The amino Acid sequence of spinach ferredoxin

Zyxin and cCRP: two interactive LIM domain proteins associated with the cytoskeleton

Interaction with extracellular matrix can trigger a variety of responses by cells including changes in specific gene expression and cell differentiation. The mechanism by which cell surface events are coupled to the transcriptional machinery is not understood, however, proteins localized at sites of cell-substratum contact are likely to function as signal transducers. We have recently purified and characterized a low abundance adhesion plaque protein called zyxin (Crawford, A. W., and M. C. Beckerle. 1991. J. Biol. Chem. 266:5847-5853; Crawford, A. W., J. W. Michelsen, and M. C. Beckerle. 1992. J. Cell Biol. 116:1381-1393). We have now isolated and sequenced zyxin cDNA and we report here that zyxin exhibits an unusual proline-rich NH2-terminus followed by three tandemly arrayed LIM domains. LIM domains have previously been identified in proteins that play important roles in transcriptional regulation and cellular differentiation. LIM domains have been proposed to coordinate metal ions and we have demonstrated by atomic absorption spectroscopy that purified zyxin binds zinc, a result consistent with the idea that zyxin has zinc fingers. In addition, we have discovered that zyxin interacts in vitro with a 23-kD protein that also exhibits LIM domains. Microsequence analysis has revealed that the 23-kD protein (or cCRP) is the chicken homologue of the human cysteine-rich protein (hCRP). By double-label indirect immunofluorescence, we found that zyxin and cCRP are extensively colocalized in chicken embryo fibroblasts, consistent with the idea that they interact in vivo. We conclude that LIM domains are zinc-binding sequences that may be involved in protein-protein interactions. The demonstration that two cytoskeletal proteins, zyxin and cCRP, share a sequence motif with proteins important for transcriptional regulation raises the possibility that zyxin and cCRP are components of a signal transduction pathway that mediates adhesion-stimulated changes in gene expression.

Examination of protein sequence homologies: V. New perspectives on evolution between bacterial and chloroplast-type ferredoxins inferred from sequence evidence

Sequence homologies among 34 chloroplast-type ferredoxins were examined using a computer program that quantitatively evaluates the extent of sequence similarity as a correlation coefficient. The resultant alignment contains six gaps representing insertions or deletions of some residues, all of which are located such that they precisely preserve the domains of structural fragments as determined by crystallographic data on Spirulina platensis ferredoxin. In the search for any total correlation between the chloroplast-type and 27 bacterial ferredoxins, 1891 comparison matrices prepared for possible combinations indicated that the bacterial basal sequence of 55 residues has been conserved evolutionarily in the chloroplast-type sequences corresponding to residue positions 36-90 of Spirulina platensis ferredoxin. In addition, the bacterial "connector sequence" region was found to be conserved. These findings strongly suggest that the bacterial and chloroplast-type ferredoxins descended from a common ancestor, and branched off after the bacterial gene duplication, whereas the chloroplast-type ferredoxins originally were generated by duplicating the already duplicated bacterial gene, i.e., by "double-duplication."

On the specificity of pig adrenal ferredoxin (adrenodoxin) and spinach ferredoxin in electron-transfer reactions

Spinach leaf ferredoxin and ferredoxin:NADP oxidoreductase as well as pig adrenodoxin and adrenodoxin reductase have been purified to homogeneity. Ferredoxin-NADP reductase and adrenodoxin-NADP reductase can perform the same diaphorase reactions (dichloroindophenol, ferricyanide and cytochrome c reduction) albeit not with the same efficiency. Despite the differences in their redox potentials, animal and plant ferredoxins can be used as heterologous substrates by the ferredoxin-NADP reductases from both sources. In heterologous systems, however, the ferredoxin/adrenodoxin concentrations must be increased approximately 100-fold in order to reach rates similar to those obtained in homologous systems. Ferredoxin and adrenodoxin can form complexes with the heterologous reductases as demonstrated by binding experiments on ferredoxin-Sepharose or ferredoxin-NADP-reductase-Sepharose and by the realization of difference spectra. Adrenodoxin also weakly substitutes for ferredoxin in NADP photoreduction, and can be used as an electron carrier in the light activation of the chloroplastic enzyme NADP-dependent malate dehydrogenase. In addition adrenodoxin is a good catalyst of pseudocyclic photophosphorylation, but not of cyclic phosphorylation and can serve as a substrate of glutamate synthase. These results are discussed with respect to the known structures of plant and animals ferredoxins and their respective reductases.

Purification, properties and complete amino acid sequence of the ferredoxin from a green alga, Chlamydomonas reinhardtii

The ferredoxin was purified from the green alga, Chlamydomonas reinhardtii. The protein showed typical absorption and circular dichroism spectra of a [2Fe-2S] ferredoxin. When compared with spinach ferredoxin, the C. reinhardtii protein was less effective in the catalysis of NADP+ photoreduction, but its activity was higher in the light activation of C. reinhardtii malate dehydrogenase (NADP). The complete amino acid sequence was determined by automated Edman degradation of the whole protein and of peptides obtained by trypsin and chymotrypsin digestions and by CNBr cleavage. The protein consists of 94 residues, with Tyr at both NH2 and COOH termini. The positions of the four cysteines binding the two iron atoms are similar to those found in other [2Fe-2S] ferredoxins. The primary structure of C. reinhardtii ferredoxin showed a great homology (about 80%) with ferredoxins from two other green algae.

Amino acid sequence of [2Fe-2S] ferredoxin from Clostridium pasteurianum

The complete amino acid sequence of the [2Fe-2S] ferredoxin from the saccharolytic anaerobe Clostridium pasteurianum has been determined by automated Edman degradation of the whole protein and of peptides obtained by tryptic and by staphylococcal protease digestion. The polypeptide chain consists of 102 amino acids, including 5 cysteine residues in positions 11, 14, 24, 56, and 60. The sequence has been analyzed for hydrophilicity and for secondary structure predictions. In its native state the protein is a dimer, each subunit containing one [2Fe-2S] cluster, and it has a molecular weight of 23,174, including the four iron and inorganic sulfur atoms. The extinction coefficient of the native protein is 19,400 M-1 cm-1 at 463 nm. The positions of the cysteine residues, four of which are most probably the ligands of the [2Fe-2S] cluster, on the polypeptide chain of this protein are very different from those found in other [2Fe-2S] proteins, and in other ferredoxins in general. In addition, whole sequence comparisons of the [2Fe-2S] ferredoxin from C. pasteurianum with a number of other ferredoxins did not reveal any significant homologies. The likely occurrence of several phylogenetically unrelated ferredoxin families is discussed in the light of these observations.

Universal regularities in protein primary structure: preference in bonding and periodicity

Utilizing the whole protein data base as well as parts of it (groups and individual representatives), the universal character of the regularities in protein primary structure - preference in bonding (self-ordering) and periodicity - is shown by means of an improved procedure of checking statistical significance. In the vast majority of the cases there is a preference in bonding with the same or with very similar amino acid. Taken as a whole, both regularities show a universal character. The results obtained provide evidence in favour of the conception about the priority of proteins as information polymers.

Molecular interpretation of kinetic-ionic strength effects

A recent and important approach to investigating electron transfer mechanisms of redox proteins has been through kinetic-ionic strength studies. There is, however, significant controversy as to whether such studies (1) yield information regarding the charge (or location) of the electron transfer site or (2) more simply reflect the influence of net or overall protein charge on the electrostatic interactions. A critical analysis using different theoretical approaches is made of our recent work and of the bulk of the published non-physiological small molecule-protein and protein-protein kinetic ionic strength studies; it is concluded that (1) the approximated Bronsted-Debye-Huckel equation can not be used at all for protein redox reactions, (2) irrespective of the theoretical approaches discussed, such studies do not provide information regarding the charge of the electron transfer site, (3) it is the net charge of the reactants that control the electrostatic interactions, (4) both the equation derived by Wherland and Gray and the full Bronsted-Debye-Huckel equation provide reasonably good approximations of net protein charge, (5) pH changes quantitatively modulate net protein charge, and (6) thus, protein redox rates need to be electrostatically corrected if relevant interpretations of kinetic-ionic strength experiments are to be made.

Some evidence for the universality of structural periodicity in proteins

A new simple and sensitive method for detecting small periodicity (repetition of a small segment along the chain) in proteins is developed, based on the repetition of identical residues. 38 proteins from organisms representing different levels of evolutionary development have been tested for small periodicity. The same is done with the nodal ancestors of 25 of them. The results are presented graphically (the periodicity curves). The statistical significance of the observed periodicity is confirmed by a modified version of the chi-square test. All the results obtained support the conception that the small periodicity of the contemporary proteins is a reflection of their evolutionary history and that the most ancient proteins have arisen through a polycondensation of short peptides or through transcription and translation of satellite-type repeat sequence DNA.

Complex-forming properties of spinach NADP+ reductase with ferredoxin, ferrocyanide and NADP+

The flavoprotein NADP+ reductase from spinach chloroplasts may form a ternary complex with one molecule of NADP+ and one molecule of ferredoxin. Spectroscopic titration studies show that the NADP+ binding site and the ferredoxin binding site are totally independent, that is previous binding of ferredoxin does not modify binding of NADP+, and conversely. Since NADP+ reductase conditions the diaphorase reaction, that is an electron transfer between NADPH and various acceptors such as ferricyanide, the binding of ferrocyanide and its possible interaction with NADP+ and ferredoxin has been studied. Ferrocyanide behaves as a competitive inhibitor with respect to both NADP+ and ferredoxin. This seems paradoxical since NADP+ and ferredoxin are independently bound at two different non-overlapping sites of the flavoprotein. This apparent paradox may be resolved by a theoretical analysis of the interactions between either ferrocyanide and NADP+, or ferrocyanide and ferredoxin. Theory shows that if ferrocyanide is non-specifically bound at two independent sites, namely the NADP+ and the ferredoxin binding sites, it appears competitive with respect to both NADP+ and ferredoxin, although ternary flavoprotein-ferredoxin-ferrocyanide and flavoprotein-NADP+-ferrocyanide complexes are formed. The binding constants of NADP+, ferredoxin and ferrocyanide for the enzyme have been determined. These results are discussed in connection with the possible mechanism of the diaphorase reaction.

Structural and evolution of chloroplast- and bacterial-type ferredoxins

Comparisons have been made between amino acid sequences of 26 chloroplast-type ferredoxins and 16 bacterial-type ferredoxins. Their structural characteristics are described and related to a three-dimensional structure of a chloroplast-type ferredoxin. Aspects of molecular evolution of these ferredoxins are presented together with a phylogenetic tree including both chloroplast- and bacterial-type ferredoxins.

The amino acid sequence of cytochrome c from the locust, Schistocerca gregaria Forskal

The amino acid sequence of locust cytochrome c was determined, although the overlap between chymotryptic and tryptic peptides at residues tyrosine-97 and leucine-98 was not observed, owing to an anomalous tryptic break duplicating the chymotryptic digestion. The molecule consists of a single polypeptide chain of 107 residues, homologous with other mitochondrial cytochromes c. In common with other known insect cytochromes c, it possesses a non-acetylated, four-residue tail at the N-terminus relative to glycine-1 of the standard alignment. A molecular phylogeny for 17 species was constructed relating the cytochrome c molecules of Schistocerca gregaria and other invertebrates with those of representative taxonomic groups. Experimental details are given in a supplementary paper deposited as Supplementary Publication SUP 50077 (24 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can obtained on the terms indicated in Biochem. J. (1977) 161, 1.

Structure and function of chloroplast-type ferredoxins

Comparison of various chloroplast-type ferredoxin sequences, chemical and enzymic modifications, reconstitution experiments, and fluorescence measurement of chloroplast-type ferredoxins have led to the following conclusions. 1. Tyrosine, histidine, and tryptophan residues are not directly involved in the oxidation-reduction mechanism of ferredoxins. The four indispensible cysteine residues in spinach ferredoxin which constitutes a part of the iron-sulfur cluster are located at residues 39, 44. 47 and 77. Two out of six cysteine residues in Spirulina ferredoxin could be easily modified with vinylpyridine without the loss of reconstitutive ability i.e. the apoferredoxin could be converted to the holoform by the addition of iron and sulfide. 2. Spinach ferredoxin was digested with carboxypeptidase A and the terminal alanine could be removed without loss of the spectral properties of native ferredoxin. However, the removal of the terminal three residues gave rise to the loss of reconstitutive ability. 3. The amino groups of spinach ferredoxin were modified by acetic anhydride and four residues were acetylated. The acetylated preparation of ferredoxin had an unique spectrum. Upon the addition of high concentration of ions the spectrum of this derivative resembled the spectrum of native ferredoxin. Acetylferredoxin did not combine with ferredoxin-NADP reductase, but upon the addition of moderate concentrations of cations, it did bind to this enzyme.

Linear and inverted repetitions in protein sequences

An extensive search for internal regularities in amino acid sequences has been made, using both the genetic code and the relative frequencies of amino acid alternatives in homologous proteins. The two methods give very similar results and strongly suggest the occurrence of significant linear and inverted repetitions (similar sequences of opposite polarity) in several proteins. A hypothesis is developed to explain the occurrence of such internal regularities in proteins. This hypothesis is based on a process of duplication of an ancestral loop in which a symmetrical arrangement of amino acid allows stabilization by interaction between the amino acid side chains.

Phylogenies from amino acid sequences aligned with gaps: the problem of gap weighting

The common but generally overlooked problem of how best to construct phylogenies from orthologous amino acid sequences, when their alignment requires the placement therein of gaps denoting insertions/deletions in the evolutionary history of their genes since their common ancestor, has been studied. Three diverse methods were examined: 1. each missing residue in a gap is weighted as equivalent to the average number of minimum nucleotide replacements in known conjugate amino acid pairs of those same two sequences, which weight necessarily differs for each pair of sequences; 2. each missing residue in a gap is weighted as equivalent to a fixed number of nucleotide replacements; and 3. each gap, regardless of length, is weighted as equivalent to a fixed number of nucleotide replacements. For the flavodoxins, each method yielded a different best tree and suggests that the choice of method may be crucial. For the plant ferredoxins, all methods give results inconsistent with botanical classification and suggests the sequences may not all be orthologous. For the bacterial ferredoxins, the method was less germane than the actual weight used, five different best trees being obtained depending upon the weight. The best tree for all ferredoxins (prokaryotic plus eukaryotic) combined proved to be greatly dependent upon the gap locations with several reasonable aligments yielding different best trees. They also suggest that functional equivalence may well prove to be a poor guide to which residues have a common ancestral codon. The rubredoxin sequences show that a partial internal gene duplication occurred in the Pseudomonas line, probably very soon after its divergence from the other genera. Together, the results clearly indicate that the phylogenetic answer one gets may greatly depend upon how one treats the gaps but they fail to indicate what treatment may be best.

Proton magnetic resonance studies of the ferredoxins from spinach and parsley

Contact-shifted resonances have been detected in the pmr spectra of both oxidized and reduced forms of spinach and parsley ferredoxins. These resonances are assigned to the beta-CH(2) protons of four cysteine residues that are thought to bind the iron-sulfur redox center to the polypeptide chain. Temperature dependences of contact shifts reveal that the two iron atoms are antiferromagnetically coupled in both redox forms of each of these proteins. Thermal population of magnetic states gives rise to the contact shifts observed in the formally diamagnetic oxidized forms of these ferredoxins and accounts for the failure of contact shifts in the reduced forms exhibit to a Curie Law temperature dependence. It appears that the unpaired electron of reduced spinach and parsley ferredoxin is unequally distributed over the two iron centers. Valence states for the iron pairs of high-spin Fe(+3)-Fe(+3) and Fe(+2)-Fe(+3) for the oxidized and reduced forms, respectively, are compatible with the nmr results.