Conformational stability of bovine holo and apo adrenodoxin--a scanning calorimetric study

Predicting melting temperature directly from protein sequences

Proteins of both hyperthermophilic and mesophilic microorganisms generally constitute from the same 20 amino acids; however, the extent of thermal tolerance of any given protein is an inherent property of its amino acid sequence. The present study is the first to report a rapid method for predicting Tm (melting temperature), the temperature at which 50% of the protein is unfolded, directly from protein sequences (the Tm Index program is available at http://tm.life.nthu.edu.tw/). We examined 75 complete microbial genomes using the Tm Index, and the analysis clearly differentiated hyperthermophilic from mesophilic microorganisms on this global genomic basis. These results are consistent with the previous hypothesis that hyperthermophiles express a greater number of high Tm proteins compared with mesophiles. The Tm Index will be valuable for modifying existing proteins (enzymes, protein drugs and vaccines) or designing novel proteins having a desired melting temperature.

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.

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.

Iron-sulfur cluster biosynthesis: biochemical characterization of the conformational dynamics of Thermotoga maritima IscU and the relevance for cellular cluster assembly

Important for the understanding of the functional properties of the iron-sulfur scaffold IscU is knowledge of the structure and dynamics of this protein class. Structural characterization of Thermotoga maritima IscU by CD (Mansy, S. S., Wu, G., Surerus, K. K., and Cowan, J. A. (2002) J. Biol. Chem. 277, 21397-21404) and high resolution NMR (Bertini, I., Cowan, J. A., Del Bianco, C., Luchinat, C., and Mansy, S. S. (2003) J. Mol. Biol. 331, 907-924) yielded data indicating a high degree of secondary structure. However, the latter also revealed IscU to exist in a dynamic equilibrium between two or more distinct conformations, possibly existing in a molten globule state. Herein, we further characterize the molten globule characteristics of T. maritima IscU by near-ultraviolet circular dichroism, 1-anilino-8-naphthalenesulfonic acid binding, free energy of unfolding, hydrodynamic radius measurements, and limited tryptic digestion. The data suggest unusual dynamic behavior that is not fully consistent with typical protein states such as fully folded, fully unfolded, or molten globule. For instance, the existence of a stable tertiary fold is supported by near-UV CD spectra and hydrodynamic radius measurements, whereas other data are less clearly interpretable and may be viewed as consistent with either a molten globule or fully folded state. However, all of the data are consistent with our previous hypothesis of a protein sampling multiple discrete tertiary conformations in which these structural transitions occur on a "slow" time scale. To describe such proteins, we introduce the term multiple discrete conformers.

Deletions in the loop surrounding the iron-sulfur cluster of adrenodoxin severely affect the interactions with its native redox partners adrenodoxin reductase and cytochrome P450(scc) (CYP11A1)

The redox active iron-sulfur center of bovine adrenodoxin is coordinated by four cysteine residues in positions 46, 52, 55 and 92 and is covered by a loop containing the residues Glu-47, Gly-48, Thr-49, Leu-50 and Ala-51. In plant-type [2Fe-2S] ferredoxins, the corresponding loop consists of only four amino acids. The loop is positioned at the surface of the proteins and forms a boundary separating the [2Fe-2S] cluster from solvent. In order to analyze the biological function of the five amino acids of the loop in adrenodoxin (Adx) for this electron transfer protein each residue was deleted by site-directed mutagenesis. The resulting five recombinant Adx variants show dramatic differences among each other regarding their spectroscopic characteristics and functional properties. The redox potential is affected differently depending on the position of the conducted deletion. In contrast, all mutations in the protein loop influence the binding to the redox partners adrenodoxin reductase (AdR) and cytochrome P450(scc) (CYP11A1) indicating the importance of this loop for the physiological function of this iron--sulfur protein.

Contribution of a salt bridge to the thermostability of adrenodoxin determined by site-directed mutagenesis

We identified a unique conserved salt bridge Arg89-Glu74 inside the protein core of adrenodoxin, which ensures proper orientation between the [2Fe-2S] cluster-containing domain and the recognition helix. Incorporation and geometry of the redox center were essentially preserved in the mutants E74D, R89A, and R89K as judged by EPR spectroscopy. However, absorption and CD spectra pointed out essential conformational changes in the protein vicinity of the [2Fe-2S] cluster. Judged by essentially increased K(m) and K(d) values and changed redox properties, mutations resulted in displacement of the recognition helix and hindered proper docking of the protein with both adrenodoxin reductase and CYP11A1. Substitutions of Arg89 and Glu74 induce thermodynamic destabilization attested by dramatically decreased unfolding temperature (T(d)) and enthalpy (Delta(d)H(T(d))). The heat capacity change of denaturation (Delta(d)C(p)) was significantly decreased for the mutants, suggesting that parts of the polypeptide chain normally hidden inside the protein core are exposed to the solvent in these variants.

The loop region covering the iron-sulfur cluster in bovine adrenodoxin comprises a new interaction site for redox partners

The amino acid in position 49 in bovine adrenodoxin is conserved among vertebrate [2Fe-2S] ferredoxins as hydroxyl function. A corresponding residue is missing in the cluster-coordinating loop of plant-type [2Fe-2S] ferredoxins. To probe the function of Thr-49 in a vertebrate ferredoxin, replacement mutants T49A, T49S, T49L, and T49Y, and a deletion mutant, T49Delta, were generated and expressed in Escherichia coli. CD spectra of purified proteins indicate changes of the [2Fe-2S] center geometry only for mutant T49Delta, whereas NMR studies reveal no transduction of structural changes to the interaction domain. The redox potential of T49Delta (-370 mV) is lowered by approximately 100 mV compared with wild type adrenodoxin and reaches the potential range of plant-type ferredoxins (-305 to -455 mV). Substitution mutants show moderate changes in the binding affinity to the redox partners. In contrast, the binding affinity of T49Delta to adrenodoxin reductase and cytochrome P-450 11A1 (CYP11A1) is dramatically reduced. These results led to the conclusion that Thr-49 modulates the redox potential in adrenodoxin and that the cluster-binding loop around Thr-49 represents a new interaction region with the redox partners adrenodoxin reductase and CYP11A1. In addition, variations of the apparent rate constants of all mutants for CYP11A1 reduction indicate the participation of residue 49 in the electron transfer pathway between adrenodoxin and CYP11A1.

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.

Structural and functional consequences of substitutions at the Pro108-Arg14 hydrogen bond in bovine adrenodoxin

Elimination of Pro108 in bovine adrenodoxin is known to result in the formation of a misfolded protein that is not able to incorporate a [2Fe-2S] cluster and rapidly degrades upon expression in E. coli. However, no experimental explanation for this phenomenon has been demonstrated so far. Using the recently obtained 3D structure of the truncated mutant Adx(4-108) we have studied the reasons of the protein stabilization by the proline residue by means of site-directed muta-genesis. Two main results have been obtained (i) the conserved hydrogen bond Pro108-Arg14, that connects different structural domains of Adx, contributes 6 kJ/mol into the protein stability and (ii) the presence of proline at position 108 provides a low conformational entropy of the unfolded state, supporting a gain in the Gibbs energy of 5.4 kJ/mol at 37 degrees C.

Heat capacities of amino acids, peptides and proteins

The heat capacity is one of the fundamental parameters describing thermodynamic properties of a system. It has wide applications in a number of areas such as polymer chemistry, protein folding and DNA stability. To aid the scientific community in the analysis of such data, I have compiled a database on the experimentally measured heat capacities of amino acids, polyamino acids, peptides, and proteins in solid state and in aqueous solutions.

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.

Effects of temperature and SDS on the structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus

The effects of temperature and SDS on the three-dimensional organization and secondary structure of beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus were investigated by CD, IR spectroscopy and differential scanning calorimetry. CD spectra in the near UV region showed that the detergent caused a remarkable change in the protein tertiary structure, and far-UV CD analysis revealed only a slight effect on secondary structure. Infrared spectroscopy showed that low concentrations of the detergent (up to 0.02%) induced slight changes in the enzyme secondary structure, whereas high concentrations caused the alpha-helix content to increase at high temperatures and prevented protein aggregation.

The conformational stability of alpha-crystallin is rather low: calorimetric results

The eye lens protein and chaperonin, alpha-crystallin, was studied by differential scanning microcalorimetry, spectroscopy and size exclusion chromatography. The thermal transition of alpha-crystallin proceeds at Ttrs = 59.8 +/- 0.6 degrees C with an enthalpy change of delta H = 336 +/- 9 kJ per mol subunit. Disagreement between previous delta H values could be attributed to a side reaction that leads, depending on the scan rate, to the formation of a non-productive folding form. The conformational stability of alpha-crystallin is rather low (delta G = 24 +/- 5 kJ/mol of subunit). The minimal cooperative unit of alpha-crystallin is the monomeric subunit.

Conformational stability of adrenodoxin mutant proteins

Adrenodoxin and the mutants at the positions T54, H56, D76, Y82, and C95, as well as the deletion mutants 4-114 and 4-108, were studied by high-sensitivity scanning microcalorimetry, limited proteolysis, and absorption spectroscopy. The mutants show thermal transition temperatures ranging from 46 to 56 degrees C, enthalpy changes from 250 to 370 kJ/mol, and heat capacity change delta Cp = 7.28 +/- 0.67 kJ/mol/K, except H56R. The amino acid replacement H56R produces substantial local changes in the region around positions 56 and Y82, as indicated by reduced heat capacity change (delta Cp = 4.29 +/- 0.37 kJ/mol/K) and enhanced fluorescence. Deletion mutant 4-108 is apparently more stable than the wild type, as judged by higher specific denaturation enthalpy and resistance toward proteolytic degradation. No simple correlation between conformational stability and functional properties could be found.

The role of threonine 54 in adrenodoxin for the properties of its iron-sulfur cluster and its electron transfer function

The amino acid in position 54 of adrenodoxin is strongly conserved among ferredoxins, consisting of a threonine or serine. Its role was studied by analyzing mutants T54S and T54A of bovine adrenodoxin. Absorption, circular dichroism, fluorescence, and electron paramagnetic resonance spectra of mutant T54S show that this substitution has no influence on the formation and stability of the ferredoxin. The redox potential of this mutant, however, was lowered by 55 mV as compared with native adrenodoxin, indicating a role for this residue in redox potential modulation. Incorporation of the iron-sulfur cluster was not impaired in the T54A mutant, although structural features of the oxidized protein were considerably changed. The decreased stability of the T54A mutant as compared with the wild type and mutant T54S indicates that a hydrogen bond donor at this position stabilizes the protein. Both mutants have been shown to be functionally active. Replacement of threonine 54 by serine or alanine, however, leads to rearrangements at the recognition sites for its redox partners. This is reflected by decreased Km and Kd values of both mutants for the cytochromes P450, whereas only T54A displayed a decreased Km value in cytochrome c reduction. Substrate conversion was accelerated (2.2- and 2.4-fold for mutants T54A and T54S, respectively) in the CYP11B1-, but not in the CYP11A1-dependent reaction.

The role of a conserved tyrosine residue in high-potential iron sulfur proteins

Conserved tyrosine-12 of Ectothiorhodospira halophila high-potential iron sulphur protein (HiPIP) iso-I was substituted with phenylalanine (Y12F), histidine (Y12H), tryptophan (Y12W), isoleucine (Y12I), and alanine (Y12A). Variants Y12A and Y12I were expressed to reasonable levels in cells grown at lower temperatures, but decomposed during purification. Variants Y12F, Y12H, and Y12W were substantially destabilized with respect to the recombinant wild-type HiPIP (rcWT) as determined by differential scanning calorimetry over a pH range of 7.0-11.0. Characterization of the Y12F variant by NMR indicates that the principal structural differences between this variant and the rcWT HiPIP result from the loss of the two hydrogen bonds of the Tyr-12 hydroxyl group with Asn-14 O delta 1 and Lys-59 NH, respectively. The effect of the loss of the latter interaction is propagated through the Lys-59/Val-58 peptide bond, thereby perturbing Gly-46. The delta delta GDapp of Y12F of 2.3 kcal/mol with respect to rcWT HiPIP (25 degrees C, pH 7.0) is entirely consistent with the contribution of these two hydrogen bonds to the stability of the latter. CD measurements show that Tyr-12 influences several electronic transitions within the cluster. The midpoint reduction potentials of variants Y12F, Y12H, and Y12W were 17, 19, and 22 mV (20 mM MOPS, 0.2 M sodium chloride, pH 6.98, 25 degrees C), respectively, higher than that of rcWT HiPIP. The current results indicate that, although conserved Tyr-12 modulates the properties of the cluster, its principle function is to stabilize the HiPIP through hydrogen bonds involving its hydroxyl group and electrostatic interactions involving its aromatic ring.