Unit Cys - Etat de Nature (Vinyl, LP, Album)

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EDIT: The migration is complete. Please report any problem you encounter to me. Since we first started to allow digital-only artists on MA over five years ago, the staff has tried to abide by a number of guidelines that were designed to prevent the Archives from getting flooded with fleeting online projects that never put out any substantial releases.

These guidelines were used because while the physical release rule has long served us well as a measuring stick of eligible bands, simply extending the general criteria of this approach to digital work comes with a number of issues; issues mainly stemming from the potentially ephemeral nature of internet releases and the relative ease of putting together an album compromising the original intent behind the physical release rule. Out of the digital release guidelines, the most visible is almost definitely the length requirement.

Their subunit 2 is intact, apart from a or residue extension of the C-terminus. While this extension is similar within members of the group, it differs substantially from that of other groups. The archaebacteria-type ferredoxins have a conserved central domain in each subunit, but further modifications are observed in regions before or after this domain, such as an extension of the N-terminus, or an insertion before the linker.

The single [4Fe-4S] group has both domains, but the conserved motif in subunit II is disrupted due to replacement of two to four of the cysteines with other nonligating residues.

Members of this group cannot be grouped further due to differences in their sequence and structure. Chemical modification studies showed that neither the N- nor C-terminal Fe—S binding motif can form a stable cluster in 2[4Fe—4S] proteins, but their combination will result in formation of a stable cluster.

The [3Fe—4S] cluster can be thought of as a cubane [4Fe—4S] cluster missing one of the irons. This class is found exclusively in bacteria, mainly anaerobic bacteria, and is involved in anaerobic metabolism. The [3Fe—4S] clusters can emerge from oxidative damage of [4Fe—4S] clusters, as in the case of aconitase, or treatment of 4Fe clusters with potassium ferricyanide or can be found as intrinsic constituents of natural proteins, such as mitochondrial complex II and nitrate reductase.

In all cases, the true reason for the presence of such clusters is not yet completely understood. It has been shown that [3Fe—4S] and [4Fe—4S] clusters can be interconverted under certain physiological conditions and the exchange between 3Fe and 4Fe can be used as a regulatory mechanism. Another common motif, Cys- Xxx 7 -Cys, is found in [3Fe-4S] cluster of 7Fe-containing proteins, some of which are thermostable and air-stable.

Another Cys following this motif serves as the third ligand to the cluster. There are examples of Asp residues and hydroxyl groups from the solvent as ligands. H-bonds play an important role in stabilizing the reduced state.

The number of these bonds is related to the extent of solvent accessibility of iron, but there are on average six such interactions that direct protons to the site. The structure has a partial 2-fold symmetry that is disrupted at the N-terminus by differences in Cys ligands to the [3Fe—4S] cluster. There are two nonligand Cys residues next to each cluster.

Although the clusters are positioned close to the surface, the presence of hydrophobic and aromatic residues protects them from the solvent. However, the protein matrix distorts the [3Fe—4S] cluster, while the [4Fe—4S] cluster is more symmetric.

Conserved hydrophobic residues are shown to be important for the stability of the protein but not for ET. In Clostridium , reduction of ferredoxin is coupled to pyruvate oxidation. The hydrogenase complex further oxidizes the reduced ferredoxin. They can bridge excitation of chlorophyll by light to reduction of NAD. Conversion of formate to CO 2 is often ferredoxin-coupled.

The role of [3Fe—4S] clusters is less well-known. It has been reported that they can act in sulfite reduction. A role as iron storage has also been proposed.

The [3Fe—4S] clusters have been observed in the monooxygenase system of Streptomyces griseolus. The 2[4Fe—4S] clusters are mainly found in anaerobic bacteria and Clostridium species. However, there are multiple reports of their occurrence in other organisms such as Micrococcus lactolyticus , Peptostreptococcus esldenii , Methanobacillus omelianski , certain photosynthetic bacteria such as Ch.

Clostridial-type ferredoxins are usually assayed using their ability to reduce NADP either in an NADP:ferredoxin reductase system or in a phosphoroclastic system. Coupling H 2 oxidation to the reduction of an organic dye is another assay used to monitor the concentration and activity of ferredoxins. Usually the greater the difference between the reduction potentials of two clusters, the lower the ET rate between the two. Mutational analyses of conserved residues that are thought to be important in the intramolecular ET showed no significant decrease, but less stability.

It was postulated that the geometry and relative orientation of the two clusters are the factors important in determining this rate. A role for amide dipoles has also been suggested. A major part of reduction potential analyses of these types of ferredoxins deal with roots of differences between them and HiPIPs.

These types of studies are discussed in detail in the section on HiPIPs section 3. Peptide models of [4Fe—4S] proteins showed that the reduction potential of the center is dependent on the number of Cys residues in the oligomer and will stabilize higher oxidation states, hence decreasing the reduction potential, with increasing cysteines.

The reduction potential of the [3Fe—4S] cluster is pH-dependent. The pH dependence is related to proton transfer via the conserved Asp next to the cluster. Other studies show a less significant role for the conserved Asp, suggesting protonation of the cluster itself as the main cause of the pH-dependent behavior.

Moreover, there are around 15 partial positive charges in ferredoxins that result in an overall positive environment of the cluster, which is suggested to be a reason for the lower reduction potential of these ferredoxins compared to their higher reduction potential counterparts, HiPIPs.

Introduction of a His near the cluster of a 7Fe protein caused a — mV increase in the reduction potential. The reduction potential of this variant was pH-dependent.

At pH values where the His was protonated, this large increase in reduction potential was attributed to placement of a positive charge next to the cluster. A dipole moment directed toward the cluster was proposed as the main cause of increased reduction potential when the His was neutral. Mutations of conserved Pro in Cp Fd resulted in changes of the reduction potentials of the two clusters. Solvent accessibility and cluster solvation also play important roles in determining the reduction potential of these clusters.

More buried clusters have higher reduction potentials. The protein dipole Langevine dipole PDLD model was used to analyze the important features of the reduction potential. On the basis of these calculations, the number and orientation of amide dipoles, and not necessarily their involvement in H-bonding, are the most important factor sin defining the reduction potential.

Addition of more amide dipoles by site-directed mutagenesis indeed resulted in a more positive reduction potential in cases where the backbone conformation did not change drastically. It seems that different factors have different degrees of importance in different proteins. While surface charges seem not to be important in Cp Fd, they showed significant effects on the reduction potential in other proteins. Although it seems that the cluster with classical geometry should be the one with a normal reduction potential, thorough mutational and electrochemical studies on this protein proved it to be the other way.

Proteins with more than one cluster are usually brown in color, with a broad absorption in the — nm region. Therefore, the temperature dependence of the EPR signal can be used as a guide to the cluster type. However, care should be taken in analysis of the signals, because spin—spin interactions between clusters can lead to an enhanced relaxation time.

A higher number of total hyperfine shifted resonances in NMR can indicate the presence of more than one cluster in a given protein. Nine or twelve contact shifts are usually observed for [3Fe—4S] or [4Fe—4S] clusters, respectively.

The [4Fe—4S] clusters are identified by the presence of peaks with anti-Curie temperature dependence, while Curie-type behavior is indicative of a [3Fe—4S] cluster. Typical 7Fe ferredoxins show five downfield peaks, two with Curie-temperature-dependent behavior. There are, however, 7Fe proteins with quite different NMR spectra and more downfield peaks.

These 7Fe proteins usually have a short symmetric motif. A peak at Also, the effects of disulfide bonds in the shifts were studied. Upon reduction, a similar pattern is observed for all [4Fe—4S] proteins, with two Cys residues showing Curie-like behavior Fe 2.

This also suggests that there are two isoforms with an Fe 2. The former is more preferred, and this preference is stronger when a disulfide bond is present, as shown by NMR studies.

NMR was also used to analyze the self-exchange rate and hence reorganization energy in ferredoxins. Resonance Raman was also used to study Se complexes of ferredoxins as well as the presence of [3Fe—3S] clusters.

A class of so-called plant ferredoxin-like proteins PLFPs has been discovered in the past few years. These proteins are known to play a role in several cellular processes. The first PFLP was discovered in sweet pepper. Phosphorylation of this domain is postulated to be important in resistance to pathogens in Arabidopsis thaliana , and PLFPs are evolved in plant defense mechanism pathways.

The ferredoxin-like protein in Rhizobium meliloti is shown to be important in nitrogen fixation. The protein is located in an operon with nif genes. Mutational analyses and molecular modeling showed the importance of extra amino acids in positioning the loop in a way that it could incorporate the cluster efficiently. This ferredoxin has similarity to plant ferredoxins with no significant similarity to bacterial ferredoxins.

Transgenic expression of PFLP from sweet pepper in calla lily resulted in more resistance to soft rot bacterial diseases. Rieske proteins are [2Fe—2S] iron—sulfur proteins that are distinguished by their unique His 2 -Cys 2 ligation motif.

Similar EPR signals were later observed in the b 6 f complex of the photosynthetic chain, the membrane of bacteria with a hydroquinone oxidizing ET chain, and soluble bacterial dioxygenases. The presence of these isoforms most likely aids the organism to adapt better to environmental changes.

The first Rieske protein to be sequenced was the Rieske protein from the bc 1 complex of Neurospora crassa. Rieske proteins can be found in bc complexes such as the bc 1 complex of mitochondria and bacteria, the b 6 f complex of chloroplast, and corresponding subunits in menaquinone oxidizing bacteria.

Three residues other than Fe—S ligands are also conserved in this class of Rieske proteins, two of which are cysteine residues that form a disulfide bond important in the stability of the protein, and the other is a Gly in a conserved Cys-Xxx-His-Xxx-Gly-Cys- Xxx 12—44 -Cys-Xxx-Cys-His motif. Mutational analysis of this class confirmed the presence of two histidines and four cysteines essential for cluster formation. Some of these proteins are within complexes that are not well identified, and some belong to organisms that are devoid of the bc complex, such as TRP from T.

Rieske-type proteins are typically part of water-soluble dioxygenases. This class of proteins can be further divided into four separate groups. They have diverse sequences, but their three-dimensional structures are very similar to those of other Rieske proteins. Bacterial Rieske-type oxygenases have a Rieske center and a mononuclear nonheme iron in their active site. In addition to four Rieske ligands, four other residues are conserved in these proteins, including two glycine residues, one tryptophan, and one arginine.

Naphthalene dioxygenase NDO is the archetype of this class. Eukaryotic homologues of bacterial Rieske-type oxygenases also have a ligand set for Rieske coordination and a site for mononuclear nonheme iron. Choline monooxygenase and CMP- N -acetylneuraminic acid hydroxylase are examples of this class.

Lastly, there are proteins that have a putative Rieske binding site , with a common motif of Cys-Pro-His- Xxx 16 -Cys-Pro-Xxx-His, but the presence of a Rieske cluster has not been confirmed in them yet. Crystal structures of several Rieske proteins from different categories have been solved. Sheet 1 consists of three conserved strands, 1, 10, and 9. Strands 2, 3, and 4 form sheet 2, and strands 5—8 are in sheet 3.

Sheet 2 is longer and interacts with both sheets 1 and 3. The interactions between sheets 2 and 1 are mostly of hydrophobic nature. In mitochondrial and chloroplast Rieske proteins, there is a disulfide bridge that connects the loops in Rieske proteins.

This disulfide bond is of prominent importance in maintaining structural integrity in these proteins because their loops are exposed to solvent. Rieske-type proteins do not have this conserved disulfide bridge.

It has been argued that this difference is due to the fact that buried Rieske complexes are stable without the need to disulfide bond. In buried Rieske complexes such as NDO, the histidines are not solvent-exposed and usually form H-bonds with acidic side chains in the active site.

In contrast to the Cys ligands which impart a tetrahedral geometry, the His ligands accommodate a geometry that is closer to octahedral Figure Multiple H-bonds constrain and stabilize the cysteine ligands, which are conserved between most bc 1 and b 6 f Rieske proteins. They are three bonds with sulfur S1, two with sulfur S2, two with S y of cysteine in loop 1, and 1 with S y of loop 2.

These H-bonds are known to stabilize type I turns. Rieske-type proteins lack three of these conserved H-bonds due to a lack of the conserved Ser and Tyr. Multiple site-directed mutagenesis studies confirmed the importance of these two H-bonds in maintaining the high reduction potential of Rieske proteins. Despite the high degree of structural similarity between different Rieske and Rieske-type proteins, each category has its unique features.

It seems that although the cluster-binding site and the minimal Rieske fold are highly conserved among all classes of Rieske and Rieske-type proteins, there are multiple insertions between elements of this minimal fold, mainly in loop regions. These significant differences make sequence alignments of Rieske proteins controversial, compared to their ribosomal RNA alignments. Rieske proteins from the b 6 f complex usually have a C-terminal extension that is known to be important in stabilizing the open conformation required for the activity.

The same role was proposed for helix—loop insertion in mitochondrial Rieske proteins. The peptide bond orientation differs in the Pro loop of bc 1 and b 6 f complexes in regard to the cis or trans configuration. These differences are required for interactions with different redox partners. Different charge distribution also reflects the variation of pH in which the proteins work, as exemplified by a net negative charge on the surface of some acidophilic proteins. The Rieske fold and the geometry of the cluster are unique to Rieske and Rieske-type proteins and differ significantly from those of the other class of [2Fe—2S] ferredoxins.

The most similar geometries are those of rubredoxins and the zinc-ribbon domain, suggesting that the Rieske fold may have arisen from a mononuclear ancestral fold. For proper function of this cycle, the hydroquinone oxidation reaction is strictly coupled. The Rieske protein is responsible for hydroquinone oxidation and acts as the first electron acceptor. Electron transfer is accomplished by direct interaction between the exposed His ligand and the quinone substrate.

Rieske-type clusters are part of aromatic ring hydroxylating dioxygenase enzymes that catalyze the conversion of aromatic compounds to cis -arenediols, a key step in aerobic degradation of aromatic compounds.

The reductase part can be of two types: ferredoxin—NADP or glutathione. The oxygenase part contains a Rieske center and a mononuclear nonheme iron center Figure The Rieske center transfers an electron from ferredoxin or reductase to the iron center.

In most cases the His ligand of the Rieske center and one of the His ligands of iron are bridged by an Asp residue, ensuring the rapid ET between the two centers Figure The removal of this conserved Asp abolishes the activity without changing the metalation. This repositioning will cause a conformational change that results in generation of a 6-coordinated iron geometry which is more active.

Mutational studies have been implemented to discover sites that are important in specific interactions between these Rieske centers and their redox partners. As with any other ET centers, the reduction potential of Rieske centers is one of the most important factors in determining its ET rate and conveying its activity. In general, any factor that selectively stabilizes either the reduced or oxidized state of a Rieske center will influence its reduction potential.

Different H-bonds to bridging or terminal sulfurs and solvent exposure of the clusters are the main determinants of different reduction potentials within the Rieske family. The reduction potential range differs depending on the type of Rieske complex: — mV in the bc 1 complex and around mV in the b 6 f complex.

The reduction potentials of menahydroquinone oxidizing complexes are mV lower than that of the ubihydroquinone bc 1 complex the same difference that is observed between the two types of quinones.

Different methods of reduction potential measurement have been applied to Rieske proteins, such as chemical redox titration monitored by EPR or CD and direct cyclic voltammetry, , which enables measurement of thermodynamic parameters. Computational studies showed that the cluster distortions caused by the protein environment play a prominent role in tuning the reduction potential of the center.

Accordingly, using active site structures determined from x-ray crystallography will result in calculations that agree much better with experimental values than idealized structures. An interesting feature of Rieske proteins is their pH-dependent reduction potential, which decreases with increasing pH and is attributed to deprotonation of a group in contact with the Rieske complex. This pH dependence can be important in interactions and binding of Rieske proteins to their redox partners.

Moreover, this redox-dependent ionization may be very important for their physiological function, as these proteins are part of proton-coupled ET systems. The biomimetic models of Rieske clusters prove the dependence of the reduction potential of the center on the protonation state of its His ligands. Addition of this ligand caused reduction of the cluster as well as an increase in the overall reduction potential, a phenomenon that was observed in the case of inhibitors such as stigmatellin, immobilizing it in the b conformation.

Moreover, if the protein was reduced first, no addition would be observed, due to a lack of available deprotonated His. The higher reduction potential in this Rieske-type protein has been attributed to the presence of amino acid substitutions in positions around the metal center. The most important residues involved in the H-bonding network in Rieske proteins are a conserved serine and a conserved tyrosine.

It has been suggested that this H-bond network stabilizes the reduced state by charge delocalization, thereby increasing the reduction potential. In one study, removal of negatively charged residues in the vicinity of the Rieske center in Rieske ferredoxin from biphenyl dioxygenase of Burkholderia sp.

Mutational analyses have been extensively used to reveal features that are important in tuning the reduction potential. GlyAsp, ProLeu, and ProLeu mutations in the Pro loop resulted in a shift of about 50— mV toward more negative reduction potentials, mostly due to distortion in the Fe—S environment and changes in the H-bond network around it.

Another study showed that mutations in the loop containing Fe-S ligands are the ones that alter reduction potential. Several site-directed mutations were made with the goal of understanding the role of H-bonds from conserved Ser and Tyr in different organisms.

It was shown that these mutations do not influence the stability of the cluster or its interaction with quinone. However, the activity was decreased, demonstrating the importance of the reduction potential in hydroquinone oxidation activity. Different effects were observed when these two residues were mutated into other amino acids.

Mutations of Tyr to nonphenolic amino acids targeted the Rieske protein to cytosolic proteolytic cleavage machinery. A Ser to Cys mutation resulted in expression of proteins that could no longer incorporate a Rieske cluster, and in cases where it could, a slight increase in the reduction potential was observed.

A Ser to Thr mutation resulted in a protein with moderate changes in the midpoint potential. Mutations of a conserved Thr that packs tightly against the Pro loop resulted in a lower reduction potential and a significant decrease in the activity.

Replacement of Leu with a neutral residue such as Ala caused a similar change in both reduction potential and p K a values of the His ligands, suggesting a causative effect of a change in water accessibility. However, placing a positive charge here resulted in a significant increase in the reduction potential.

Several mutations in a flexible linker distant from the cluster binding site have been shown to increase the reduction potential. This lower reduction potential is mainly due to removal of polarizable Cys groups and disturbance of the loop conformation and pattern of H-bonds. Explore music. Cy by Cy. Ch'monne du roi: www. Andree Anne Chose. Bearl Hoffayeur. Jean-noel Riviere. Caitlin Sellers. Paper In Fire.

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