Conformational stability of adrenodoxin mutant proteins

Raman and infrared spectroscopic evidence for the structural changes of the 2Fe2S cluster and its environment during the interaction of adrenodoxin and adrenodoxin reductase

Many biological functions involve the formation of protein-protein complexes. In the present study, we investigated the interaction of two proteins involved in electron transfer, adrenodoxin (Adx) and adrenodoxin reductase (AdR) by using Raman and infrared spectroscopies. Different shifts and splittings of the FeS_b/t stretching vibrational modes upon interaction of the two proteins can be reported pointing towards major structural changes in the [2Fe2S] cluster. These changes may be necessary for optimizing electron transfer. The assignment of the shifted modes to the [2Fe2S] cluster was confirmed by ⁵⁴Fe labeling of the truncated Adx (4-108) as well as the investigation of mutants close to the interaction site and in the vicinity of the [2Fe2S] cluster. Electrochemically induced FTIR difference spectra revealed that the flavin cofactor in AdR also changes due to the interaction with [2Fe2S] cluster in the Adx/AdR electron transfer complex.

A solution model of the complex formed by adrenodoxin and adrenodoxin reductase determined by paramagnetic NMR spectroscopy

Lanthanide tags offer the opportunity to retrieve long-range distance information from NMR experiments that can be used to guide protein docking. To determine whether sufficient restraints can be retrieved for proteins with low solubility and availability, Ln tags were applied in the study of the 65 kDa membrane-associated protein complex formed by the electron carrier adrenodoxin and its electron donor, adrenodoxin reductase. The reductase is only monomeric at low concentration, and the paramagnetic iron-sulfur cluster of adrenodoxin broadens many of the resonances of nuclei in the interface. Guided by the paramagnetic restraints obtained using two Ln-tag attachment sites, protein docking yields a cluster of solutions with an rmsd of 3.2 A. The mean structure is close to the crystal structure of the cross-linked complex, with an rmsd of 4.0 A. It is concluded that with the application of Ln tags paramagnetic NMR restraints for structure determination can be retrieved even for difficult, low-concentration protein complexes.

Studies of the molten globule state of ferredoxin: Structural characterization and implications on protein folding and iron-sulfur center assembly

The biological insertion of iron-sulfur clusters (Fe-S) involves the interaction of (metallo) chaperons with a partly folded target polypeptide. In this respect, the study of nonnative protein conformations in iron-sulfur proteins is relevant for the understanding of the folding process and cofactor assembly. We have investigated the formation of a molten globule state in the [3Fe4S][4Fe4S] ferredoxin from the thermophilic archaeon Acidianus ambivalens (AaFd), which also contains a structural zinc site. Biophysical studies have shown that, at acidic pH, AaFd retains structural folding and metal centers. However, upon increasing the temperature, a series of successive modifications occur within the protein structure: Fe-S disassembly, loss of tertiary contacts and dissociation of the Zn(2+) site, which is simultaneous to alterations on the secondary structure. Upon cooling, an apo-ferredoxin state is obtained, with characteristics of a molten globule: compactness identical to the native form; similar secondary structure evidenced by far-UV CD; no near-UV CD detected tertiary contacts; and an exposure of the hydrophobic surface evidenced by 1-anilino naphthalene-8-sulfonic acid (ANS) binding. In contrast to the native form, this apo ferredoxin state undergoes reversible thermal and chemical unfolding. Its conformational stability was investigated by guanidinium chloride denaturation and this state is approximately 1.5 kcal mol(-1) destabilised in respect to the holo ferredoxin. The single tryptophan located nearby the Fe-S pocket probed the conformational dynamics of the molten globule state: fluorescence quenching, red edge emission shift analysis and resonance energy transfer to bound ANS evidenced a restricted mobility and confinement within a hydrophobic environment. The possible physiological relevance of molten globule states in Fe-S proteins and the hypothesis that their structural flexibility may be important to the understanding of metal center insertion are discussed.

Structure of a [2Fe–2S] ferredoxin from Rhodobacter capsulatus likely involved in Fe–S cluster biogenesis and conformational changes observed upon reduction

FdVI from Rhodobacter capsulatus is structurally related to a group of [2Fe-2S] ferredoxins involved in iron-sulfur cluster biosynthesis. Comparative genomics suggested that FdVI and orthologs found in alpha-Proteobacteria are involved in this process. Here, the crystal structure of FdVI has been determined for both the oxidized and the reduced protein. The [2Fe-2S] cluster lies 6 A below the protein surface in a hydrophobic pocket without access to the solvent. This particular cluster environment might explain why the FdVI midpoint redox potential (-306 mV at pH 8.0) did not show temperature or ionic strength dependence. Besides the four cysteines that bind the cluster, FdVI features an extra cysteine which is located close to the S1 atom of the cluster and is oriented in a position such that its thiol group points towards the solvent. Upon reduction, the general fold of the polypeptide chain was almost unchanged. The [2Fe-2S] cluster underwent a conformational change from a planar to a distorted lozenge. In the vicinity of the cluster, the side chain of Met24 was rotated by 180 degrees , bringing its S atom within hydrogen-bonding distance of the S2 atom of the cluster. The reduced molecule also featured a higher content of bound water molecules, and more extensive hydrogen-bonding networks compared with the oxidized molecule. The unique conformational changes observed in FdVI upon reduction are discussed in the light of structural studies performed on related ferredoxins.

Linear three-iron centres are unlikely cluster degradation intermediates during unfolding of iron-sulfur proteins

Recent studies on the chemical alkaline degradation of ferredoxins have contributed to the hypothesis that linear three-iron centres are commonly observed as degradation intermediates of iron-sulfur clusters. In this work we assess the validity of this hypothesis. We studied different proteins containing iron-sulfur clusters, iron-sulfur centres and di-iron centres with respect to their chemical degradation kinetics at high pH, in the presence and absence of exogenous sulfide, to investigate the possible formation of linear three-iron centres during protein unfolding. Our spectroscopic and kinetic data show that in these different proteins visible absorption bands at 530 and 620 nm are formed that are identical to those suggested to arise from linear three-iron centres. Iron release and protein unfolding kinetics show that these bands result from the formation of iron sulfides at pH 10, produced by the degradation of the iron centres, and not from rearrangements leading to linear three-iron centres. Thus, at this point any relevant functional role of linear three-iron centres as cluster degradation intermediates in iron-sulfur proteins remains elusive.

Studies on the degradation pathway of iron-sulfur centers during unfolding of a hyperstable ferredoxin: cluster dissociation, iron release and protein stability

The ferredoxin from the thermoacidophile Acidianus ambivalens is a representative of the archaeal family of di-cluster [3Fe-4S][4Fe-4S] ferredoxins. Previous studies have shown that these ferredoxins are intrinsically very stable and led to the suggestion that upon protein unfolding the iron-sulfur clusters degraded via linear three-iron sulfur center species, with 610 and 520 nm absorption bands, resembling those observed in purple aconitase. In this work, a kinetic and spectroscopic investigation on the alkaline chemical denaturation of the protein was performed in an attempt to elucidate the degradation pathway of the iron-sulfur centers in respect to protein unfolding events. For this purpose we investigated cluster dissociation, iron release and protein unfolding by complementary biophysical techniques. We found that shortly after initial protein unfolding, iron release proceeds monophasically at a rate comparable to that of cluster degradation, and that no typical EPR features of linear three-iron sulfur centers are observed. Further, it was observed that EDTA prevents formation of the transient bands and that sulfide significantly enhances its intensity and lifetime, even after protein unfolding. Altogether, our data suggest that iron sulfides, which are formed from the release of iron and sulfide resulting from cluster degradation during protein unfolding in alkaline conditions, are in fact responsible for the observed intermediate spectral species, thus disproving the hypothesis suggesting the presence of a linear three-iron center intermediate. Kinetic studies monitored by visible, fluorescence and UV second-derivative spectroscopies have elicited that upon initial perturbation of the tertiary structure the iron-sulfur centers start decomposing and that the presence of EDTA accelerates the process. Also, the presence of EDTA lowers the observed melting temperature in thermal ramp experiments and the midpoint denaturant concentration in equilibrium chemical unfolding experiments, further suggesting that the clusters also play a structural role in the maintenance of the conformation of the folded state.

The interaction of bovine adrenodoxin with CYP11A1 (cytochrome P450scc) and CYP11B1 (cytochrome P45011beta ). Acceleration of reduction and substrate conversion by site-directed mutagenesis of adrenodoxin

The kinetics of protein-protein interaction and heme reduction between adrenodoxin wild type as well as eight mutants and the cytochromes P450 CYP11A1 and CYP11B1 was studied in detail. Rate constants for the formation of the reduced CYP11A1.CO and CYP11B1.CO complexes by wild type adrenodoxin, the adrenodoxin mutants Adx-(4-108), Adx-(4-114), T54S, T54A, and S112W, and the double mutants Y82F/S112W, Y82L/S112W, and Y82S/S112W (the last four mutants are Delta113-128) are presented. The rate constants observed differ by a factor of up to 10 among the respective adrenodoxin mutants for CYP11A1 but not for CYP11B1. According to their apparent rate constants for CYP11A1, the adrenodoxin mutants can be grouped into a slow (wild type, T54A, and T54S) and a fast group (all the other mutants). The adrenodoxin mutants forming the most stable complexes with CYP11A1 show the fastest rates of reduction and the highest rate constants for cholesterol to pregnenolone conversion. This strong correlation suggests that C-terminal truncation of adrenodoxin in combination with the introduction of a C-terminal tryptophan residue enables a modified protein-protein interaction rendering the system almost as effective as the bacterial putidaredoxin/CYP101 system. Such a variation of the adrenodoxin structure resulted in a mutant protein (S112W) showing a 100-fold increased efficiency in conversion of cholesterol to pregnenolone.

Interactions between redox partners in various cytochrome P450 systems: functional and structural aspects

The various types of redox partner interactions employed in cytochrome P450 systems are described. The similarities and differences between the redox components in the major categories of P450 systems present in bacteria, mitochondria and microsomes are discussed in the light of the accumulated evidence from X-ray crystallographic and NMR spectroscopic determinations. Molecular modeling of the interactions between the redox components in various P450 mono-oxygenase systems is proposed on the basis of structural and mutagenesis information, together with experimental findings based on chemical modification of key residues likely to be associated with complementary binding sites on certain typical P450 isoforms and their respective redox partners.

Adrenodoxin: structure, stability, and electron transfer properties

Adrenodoxin is an iron-sulfur protein that belongs to the broad family of the [2Fe-2S]-type ferredoxins found in plants, animals and bacteria. Its primary function as a soluble electron carrier between the NADPH-dependent adrenodoxin reductase and several cytochromes P450 makes it an irreplaceable component of the steroid hormones biosynthesis in the adrenal mitochondria of vertebrates. This review intends to summarize current knowledge about structure, function, and biochemical behavior of this electron transferring protein. We discuss the recently solved first crystal structure of the vertebrate-type ferredoxin, the truncated adrenodoxin Adx(4-108), that offers the unique opportunity for better understanding of the structure-function relationships and stabilization of this protein, as well as of the molecular architecture of [2Fe-2S] ferredoxins in general. The aim of this review is also to discuss molecular requirements for the formation of the electron transfer complex. Essential comparison between bacterial putidaredoxin and mammalian adrenodoxin will be provided. These proteins have similar tertiary structure, but show remarkable specificity for interactions only with their own cognate cytochrome P450. The discussion will be largely centered on the protein-protein recognition and kinetics of adrenodoxin dependent reactions.

A step toward understanding the folding mechanism of bovine adrenodoxin

The iron-sulfur clusters of iron-sulfur proteins are not only essential for the structure and function but they also seem to play an important role in the folding process of these proteins. So far, no data on reversible unfolding/refolding of iron-sulfur proteins under aerobic conditions have been reported. We found appropriate conditions, which might also be applicable for other iron-sulfur proteins, for reversible unfolding/refolding of bovine adrenodoxin (Adx) that prevent cluster decomposition during the unfolding process. The unfolding/refolding studies have been performed under aerobic conditions using fluorescence measurements (with mutant Y82W of Adx, providing a sensitive internal probe), absorption, and circular dichroism (CD) spectroscopy as well as activity measurements. Without protecting reagent, adrenodoxin becomes an apoprotein upon denaturation which is an irreversible process with respect to cluster rebinding. However, reversibility of unfolding/refolding can be observed after protein denaturation in the presence of dithiothreitol (DTT). Upon removal of the denaturant, we regained 65, 63, and 64% refolding from CD, fluorescence, and activity measurements, respectively. In the case of thermal denaturation, the percentage of refolding is about 60% according to CD measurements. DTT appears to stabilize the [2Fe-2S] cluster and prevents its decomposition during aerobic unfolding, providing thereby the means of correct refolding of the protein.

Impact of the presequence of a mitochondrium-targeted precursor, preadrenodoxin, on folding, catalytic activity, and stability of the protein in vitro

Bovine preadrenodoxin, an adrenocortical precursor protein destined for mitochondrial import, was expressed in Escherichia coli as an [2Fe-2S] cluster-containing protein. It was found in inclusion bodies, purified from there, and finally reconstituted to obtain soluble holo-protein. The impact of the presequence on folding of the protein using biochemical and biophysical approaches has been investigated. Upon unfolding the preprotein reveals a decrease in the denaturational enthalpy and heat capacity compared with mature adrenodoxin, indicating an incomplete unfolding of the preprotein with remaining residual structure. Moreover, the data obtained show that the presequence is solvent exposed in aqueous solution with no preference for secondary structure elements and that it does not disturb the accurate folding of the mature part of the protein. The latter conclusion is also based on the finding that the precursor in vitro exhibits electron transfer function comparable to the mature protein, adrenodoxin. While the reduction of cytochrome c, reflecting the interaction between adrenodoxin and its reductase, and the interaction with CYP11B1 have not been significantly affected by the presence of the presequence, the binding affinity of preadrenodoxin to CYP11A1 is 5.5-fold lower than that of the mature form.

Structure of adrenodoxin and function in mitochondrial steroid hydroxylation

The three-dimensional structure of a truncated mutant of bovine adrenodoxin has been resolved at 1.85 A resolution by MAD. The protein consists of a large core region and a more flexible hairpin loop bearing residues which have been previously described as being involved in redox partner recognition. To study the role of distinct protein domains and amino acids of adrenodoxin in interaction with adrenodoxin reductase (AdR), CYP11A1 and CYP11B1, as well as in electron transfer, mutants of adrenodoxin have been prepared by site-directed mutagenesis and produced in Escherichia coli, and their structural and functional properties have been characterized in detail. It could be demonstrated that Tyr82 is located at the edge of the flexible interaction loop of adrenodoxin participating in interactions with AdR and P450s. His56, being close to Tyr82, forms a bridge between the core region of adrenodoxin and the interaction loop. Its role in transmitting changes of the cluster region to the interaction site has also been supported by functional studies. Pro108 of adrenodoxin, the only proline residue contained in the protein and being conserved in this position among several other vertebrate-type ferredoxins, has been demonstrated to be of importance for the correct folding of this protein.

New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108)

BACKGROUND

Adrenodoxin (Adx) is a [2Fe-2S] ferredoxin involved in steroid hormone biosynthesis in the adrenal gland mitochondrial matrix of mammals. Adx is a small soluble protein that transfers electrons from adrenodoxin reductase (AR) to different cytochrome P450 isoforms where they are consumed in hydroxylation reactions. A crystallographic study of Adx is expected to reveal the structural basis for an important electron transfer reaction mediated by a vertebrate [2Fe-2S] ferredoxin.

RESULTS

The crystal structure of a truncated bovine adrenodoxin, Adx(4-108), was determined at 1.85 A resolution and refined to a crystallographic R value of 0.195. The structure was determined using multiple wavelength anomalous dispersion phasing techniques, making use of the iron atoms in the [2Fe-2S] cluster of the protein. The protein displays the compact (alpha + beta) fold typical for [2Fe-2S] ferredoxins. The polypeptide chain is organized into a large core domain and a smaller interaction domain which comprises 35 residues, including all those previously determined to be involved in binding to AR and cytochrome P450. A small interdomain motion is observed as a structural difference between the two independent molecules in the asymmetric unit of the crystal. Charged residues of Adx(4-108) are clustered to yield a strikingly asymmetric electric potential of the protein molecule.

CONCLUSIONS

The crystal structure of Adx(4-108) provides the first detailed description of a vertebrate [2Fe-2S] ferredoxin and serves to explain a large body of biochemical studies in terms of a three-dimensional structure. The structure suggests how a change in the redox state of the [2Fe-2S] cluster may be coupled to a domain motion of the protein. It seems likely that the clearly asymmetric charge distribution on the surface of Adx(4-108) and the resulting strong molecular dipole are involved in electrostatic steering of the interactions with AR and cytochrome P450.

Ferredoxin from the hyperthermophile Thermotoga maritima is stable beyond the boiling point of water

Heat-stable proteins from hyperthermophilic microorganisms are ideally suited for investigating protein stability and evolution. We measured with differential scanning calorimetry and optical absorption spectroscopy the thermal stability of [4Fe-4S] ferredoxin from Thermotoga maritima (tfdx), which is a small electron transfer protein. The results are consistent with two-state unfolding at the record denaturation temperature of 125 degrees C. According to the crystal structure at 1.75 A resolution, T. maritima ferredoxin contains a significantly increased number of hydrogen bonds that involve charged amino acid side-chains, compared to thermolabile ferredoxins. Thus, our results suggest that polar interactions substantially contribute to protein stability at very high temperatures. Moreover, because small [4Fe-4S] ferredoxins seem to have occurred early in evolution, the extreme thermostability of tfdx supports the hypothesis that life originated at high temperatures.

Pro108 is important for folding and stabilization of adrenal ferredoxin, but does not influence the functional properties of the protein

The truncated mutant Met-adrenodoxin-(4-107)-peptide of bovine adrenal ferredoxin was expressed as apoprotein in Escherichia coli BL21 and could be reconstituted to the holoform by chemical or enzymatic methods. The reconstituted protein had spectroscopic, functional and redox properties similar to the Met-adrenodoxin-(4-108)-peptide of adrenal ferredoxin, into which the cluster was inserted upon expression in the same Escherichia coli strain. Rate of in vitro cluster insertion into the Met-adrenodoxin-(4-107) apoprotein was much lower than for the Met-adrenodoxin-(4-108) apoprotein under identical conditions. Comparative thermodynamic studies with the Met-adrenodoxin-(4-108)-peptide indicated that removal of Pro108 resulted in an extensive decrease of the overall stability of the protein in either oxidation state. The Met-adrenodoxin-(4-107)-peptide showed a higher sensitivity to urea denaturation and had a sensibly lower denaturation temperature, 44.8 degrees C, compared with 51.7 degrees C for mutant Met-adrenodoxin-(4-108). The stability of the reduced state of both mutants is slightly lower than that of the oxidized state indicating that this protein region does not undergo major structural changes upon reduction.

Specific aspects of electron transfer from adrenodoxin to cytochromes p450scc and p45011beta

An analysis of the electron transfer kinetics from the reduced [2Fe-2S] center of bovine adrenodoxin and its mutants to the natural electron acceptors, cytochromes P450scc and P45011beta, is the primary focus of this paper. A series of mutant proteins with distinctive structural parameters such as redox potential, microenvironment of the iron-sulfur cluster, electrostatic properties, and conformational stability was used to provide more detailed insight into the contribution of the electronic and conformational states of adrenodoxin to the driving forces of the complex formation of reduced adrenodoxin with cytochromes P450scc and P45011beta and electron transfer. The apparent rate constants of P450scc reduction were generally proportional to the adrenodoxin redox potential under conditions in which the protein-protein interactions were not affected. However, the effect of redox potential differences was shown to be masked by structural and electrostatic effects. In contrast, no correlation of the reduction rates of P45011beta with the redox potential of adrenodoxin mutants was found. Compared with the interaction with P450scc, however, the hydrophobic protein region between the iron-sulfur cluster and the acidic site on the surface of adrenodoxin seems to play an important role for precise complementarity in the tightly associated complex with P45011beta.