Biomedical subjects
Publications and source records attributed to M D Kamen.
A brief description of the informal workshop on non-mitochondrial cytochromes c is given. The organization of the meeting, the personnel participating and the scope of research effort are discussed. A brief historical account is included to place the Symposium reports in context.
The Order Euglenida comprises many species and perhaps 40 genera, but almost all biochemical and genetic studies have been limited to a single species. Euglena gracilis, because of its ease of growth in the laboratory. Sequence studies of chloroplast and mitochondrial proteins from E. gracilis show that they have diverged widely from other eukaryotic lines. In the present paper we report the sequences of three proteins from another euglenoid, Euglena viridis, using material isolated from a natural bloom. The mitochondrial cytochrome c shows more than 90% sequence identity with that from E. gracilis, and contains the same characteristic features. The chloroplast cytochrome c6 has diverged to a greater extent and shows only 77% identity. The chloroplast ferredoxin from E. viridis is similar in sequence to those of cyanobacteria and algal chloroplasts, with sequence identities of up to 75%. Details of the purification, analysis and sequence determination experiments on the peptides have been deposited as Supplementary Publication SUP 50163 (32 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.
The effect of chelation on rate or air inactivation of hydrogenase from Clostridium pasteurianum has been investigated. All chelating agents used, whether water-soluble or water-insoluble, afforded protection against oxygen inactivation. EDTA appeared to be the most effective. Thus, in the absence of EDTA, hydrogenase in aqueous solution was nearly totally inactivated after 1 hour incubation in air, whereas 0.5 M EDTA (which did not affect significantly catalytic activity) allowed 41% retention of the initial activity even after 3 days incubation.
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The amino acid sequence of a high oxidation-reduction potential iron-sulfur protein (HiPIP) isolated from the purple photosynthetic bacterium Rhodospirillum tenue has been determined. This is the smallest of the HiPIP's, containing 63 residues, with only 3 residues apparently conserved in addition to the 4 cluster-binding cysteines. A minimum of four internal genetic gaps is postulated to align tenue high potential iron-sulfur protein with the previously known proteins. It is the most divergent of its class, with an average of only 25% identically matching residues in common with any of the other species.
An amino acid sequence is proposed for the cytochrome c' from the photosynthetic purple sulphur bacterium Chromatium vinosum strain D. It is single polypeptide chain of 131 residues, with haem-attachment cysteine residues at positions 121 and 124. The results discredit an earlier report [Dus, Bartsch & Kamen (1962) J. Biol. Chem 237, 3083--3093] of a di-haem peptide sequence from this protein. The sequence belongs to the same class as the published Alcaligenes and Rhodospirillum rubrum cytochrome c' squences, but the resemblance is not close. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50,093 (15 pp.) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1978) 169, 5.
The cytochromes c2 of the Rhodospirillaceae show a much greater variation in redox potential and its pH dependence than the mitochondrial cytochromes c that have been studied. It is proposed that the range of redox potential for cytochromes c2 functioning as the immediate electron donor to photo-oxidised bacteriochlorophyll may be 345-395 mV at pH 5. Closely related cytochromes c2 with different redox potentials show patterns of amino acid substitution which are consistent with changes in hydrophobicity near the haem being at least a partial determinant of redox potential. More distantly related cytochromes are difficult to compare because of the large number of amino acid substitutions and the probability that there are subtle changes in overall peptide chain folding. The redox potential versus pH curves can be analysed in terms of either one ionisation in the oxidised form or two in the oxidised form and one in the reduced. The pK in the oxidised form at higher pH values can be correlated with the pK for the disappearance or shift of the near infrared absorption band located near 695 nm. The structural bases of these ionisations are not known but the possible involvement of the haem propionate residues is discussed.
Kinetic studies of the reactions of selected eukaryotic and prokaryotic cytochromes c with mitochondrial cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase (EC 1.9.3.1) using a standardized complex IV preparation from beef heart are reported. Data on reactions with NADH-linked cytochrome c reductase (complexes I and III) are included. The concentration ranges employed provide a basis for quantitative demonstration of a general rate law applicable to oxidase reactions of cytochrome c of greatly differing reactivities. Results are interpreted on the basis of a modified Minnaert mechanism (Minnaert, K. (1961) Biochim. Biophys. Acta 50, 23), assuming productive complex formation between cytochrome c and free oxidase in addition to further complex binding of a second cytochrome c molecule to the initially formed oxidase complex. Kinetic constants so obtained are consistent with the assumption that binding is the dominant parameter in reactivity, and can be rationalized most simply on this basis.
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A general procedure for stabilization of O2-labile enzymes exploiting "salting out" of oxygen from the microenvironment in the molecular layers immediately adjacent to charged surfaces of polyionic solid adsorbents has been developed. Empirical verification of this rationale is provided. The half-life of air inactivation of the O2-labile hydrogenase (EC 1.12.7.1) from Clostridium pasteurianum is increased 20- to 25-fold simply by adsorption (noncovalent binding) in dilute Tris.HCl buffer on common anion exchange supports such as DEAE-cellulose or Dowex 1-X2. Predicted increases in degree of stabilization by using more densely charged adsorbents (such as polyethyleneimine-cellulose), as well as bulkier solvent counter-anions, are found; half-lives for air inactivation for the bound hydrogenase can be increased to 3000-fold longer than that of the free enzyme. Most of the total catalytic activity, assayed as H2 evolution from dithionite mediated by methyl viologen or ferredoxin, is retained, whereas the expected suppression of H2 uptake in the reverse reaction is observed.
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The occurrence of a specific high potential iron-sulfur protein in a halophilic, denitrifying coccus provisionally assigned to the genus Paracoccus has been confirmed through primary structure determination. This protein, known as "HiPIP", has been found previously only in photosynthetic bacteria. The sequence of this 71-residue protein is as similar to the HiPEPs from photosynthetic bacteria as they, in turn, are to one another (average number of identically matching residues is 38%). Paracoccus HiPIP is a highly acidic protein in accord with general observations on the proteins of halophilic bacteria. A possible explanation for its occurrence in Paracoccus is that gene transfer is involved.
The near-infrared magnetic circular dichroism (MCD) of Rhodospirillum rubrum, Chromatium vinosum, and Rhodopseudomonas palustris cytochromes c' are reported. The spectra of the reduced protein are very similar to those of deoxymyoglobin. The spectra of the oxidized proteins in the pD range 1-13 can be analyzed on the basis of four species A, B, C, and D. The existence of nine species, reported in a recent electron paramagnetic resonance study, is not substantiated. The MCD spectra support the assignment of B as high spin and C and D as low spin. The MCD of species A is close to that of high-spin proteins and does not support the recently proposed assignment of a mixed high- and intermediate-spin ground state for this species. The energies of the near-IR electronic transitions of all four oxidized species point to axial ligation via oxygen, assuming histidine to be the opposite axial ligand. Unfortunately, insufficient model compounds with ligation by carboxyl or hydroxyl moieties exist to enable more precise assignments.
Previous reports of a relatively air-stable soluble hydrogenase from the photosynthetic anaerobe, Chromatium vinosum, have been substantiated. The properties of this enzyme, as seen in highly purified samples prepared by procedures that permit improved yields, are described. A possible role for flavin mediation is noted.
The pH dependence of the spectra and of the oxidation-reduction potential of three cytochromes c2, from Rhodopseudomonas capsulata, Rhodopseudomonas sphaeroides and Rhodomicrobium vannielii, were studied. A single alkaline pK was observed for the spectral changes in all three ferricytochromes. In Rps. capsulata cytochrome c2 this spectroscopic pK corresponds to the pK observed in the dependence of oxidation-reduction potential on pH. For the other two cytochromes the oxidation-reduction potential showed a complex dependency on pH which can be fitted to theoretical curves involving three ionizations. The third ionization corresponds to the ionization observed in the spectroscopic studies but the first two occur without changes in the visible spectra. The possible structural bases for these ionizations are discussed.
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The third amino acid sequence of a high potential iron-sulfur protein, that of the non-sulfur purple photosynthetic bacterium Rhodopseudomonas gelatinosa, has been determined. It consists of a single polypeptide chain of 74 amino acid residues, which is slightly smaller than the high potential iron-sulfur proteins from the sulfur purple bacteria Chromatium vinosum (85 residues) and Thiocapsa pfennigii (81 residues). The sequence of the gelatinosa protein is similar to the C. vinosum and T. pfennigii proteins with 38% and 37% identically matching residues, although six gaps are proposed for the comparison (the C. vinosum and T. pfennigii proteins have 44% identically matching residues out of 73 positions compared with only one 4-residue gap). Only 17 redisues, including the 4 cystein residues essential for binding the four-iron-sulfur chromophore, are invariant in the three known sequences. A discussion of the role of conserved residues in maintenance of the three-dimensional structure and in electron transport is presented.