Pressure dependence of peroxynitrite reactions. Support for a radical mechanism.

Activation volumes (delta V++) have been determined for several reactions of peroxynitrite using the stopped-flow technique. Spontaneous decomposition of ONOOH to NO3- in 0.15 M phosphate, pH 4.5, gave delta V++ = 6.0 +/- 0.7 and 14 +/- 1.0 cm3 mol-1 in the presence of 53 microM and 5 mM nitrite ion, respectively. One-electron oxidations of Mo(CN)8(4-) and Fe(CN)6(4-), which are first order in peroxynitrite and zero order in metal complex, gave delta V++ = 10 +/- 1 and 11 +/- 1 cm3 mol-1, respectively, at pH 7.2. The limiting yields of oxidized metal complex were found to decrease from 61 to 30% of the initially added peroxynitrite for Mo(CN)8(3-) and from 78 to 47% for Fe(CN)6(3-) when the pressure was increased from 0.1 to 140 MPa. The bimolecular reaction between CO2 and ONOO- was determined by monitoring the oxidation of Fe(CN)6(4-) by peroxynitrite in bicarbonate-containing 0.15 M phosphate, pH 7.2, for which delta V++ = -22 +/- 4 cm3 mol-1. The Fe(CN)6(3-) yield decreased by approximately 20% upon increasing the pressure from atmospheric to 80 MPa. Oxidation of Ni(cyclam)2+ by peroxynitrite, which is first order in each reactant, was characterized by delta V++ = -7.1 +/- 2 cm3 mol-1, and the thermal activation parameters delta H++ = 4.2 +/- 0.1 kcal mol-1 and delta S++ = -24 +/- 1 cal mol-1 K-1 in 0.15 M phosphate, pH 7.2. These results are discussed within the context of the radical cage hypothesis for peroxynitrite reactivity.

Intramolecular electron transfer in ascorbate oxidase is enhanced in the presence of oxygen.

Intramolecular electron transfer from the type 1 copper center to the type 3 copper(II) pair is induced in the multi-copper enzyme, ascorbate oxidase, following pulse radiolytic reduction of the type 1 Cu(II) ion. In the presence of a slight excess of dioxygen over ascorbate oxidase, interaction between the trinuclear copper center and O2 is observed even with singly reduced ascorbate oxidase molecules. Under these conditions, the rate constant for intramolecular electron transfer from type 1 Cu(I) to type 3 Cu(II) increases 5-fold to 1100 +/- 300 s-1 (20 degrees C, pH 5.8) as compared to that of the same process under anaerobic conditions. This observation constitutes evidence for control of the internal electron transfer process by one of its substrates. The structural and functional significance of these findings are discussed.

A 3D building blocks approach to analyzing and predicting structure of proteins.

A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of C alpha coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set of standard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can "replace" about 76% of all hexamers in well-refined known proteins with an error of less than 1 A, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.

Three-dimensional model of stellacyanin and its implications for electron transfer reactivity.

Experimental data were combined with computational methods in constructing a hypothetical three-dimensional model for the blue single copper protein Rhus stellacyanin (St). The known sequence of stellacyanin and its homology with plastocyanin (Pc) were used together with the results of spectroscopic studies of the protein that yielded the current assignment of two histidines, one cysteine and a disulfide sulfur as copper ligands in stellacyanin. By computer graphics and energy minimization the folding of the protein was predicted. The model structure is somewhat less regular than Pc as judged by surface area and energy comparisons, but it is a stable structure. Besides rotation of one imidazole ring the copper site undergoes no change even in the absence of the copper ion and the model shows that the site can be constructed with the four assumed copper ligands without forming a strained system. The structure also indicates that a carbonyl oxygen atom is near the copper, thus the site may have analogy to the Alcaligenes denitrificans azurin (Az) site, although the amino acid sequence is more homologous to that of Pc. The model indicates that aspartate 49, reductively labeled by Cr(III), is near the copper center and homologous to the site labeled by Cr(III) on Pc. Also homologous to Pc is a tyrosine residue adjacent to the aspartate. This tyrosine has been implicated in Pc electron transfer and thus is probably involved in electron transfer reactivity of St as well. The higher reactivity of St with small-molecule redox reagents compared to Az and Pc, may be due to the proximity of the above-mentioned aspartate 49 to the Cu, or the greater exposure of one of the Cu cysteine ligands, in the predicted structure as compared to that in the known Pc and Az structures.

Nitrogenase reactivity: insight into the nitrogen-fixing process through hydrogen-inhibition and HD-forming reactions.

The dihydrogen reactions of nitrogenase are H2 evolution, H2 inhibition of N2 reduction, and HD production from H2/D2O or D2/H2O. The relationships among these dihydrogen reactions are studied to gain insight into the mechanism of N2 reduction. Detailed studies have probed (1) the formation of HD by nitrogenase as a function of partial pressures of N2, D2, and CO, (2) the formation of TOH from T2 under N2-fixing conditions, and (3) the reduction of hydrazine by nitrogenase. Experiments under T2 demonstrate that negligible tritium is incorporated into water compared to the HD produced under similar conditions. Studies of total electron flow, in the presence or absence of D2, establish a requirement of 1 mol of electrons/mol of HD formed. These findings show definitively that HD formation is not due to a simple H2O/D2 exchange mechanism. Kinetic analysis shows that HD is produced by two separate processes. In the minor process, the HD formed is proportional to the H2 evolved, electron requiring, and partially inhibited by 1% CO. In the major process, HD formation is dependent on N2 pressure, electron requiring, and completely inhibited by CO. A mechanism is proposed whereby HD from the N2-dependent process is formed from a bound, reduced dinitrogen intermediate. This mechanism is supported by studies using hydrazine as a substrate for nitrogenase and leads to the conclusion that H2 inhibition of nitrogen fixation and N2-dependent HD formation are manifestations of the same molecular process.

Reductant-dependent electron distribution among redox sites of laccase.

Rhus laccase (monophenol monooxygenase, monophenol,dihydroxyphenylalanine:oxygen oxidoreductase, EC 1.14.18.1) an O2/H2O oxidoreductase containing four copper ions bound to three redox sites (type 1, type 2, and type 3 Cu pair), was titrated anaerobically with several reductants having various chemical and thermodynamic properties. The distribution of electron equivalents among the redox sites was found to be reductant dependent. When the data for titration by various reductants of the type 3 site were plotted against those of the type 1 site according to the Nernst formalism, the slope n varied from 2.0 to 1.0. The redox potential of the reductant's first oxidation step is qualitatively correlated with the value of n and is suggested as the factor that modulates the electron distribution. Such a behavior implies a nonequilibrium situation. A very good simulation of the data was provided by an analysis assuming a formally variable cooperativity between the two type 3 copper ions. This apparent variability is suggested to result from a process whereby sufficiently strong reductants induce a transition of the type 3 site from a cooperative two-electron acceptor to a pair of independent one-electron acceptors. This uncoupled state of the type 3 site is considered metastable. Other possible models were also investigated. Summarizing the available data, we conclude that the two-electron accepting behavior of the 330-nm chromophore is the exception rather than the rule.

Metalloprotein electron transfer reactions: analysis of reactivity of horse heart cytochrome c with inorganic complexes.

The reactions of horse heart cytochrome c with Fe(ethylenediaminetetraacetate)2-, Co(1,10-phenanthroline)3(3+), Ru(NH3)6(2+), and Fe(CN)6(3-) have been analyzed within the formalism of the Marcus theory of outer-sphere electron transfer, including compensation for electrostatic interactions. Calculated protein self-exchange rate constants based on crossreactions are found to vary over three orders of magnitude, decreasing according to Fe(CN)6(3-) greater than Ru(NH3)6(2+) greater than Fe(EDTA)2-. The reactivity order suggests that the mechanism of electron transfer involves attack by the small molecule reagents near the most nearly exposed region of the heme; this attack is affected by electrostatic interactions with the positively charged protein, by hydrophobic interactions that permit reagent penetration of the protein surface, and by the availability of pi symmetry ligand (or extended metal) orbitals that can overlap with the pi redox orbitals of the heme group.