Site-directed mutants of Escherichia coli fumarate reductase in which each of the four N-terminal cysteine residues in the FrdB subunit, residues 57, 62, 65, and 77, was mutated individually to serine have been constructed, overexpressed, and investigated in terms of enzymatic activity as well as the EPR and redox properties of the iron-sulfur centers. In each case, the mutant contains a functional fumarate reductase in which all three of the constituent iron-sulfur clusters (i.e., The menaquinol-fumarate oxidoreductase (EC 1.3.99.1) of Escherichia coli is a four-subunit membrane-bound complex that catalyzes the final step in anaerobic respiration when fumarate is the terminal electron acceptor (1, 2). The membrane-extrinsic fumarate reductase domain comprises a flavoprotein (Fp), FrdA (66 kDa), with a covalently bound FAD (3), and an iron-sulfur protein (Ip), FrdB (27 kDa). Two small hydrophobic peptides (4), FrdC (15 kDa) and FrdD (13 kDa), anchor the enzyme to the membrane and are essential for interaction with quinones (5-7). The combination ofmagnetic CD and EPR spectroscopies has provided evidence for three types of iron-sulfur clusters, each stoichiometric with FAD, in the two-subunit fumarate reductase: center 1, [2Fe-

Site-directed mutants of Escherichia coli fumarate reductase in which FrdB Cys204, Cys210, and Cys214 were individually replaced by Ser and in which Val207 was replaced by Cys were constructed and overexpressed in a strain of E. coli lacking a wild-type copy of fumarate reductase and succinate dehydrogenase. The consequences of these mutations on bacterial growth, enzymatic activity, and the EPR properties of the constituent iron-sulfur clusters were investigated. The FrdB Cys204Ser, Cys210Ser, and Cys214Ser mutations result in enzymes with negligible activity that have dissociated from the membrane and consequently are incapable of supporting cell growth under conditions requiring a functional fumarate reductase. EPR studies indicate that these effects are associated with loss of both the [3Fe-4S] and [4Fe-4S] clusters, centers 3 and 2, respectively. In contrast, the FrdB Val207Cys mutation results in a functional membrane-bound enzyme that is able to support growth under anaerobic and aerobic conditions. However, EPR studies indicate that the indigenous [3Fe-4S]+,0 cluster (Em = -70 mV), center 3, has been replaced by a much lower potential [4Fe-4S]2+,+ cluster (Em = -350 mV), indicating that the primary sequence of the polypeptide determines the type of clusters assembled. The results of these studies afford new insights into the role of centers 2 and 3 in mediating electron transfer from menaquinol, the residues that ligate these clusters, and the intercluster magnetic interactions in the wild-type enzyme.

The ground and excited state properties of Co(II) substituted for Zn(II) at the catalytic (c) and the noncatalytic (n) sites of horse liver alcohol dehydrogenase EE isozyme have been investigated by parallel EPR and UV/ visible variable-temperature magnetic circular dichroism (VTMCD) spectroscopies. Samples were investigated as prepared and after formation of a ternary complex with NAD+ and the potent inhibitor pyrazole. In accord with the structural role proposed for the noncatalytic metal, the spectroscopic properties of Co(II) at the noncatalytic site were unperturbed by formation of the ternary complex. The EPR spectra were readily analyzed in terms of a S = 3/2 spin Hamiltonian using anisotropic intrinsic g-values in the range characteristic of tetrahedral Co(II), i.e. g = 2.1-2.4; E/D 0), and 0 (with D > 0) for Co(c)Zn(n)-HLADH, Co(c)Zn(n)-HLADH/NAD+/pyrazole, and Zn(c)Co(n)-HLADH, respectively. VTMCD studies facilitated resolution and assignment of S -Co(II) charge transfer bands (300-400 nm) and the components of the 4A2 -'Tl(P) tetrahedral d-d band (500-800 nm) that are split by spin-orbit coupling and low-symmetry distortions. The splittings of the highest energy d-d band are indicative of a much more distorted coordination environment for Co(I1) at the catalytic site than the noncatalytic site. This is also reflected in the magnitude of ground state zero-field splitting, A, determined by analysis of the temperature dependence of discrete MCD bands, IA( = 33, 56, and 7 cm-* for Co(c)Zn(n)-HLADH, Co(c)Zn(n)-HLADH/NAD+/pyrazole, and Zn(c)Co(n)-HLADH, respectively. MCD magnetization data are rationalized in terms of the EPR-determined ground state effective g-values, ground state zero-field splitting, and the polarization of the electronic transitions. The zero-field splittings for the samples with Co(I1) at the catalytic site determined by VTMCD are quite different from those determined by EPR from the temperature dependence of the spin relaxation (Makinen, M. W.; Yim, M. B. Proc. Nutl. Acad. Sci. U S A . 1981 78, 6221-6225), and the origin of this discrepancy is discussed. In accord with X-ray crystallographic studies, the EPR and VTMCD data are rationalized in terms of a highly distorted tetrahedral coordination environment for Co(I1) at the catalytic site (two cysteines, one histidine, and one H20 for Co(c)Zn(n)-HLADH and two cysteines, one histidine and one pyrazole for Co(c)Zn(n)-HLADWNAD+/pyrazole) and a more regular tetrahedral environment for Co(I1) at the noncatalytic site (four cysteines). 0.33, 0.05 (with D

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Large amounts of data from high throughput metabolomic experiments are commonly visualized using a principal component analysis (PCA) 2D scores plot. The question of the similarity or difference between multiple metabolic states then becomes a question of the degree of overlap between their respective data point clusters in PC scores space. A qualitative visual inspection of the clustering pattern in PCA score plots is a common protocol. This report describes the application of tree diagrams and bootstrapping techniques for an improved quantitative analysis of metabolic PCA data clustering. Our PCAtoTree program creates a distance matrix with 100 bootstrap steps that describes the separation of all clusters in a metabolic dataset. Using accepted phylogenetic software, the distance matrix resulting from the various metabolic states is organized into a phylogenetic-like tree format, where bootstrap values ≥ 50 indicate a statistically relevant branch separation. PCAtoTree analysis of two previously published data sets demonstrates the improved resolution of metabolic state differences using tree diagrams. In addition, for metabolomic studies of large numbers of different metabolic states, the tree format provides a better description of similarities and differences between each metabolic state. The approach is also tolerant of sample size variations between different metabolic states.