ca than the open water plots. Plant tissue analysis indicated that between species elemental variation existed as well. Water lily tissue had higher concentrations of N, P, Mn, Zn, Ca, K and Mg than that of wild rice. It was postulated that aquatic macrophytes can influence the redox level of sediments and thereby dramatically alter the overlying water column forming microchemical environments in stagnant regions of the littoral zone.     

Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface

The sediment–water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment–water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NO_x. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment–water interface.     

Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes

The chemical sequence of the [2Fe-2S] ferredoxin from the cyanobacterium AnabaenaPCC7119 (Fd7119) and its high-resolution X-ray structures in the oxidized and reduced states have been determined. The Fd7119 sequence is identical to that of the ferredoxin from the PCC7120 strain (Fd7120). X-ray diffraction data were collected at 100 K with an oxidized trigonal Fd7119 crystal, at 1.3 A resolution, and with an orthorhombic crystal, previously reduced with dithionite and flash frozen under anaerobic conditions, at 1.17 A resolution. The two molecular models were determined by molecular replacement with the [2Fe-2S] ferredoxin from the strain PCC7120 (Rypniewski, W. R., Breiter, D. R., Benning, M. M., Wesenberg, G., Oh, B.-H., Markley, J. L., Rayment, I., and Holden, H. M. (1991) Biochemistry 30, 4126-4131.) The final R-factors are 0. 140 (for the reduced crystal) and 0.138 (for the oxidized crystal). The [2Fe-2S] cluster appears as a significantly distorted lozenge in the reduced and oxidized redox states. The major conformational difference between the two redox forms concerns the peptide bond linking Cys46 and Ser47 which points its carbonyl oxygen away from the [2Fe-2S] cluster ("CO out") in the reduced molecule and toward it ("CO in") in the oxidized one. The "CO out" conformation could be the signature of the reduction of the iron atom Fe1, which is close to the molecular surface. Superposition of the three crystallographically independent molecules shows that the putative recognition site with the physiological partner (FNR) involves charged, hydrophobic residues and invariant water molecules.     

Anti-oxidant activity of spermine and spermidine re-evaluated with oxidizing systems involving iron and copper ions

This study was designed to investigate the direction of redox reactions of spermine and spermidine in the presence of iron and copper. The redox activity of spermine and spermidine was assessed using a variety of methods, including their ability to: (1) reduce Fe(3+) to Fe(2+) ions; (2) protect deoxyribose from oxidation by Fe(2+)-ethylene diaminetetraacetic acid, Fe(3+)-ethylene diaminetetraacetic acid systems with and without H(2)O(2); (3) protect DNA from damage caused by Cu(2+)-H(2)O(2), and Fe(2+)-H(2)O(2) with and without ascorbic acid; (4) inhibit H(2)O(2)-peroxidase-induced luminol dependent chemiluminescence; (5) scavenge diphenyl-picryl-hydrazyl radical. Spermine and spermidine at concentration 1mM reduced 1.8+/-0.3 and 2.5+/-0.1 nmol of Fe(3+) ions during 20 min incubation. Both polyamines enhanced deoxyribose oxidation. The highest enhancement of 7.6-fold in deoxyribose degradation was found for combination of spermine with Fe(3+)-ethylene diaminetetraacetic acid. An 10mM spermine and spermidine decreased CuSO(4)-H(2)O(2)-ascorbic acid- and FeSO(4)-H(2)O(2)-ascorbic-induced DNA damage by 73+/-6, 69+/-4% and 90+/-5, 53+/-4%, respectively. They did not protect DNA from CuSO(4)-H(2)O(2) and FeSO(4)-H(2)O(2). Spermine apparently increased the CuSO(4)-H(2)O(2)-dependent injury to DNA. Polyamines attenuated H(2)O(2)-peroxidase-induced luminol dependent chemiluminescence. Total light emission from specimens containing 10mM spermine or spermidine was attenuated by 85.3+/-1.5 and 87+/-3.6%. During 20 min incubation 1mM spermine or spermidine decomposed 8.1+/-1.4 and 9.2+/-1.8% of diphenyl-picryl-hydrazyl radical. These results demonstrate that polyamines of well known anti-oxidant properties may act as pro-oxidants and enhance oxidative damage to DNA components in the presence of free iron ions and H(2)O(2).     

Water-sensitive low-frequency vibrations of reaction intermediates during S-state cycling in photosynthetic water oxidation

In photosynthetic water oxidation, two water molecules are converted to an oxygen molecule through five reaction intermediates, designated S(n) (n = 0-4), at the catalytic Mn cluster of photosystem II. To understand the mechanism of water oxidation, changes in the chemical nature of the substrate water as well as the Mn cluster need to be defined during S-state cycling. Here, we report for the first time a complete set of Fourier transform infrared difference spectra during S-state cycling in the low-frequency (670-350 cm(-1)) region, in which interactions between the Mn cluster and its ligands can be detected directly, in PS II core particles from Thermosynechococcus elongatus. Furthermore, vibrations from oxygen and/or hydrogen derived from the substrate water and changes in them during S-state cycling were identified using multiplex isotope-labeled water, including H2(18)O, D2(16)O, and D2(18)O. Each water isotope affected the low-frequency S-state cycling spectra, characteristically. The bands sensitive only to (16)O/(18)O exchange were assigned to the modes from structures involving Mn and oxygen having no interactions with hydrogen, while the bands sensitive only to H/D exchange were assigned to modes from amino acid side chains and/or polypeptide backbones that associate with water hydrogen. The bands sensitive to both (16)O/(18)O and H/D exchanges were attributed to the structure involving Mn and oxygen structurally coupled with hydrogen in a direct or an indirect manner through hydrogen bonds. These bands include the changes of intermediate species derived from substrate water during the process of photosynthetic water oxidation.     

Resuspension studies in cylindrical microcosms: Effects of stirring velocity on the dynamics of redox sensitive elements in a coastal sediment

Effects of resuspension on the release of dissolved, redox sensitive elements (Fe, Mn) was studied in cylindrical microcosms. Effects from changing water stirring velocity in sediment pools were evaluated through measurements of pore water profiles of dissolved Mn, Fe and redox potential. Mn was a good natural marker to follow such effects. At current velocities below the threshold velocity for resuspension (37 cm s-1), Mn release rates to overlying water were 100 times higher compared to steady-state values. Pulse increases in Mn concentration were the result of convective currents inside flow chambers. These results were strongly supported by measurements of Eh profiles in the sediment pore water. Furthermore, impacts from increasing stirring velocity were found down to 1.9 cm depth below the resuspended layer of sediment.     

Changes in the physical and chemical properties of floodwater and sediment in an experimental ricefield (Reggio Emilia,Italy)

Changes in time and space in the physical and chemical variables connected to the oxygen P/R ratio were studied.Temperature, light transmission, dissolved oxygen and its day-night cycles were measured periodically in the floodwater; in addition, concentrations of total phosphorus, proteins and chlorophyll-a in the particulate suspended matter were measured. Finally, the seasonal evolution of the redox conditions in the water and in the sediment were analysed.Highly significant correlations between pH and D.O. in the water, and oxygen production were found; the pH and Eh values of the water/sediment interface were strictly related to the corresponding values reached in the water. The composition and the size of the particulate suspended matter pool seemed to be relatively stable and unrelated to the physical and chemical characteristics of the water.     

Colorless Sulfur Bacteria, Beggiatoa spp. and Thiovulum spp., in O(2) and H(2)S Microgradients

The interactions between colorless sulfur bacteria and the chemical microgradients at the oxygen-sulfide interface were studied in Beggiatoa mats from marine sediments and in Thiovulum veils developing above the sediments. The gradients of O(2), H(2)S, and pH were measured by microelectrodes at depth increments of 50 mum. An unstirred boundary layer in the water surrounding the mats and veils prevented microturbulent or convective mixing of O(2) and H(2)S. The two substrates reached the bacteria only by molecular diffusion through the boundary layer. The bacteria lived as microaerophiles or anaerobes even under stirred, oxic water. Oxygen and sulfide zones overlapped by 50 mum in the bacterial layers. Both compounds had concentrations in the range of 0 to 10 mumol liter and residence times of 0.1 to 0.6 s in the overlapping zone. The sulfide oxidation was purely biological. Diffusion calculations showed that formation of mats on solid substrates or of veils in the water represented optimal strategies for the bacteria to achieve a stable microenvironment, a high substrate supply, and an efficient competition with chemical sulfide oxidation. The continuous gliding movement of Beggiatoa cells in mats or the flickering motion of Thiovulum cells in veils were important for the availability of both O(2) and H(2)S for the individual bacteria.     

Near-infrared-induced transitions in the manganese cluster of photosystem II: action spectra for the S2 and S3 redox states

The Mn4Ca complex that is involved in water oxidation in PSII is affected by near-infrared (NIR) light in certain redox states and these phenomena can be monitored by electron paramagnetic resonance (EPR) at low temperature. Here we report the action spectra of the NIR effects in the S2 and S3 states in PSII from plants and the thermophilic cyanobacterium Thermosynechococcus elongatus. The action spectra obtained are very similar in both S states, indicating the presence of the same photoactive form of the Mn4Ca complex in both states. Since the chemical nature of the photoactive species is not known, an unequivocal interpretation of this result cannot be made; however, it appears to be more easily reconciled with the view that the redox state of the Mn4Ca cluster does not change from the S2 to the S3 transition, at least in those centers sensitive to NIR light. The temperature dependence of the NIR effect and the action spectra for S2 indicate the presence of structural heterogeneity in the Mn4Ca cluster.     

Associations between redox‐sensitive trace metals and microbial communities in a Proterozoic ocean analogue

Constraints on Precambrian ocean chemistry are dependent upon sediment geochemistry. However, diagenesis and metamorphism can destroy primary biosignatures, making it difficult to consider biology when interpreting geochemical data. Modern analogues for ancient ecosystems can be useful tools for identifying how sediment geochemistry records an active biosphere. The Middle Island Sinkhole (MIS) in Lake Huron is an analogue for shallow Proterozoic waters due to its low oxygen water chemistry and microbial communities that exhibit diverse metabolic functions at the sediment–water interface. This study uses sediment trace metal contents and microbial abundances in MIS sediments and an oxygenated Lake Huron control site (LH) to infer mechanisms for trace metal burial. The adsorption of trace metals to Mn‐oxyhydroxides is a critical burial pathway for metals in oxic LH sediments, but not for the MIS mat and sediments, consistent with conventional understanding of Mn cycling. Micronutrient trace metals (e.g., Zn) are associated with organic matter regardless of oxygen and sulfide availability. Although U and V are conventionally considered to be organically complexed in suboxic and anoxic conditions, U and organic covary in oxic LH sediments, and Mn‐oxyhydroxide cycling dominates V deposition in the anoxic MIS sediments. Significant correlations between Mo and organic matter across all redox regimes have major implications for our interpretations of Mo isotope systematics in the geologic record. Finally, while microbial groups vary between the sampling locales (e.g., the cyanobacteria in the MIS microbial mat are not present in LH sediments), LH and MIS ultimately have similar relationships between microbial assemblages and metal burial, making it difficult to link trace metal burial to microbial metabolisms. Together, these results indicate that bulk sediment trace metal composition does not capture microbiological processes; more robust trace metal geochemistry such as isotopes and speciation may be critical for understanding the intersections between microbiology and sediment geochemistry.     

The oxidised histone octamer does not form a H3 disulphide bond

A H3 dimer band is produced when purified native histone octamers are run on an SDS-PAGE gel in a beta-mercaptoethanol-free environment. To investigate this, native histone octamer crystals, derived from chicken erythrocytes, and of structure (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A'), were grown in 2 M KCl, 1.35 M potassium phosphates and 250-350 microM of the oxidising agent S-nitrosoglutathione, pH 6.9. X-ray diffraction data were acquired to 2.10 A resolution, yielding a structure with an Rwork value of 18.6% and an Rfree of 22.5%. The space group is P6(5), the asymmetric unit of which contains one complete octamer. Compared to the 1.90 A resolution, unoxidised native histone octamer structure, the crystals show a reduction of 2.5% in the c-axis of the unit cell, and free-energy calculations reveal that the H3-H3' dimer interface in the latter has become thermodynamically stable, in contrast to the former. Although the inter-sulphur distance of the two H3 cysteines in the oxidised native histone octamer has reduced to 6 A from the 7 A of the unoxidised form, analysis of the hydrogen bonds that constitute the (H4-H3)-(H3'-H4') tetramer indicates that the formation of a disulphide bond in the H3-H3' dimer interface is incompatible with stable tetramer formation. The biochemical and biophysical evidence, taken as a whole, is indicative of crystals that have a stable H3-H3' dimer interface, possibly extending to the interface within an isolated H3-H3' dimer, observed in SDS-PAGE gels.     

Versatile peroxidase oxidation of high redox potential aromatic compounds: site-directed mutagenesis, spectroscopic and crystallographic investigation of three long-range electron transfer pathways

Versatile peroxidases (VP), a recently described family of ligninolytic peroxidases, show a hybrid molecular architecture combining different oxidation sites connected to the heme cofactor. High-resolution crystal structures as well as homology models of VP isoenzymes from the fungus Pleurotus eryngii revealed three possibilities for long-range electron transfer for the oxidation of high redox potential aromatic compounds. The possible pathways would start either at Trp164 or His232 of isoenzyme VPL, and at His82 or Trp170 of isoenzyme VPS1. These residues are exposed, and less than 11 A apart from the heme. With the purpose of investigating their functionality, two single mutations (W164S and H232F) and one double mutation (W164S/P76H) were introduced in VPL that: (i) removed the two pathways in this isoenzyme; and (ii) incorporated the absent putative pathway. Analysis of the variants showed that Trp164 is required for oxidation of two high redox potential model substrates (veratryl alcohol and Reactive Black 5), whereas the two other pathways (starting at His232 and His82) are not involved in long-range electron transfer (LRET). None of the mutations affected Mn2+ oxidation, which would take place at the opposite side of the enzyme. Substitution of Trp164 by His also resulted in an inactive variant, indicating that an indole side-chain is required for activity. It is proposed that substrate oxidation occurs via a protein-based radical. For the first time in a ligninolytic peroxidase such an intermediate species could be detected by low-temperature electron paramagnetic resonance of H2O2-activated VP, and was found to exist at Trp164 as a neutral radical. The H2O2-activated VP was self-reduced in the absence of reducing substrates. Trp164 is also involved in this reaction, which in the W164S variant was blocked at the level of compound II. When analyzing VP crystal structures close to atomic resolution, no hydroxylation of the Trp164 Cbeta atom was observed (even after addition of several equivalents of H2O2). This is in contrast to lignin peroxidase Trp171. Analysis of the crystal structures of both peroxidases showed differences in the environment of the protein radical-forming residue that could affect its reactivity. These variations would also explain differences found for the oxidation of some high redox potential aromatic substrates.     

Electron paramagnetic resonance studies of a ras p21-MnIIGDP complex in solution.

The number of water molecules bound to Mn2+ in the complex with a variant of Ha ras p21 and GDP has been determined by electron paramagnetic resonance (EPR) measurements in 17O-enriched water. A resolution enhancement method has been used to improve quantitation of the spectral data. These spectroscopic measurements show that Mn2+ has four water ligands in this complex, a result in agreement with the conclusions of a previous paper [Smithers, G. W., Poe, M., Latwesen, D. G., & Reed, G. H. (1990) Arch. Biochem. Biophys. 280, 416-420]. The resolution enhancement method has also been applied in a measurement of the 17O-Mn2+ superhyperfine coupling constant of 17O in the beta-phosphate of the GDP in the ras p21 complex. The intrinsically narrow EPR signals of Mn2+ in the complex with ras p21 and GDP in 2H2O respond to resolution enhancement such that the superhyperfine splitting from the 17O nuclear spin (I = 5/2) becomes visible in the EPR signals. An 17O-Mn2+ superhyperfine coupling constant is obtained from simulation of the resolution-enhanced EPR spectrum.     

Theoretical investigation on peripheral ligands of oxygen-evolving center in photosystem II

The interaction between the Mn-cluster and its peripheral ligands in oxygen-evolving center is still unclear. Theoretical investigation on the coordination of histidine, H2O, and Cl to Mn2O2 units in OEC is conducted. The following conclusions are obtained: (i) both histidine and H2O molecule, bound to the two Mn ions, respectively, are vertical to the Mn2O2 plane, and maintain a large distance; (ii) the two H2O molecules cannot bind to the same Mn2O2 unit. Based on Mn-cluster structure in OEC, we theoretically predict that two H2O molecules bind to the two Mn ions at the "C"-shaped open end in S0 state, while two His residues at the closed end. Cl ion can only terminally ligate at the open end. Individual valence for the four Mn ions in S0 state is assigned.     

Theoretical investigation on peripheral ligands of oxygen-evolving center in photosystem II

The interaction between the Mn-cluster and its peripheral ligands in oxygen-evolving center is still unclear. Theoretical investigation on the coordination of histidine, H2O, and Cl to Mn2O2 units in OEC is conducted. The following conclusions are obtained: (i) both histidine and H2O molecule, bound to the two Mn ions, respectively, are vertical to the Mn2O2 plane, and maintain a large distance; (ii) the two H2O molecules cannot bind to the same Mn2O2 unit. Based on Mn-cluster structure in OEC, we theoretically predict that two H2O molecules bind to the two Mn ions at the "C"-shaped open end in S0 state, while two His residues at the closed end. Cl ion can only terminally ligate at the open end. Individual valence for the four Mn ions in S0 state is assigned.