Kinetics of oxidation and reduction of high-potential iron-sulfur proteins with nonphysiological reactants

We have investigated the kinetic and equilibrium oxidation-reduction properties of HIPIP's from four sources: Chromatium vinosum, Thiocapsa pfennigii, Rhodopseudomonas gelatinosa, and a paracoccus sp. These studies focused on the interaction of the various HIPIP's and the iron hexacyanides as a function of ionic strength, pH, and temperature. On the basis of the kinetic and equilibrium data obtained and the known structrual properties of the various HIPIP's a number of conclusions concerning the mechanism of electron transfer by HIPIP can be inferred. (1) The oxidation and reduction of HIPIP by the iron hexacyanides show no kinetic complexity due to heterogeneity or changes in rate-limiting step. (2) The kinetic and equilibrium studies (oxidation-reduction potential) are in good agreement, although a rapid binding equilibrium between HIPIP and the iron hexacyanides is possible. (3) The kinetics of oxidation and reduction of the various HIPIP's studied do not correlate with their oxidation-reduction potentials. (4) The electrostatic interactions between a particular HIPIP and the iron hexacyanides appear to be influenced by the charge on the iron-sulfur cluster with specific amino acid side chains playing a significant but limited role in the interactions leading to electron transfer. (5) The iron-sulfur cluster charge is apparently distributed on the surface of the HIPIP molecule through a network of hydrogen bonds. (6) On the basis of an analysis of the known primary and tertiary structure of the HIPIP's studied, it is concluded that peptide backbone carbonyls and amino acid side chains for the amino acid sequence positions 46-49, 63-65, 78-82, 31-34, and 16-17 define the interaction site of HIPIP and the iron hexacyanides irrespective of the HIPIP source. This is a structural region at which the iron-sulfur cluster is near to the protein surface and in this respect resembles the active site in mitochondrial cytochrome c.

Primary structure of a high potential, four-iron-sulfur ferredoxin from the photosynthetic bacterium Rhodospirillum tenue

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.

The amino acid sequence of cytochrome c' from the purple sulphur bacterium Chromatium vinosum

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.

Redox potentials of the photosynthetic bacterial cytochromes c2 and the structural bases for variability

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.

Primary structure of a high potential iron sulfur protein from a moderately halophilic denitrifying coccus

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 amino acid sequences of the cytochromes c-555 from two green sulphur bacteria of the genus Chlorobium

Amino acid seauences are proposed for the cytochromes c-555 from Chlorobium thiosulphatophilum and from the Chlorobium limicola component of "Chloropseudomonas ethylica 2K". Each is a sincle polypeptide chain, the former of 86, the latter of 99 residues, and, when aligned so as to give the best match, 47 residues are common to the two sequences. The sequences show some resemblance to those of cytochromes c5 and f. The bacteriochlorophyll a-proteins were also isolated and purified, and their amino acid compositions compared (see the Appendix). There are significant differences in the compositions, but not as great as those found for the cytochromes c-555. The significance of these observations for the taxonomy of the Chlorobiaceae and for the further development of the comparative biochemistry of cytochrome c is discussed. Detailed evidence for the sequences of the cytochromes c-555 has been deposited as Supplementary Publication SUP 50073 (36 pages) 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. (1976) 153, 5.

pH dependence of the oxidation-reduction potential of cytochrome c2

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.

Primary structure determination of two cytochromes c2: close similarity to functionally unrelated mitochondrial cytochrome C

The amino-acid sequences of the cytochromes c2 from the photosynthetic non-sulfur purple bacteria Rhodomicrobium vannielii and Rhodopseudomonas viridis have been determined. Only a single residue deletion (at position 11 in horse cytochrome c) is necessary to align the sequences with those of mitochondrial cytochromes c. The overall sequence similarity between these cytochromes c2 and mitochondrial cytochromes c is closer than that between mitochondrial cytochromes c and the other cytochromes c2 of known sequence, and in the latter multiple insertions and deletions must be postulated before a match can be obtained. Nevertheless, these two cytochromes c2 show no better reactivity with the mitochondrial cytochrome c oxidase than do the less well-matched cytochromes c2. The bearing of these findings on possible evolutionary relationship between mitochondria and prokaryotes is discussed.

Primary structure of a high potential iron-sulfur protein from the purple non-sulfur photosynthetic bacterium Rhodopseudomonas gelatinosa

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.

Amino acid sequence of cytochrome c' from the purple photosynthetic bacterium Rhodospirillum rubrum S1

The amino acid sequence of cytochrome c' from the purple photosynthetic bacterium Rhodospirillum rubrum S1 has been determined and is consistent with homology to cytochrome c' from the nonphotosynthetic bacterium Alcaligenes sp. NCIB 11015. There is 29% identity in the chosen alignment of these two proteins. R. rubrum cytochrome c' is composed of a single peptide chain of 126 amino acid residues with a single heme covalently bound near the COOH terminus. There is no sequence similarity to mitochondrial cytochrome c, except at the heme binding site.

Purification, properties and amino acid sequence of atypical cytochrome c from two protozoa, Euglena gracilis and Crithidia oncopelti

A basic cytochrome was isolated from the phytomastigophorean protozoan Euglena gracilis and a similar protein from the zoomastigophorean protozoan Crithidia oncopelti. In both cases chromatography on CM-cellulose in first the reduced and then the oxidized form proved to be an efficient means of purification. The two cytochromes can be classed in the cytochrome c family but they have certain atypical features. The alpha peak of the absorption spectrum is shifted towards the red and is asymmetrical. The pyridine ferrohaemochrome has an alpha-peak maximum intermediate between that of c-type cytochromes and proteins containing protohaem IX. The test for free vinyl groups was positive. The amino acid sequences of the two cytochromes were determined. Attention is drawn in the text to those parts of the evidence that are less satisfactory. Both sequences are homologous with the family of cytochrome c, but are unusual in having only one cysteine residue so that the haem is attached through only one thioether bond. Detailed evidence for the amino acid dequences of the two proteins has been deposited as Supplementary Publication SUP 50042 (70 pages) at the British Library (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Wetherby, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1975) 145, 5.

On the monohene character of cytochromes c'

Interpretations of data bearing on structures of cytochromes cc'-a class of variant c-type heme proteins from bacteria-in support of a diheme-bearing single chain as a basic structural unit, appear to be invalid in the light of recent studies. These reveal that nearly all members of this class exist as dimers that can be dissociated into, if they do not already exist as, monoheme-bearing monomers. The particular case of the Chromatium protein, held to be the source of a peptic-"core" peptide containing two covalently-bonded heme groups, has been re-examined by preparation of tryptic and chymotryptic peptides derived from the heme-bearing region of the protein, as well as by repetition of experiments on peptic digestion, with more rigorous purification of the resultant peptides than was previously done. It is shown that this protein can also be dissociated into identical subunits, bearing a single heme prosthetic group, and accounting essentially for all its heme content. Thus, the previous terminology-cytochromes cc'-based on supposition of heme group heterogeneity, is inconsistent with these findings and should be replaced by cytochromes c'.