Affitins: Ribosome Display for Selection of Aho7c-Based Affinity Proteins.

Engineered protein scaffolds have made a tremendous contribution to the panel of affinity tools owing to their favorable biophysical properties that make them useful for many applications. In 2007, our group paved the way for using archaeal Sul7d proteins for the design of artificial affinity ligands, so-called Affitins. For many years, Sac7d and Sso7d have been used as molecular basis to obtain binders for various targets. Recently, we characterized their old gifted protein family and identified Aho7c, originating from Acidianus hospitalis, as the shortest member (60 amino-acids) with impressive stability (96.5 °C, pH 0-12). Here, we describe the construction of Aho7c combinatorial libraries and their use for selection of binders by ribosome display.

In situ characterization of change in superficial organic components of thermoacidophilic archaeon Acidianus manzaensis YN-25.

For the first time, synchrotron radiation (SR) -based carbon K-edge X-ray absorption near edge structure (XANES) spectroscopy in-situ characterization was conducted to evaluate the evolution of superficial (about 10 nm) organic components of extracellular polymeric substances (EPS) of thermoacidophilic archaeon Acidianus manzaensis YN-25 acclimated with different energy substrates (FeS2, CuFeS2, S0, FeSO4). The atomic force microscopy (AFM) morphology scanning showed that the strain acclimated with different energy substrates varied a lot in EPS amount. XANES results showed clear associations between the energy substrates and the changes in organic composition in terms of typical function groups (CO, CO and CN). The chalcopyrite- and pyrite-acclimated cells contained higher proportion of proteins but less proportion of polysaccharides than the S0-acclimated cells. The FeSO4-acclimated cells contained the highest proportion of proteins, while the S0-acclimated cells contained more lipids and polysaccharides. The results of linear-combination and peak fitting of the K-edge XANES for the extracellular superficial organic component C is consistent with the trend in comparison with the results of FTIR and spectrophotometric determination, but there are significant differences in the values. These differences are caused by the inconsistencies of measurement depth between XANES and the latter two characterization methods.

Speciation of arsenic in a thermoacidophilic iron-oxidizing archaeon, Acidianus brierleyi, and its culture medium by inductively coupled plasma-optical emission spectroscopy combined with flow injection pretreatment using an anion-exchange mini-column.

The thermoacidophilic iron-oxidizing archaeon Acidianus brierleyi is a microorganism that could be useful in the removal of inorganic As from wastewater, because it simultaneously oxidizes As(III) and Fe(II) to As(V) and Fe(III) in an acidic culture medium, resulting in the immobilization of As(V) as FeAsO4. To investigate the oxidation mechanism, speciation of the As species in both the cells and its culture media is an important issue. Here we describe the successive determination of As(III), As(V), and total As in A. brierleyi and its culture medium via a facile method based on inductively coupled plasma-optical emission spectroscopy (ICP-OES) with a flow injection pretreatment system using a mini-column packed with an anion-exchange resin. The flow-injection pretreatment system consisted of a syringe pump, a selection valve, and a switching valve, which were controlled by a personal computer. Sample solutions with the pH adjusted to 5 were flowed into the mini-column to retain the anionic As(V), whereas As(III) was introduced into ICP-OES with no adsorption on the mini-column due to its electrically neutral form. An acidic solution (1 M HNO3) was then flowed into the mini-column to elute As(V) followed by ICP-OES measurement. The same sample was also subjected to ICP-OES without being passed through the mini-column in order to determine the total amounts of As(III) and As(V). The method was verified by comparing the results of the total As with the sum of As(III) and As(V). The calibration curves showed good linearity with limits of detection of 158, 86, and 211 ppb for As(III), As(V), and total As, respectively. The method was successfully applicable to the determination of the As species contained in the pellets of A. brierleyi and their culture media. The results suggested that the oxidation of As(III) was influenced by the presence of Fe(II) in the culture medium, i.e., Fe(II) enhanced the oxidation of As(III) in A. brierleyi. In addition, we found that no soluble As species was contained in the cell pellets and more than 60% of the As(III) in the culture medium was oxidized by A. brierleyi after a 6-day incubation.

Effect of sodium chloride on sulfur speciation of chalcopyrite bioleached by the extreme thermophile Acidianus manzaensis.

The influence of sodium chloride on dissolution of chalcopyrite and surface sulfur speciation during bioleaching of chalcopyrite with the extreme thermophile Acidianus manzaensis YN-25 was studied. The addition of sodium chloride accelerated the dissolution of chalcopyrite by reducing the accumulation of elemental sulfur layers on the mineral surface, resulting in an increase in the concentration of copper ions from 2.37g/L to 2.67g/L. Jarosite and elemental sulfur were found in the bioleached residues, while the amount of elemental sulfur accumulating on the mineral surface decreased drastically from 25.4% to 3.0% when 0.66g/L of sodium chloride was present during bioleaching. Therefore, the accumulation of elemental sulfur on the mineral surface is likely mainly responsible for the slowdown in the dissolution rate. The results indicated that bioleaching chalcopyrite with extreme thermophiles possessing high sulfur oxidation activity likely enhances dissolution of chalcopyrite by effectively removing elemental sulfur accumulating on the mineral surface.

Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV.

The structure of a 14 kDa structural protein from Acidianus two-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 A wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structure, one chloride ion turned out to be essential to achieve phasing. The minimal data requirements and the relative contributions of the Cl and S atoms to phasing are discussed. This work supports the feasibility of a systematic approach for the solution of protein crystal structures by SAD based on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substitution and heavy-atom derivatization.

Role of a novel disulfide bridge within the all-beta fold of soluble Rieske proteins.

Rieske proteins and Rieske ferredoxins are present in the three domains of life and are involved in a variety of cellular processes. Despite their functional diversity, these small Fe-S proteins contain a highly conserved all-beta fold, which harbors a [2Fe-2S] Rieske center. We have identified a novel subtype of Rieske ferredoxins present in hyperthermophilic archaea, in which a two-cysteine conserved SKTPCX((2-3))C motif is found at the C-terminus. We establish that in the Acidianus ambivalens representative, Rieske ferredoxin 2 (RFd2), these cysteines form a novel disulfide bond within the Rieske fold, which can be selectively broken under mild reducing conditions insufficient to reduce the [2Fe-2S] cluster or affect the secondary structure of the protein, as shown by visible circular dichroism, absorption, and attenuated total reflection Fourier transform IR spectroscopies. RFd2 presents all the EPR, visible absorption, and visible circular dichroism spectroscopic features of the [2Fe-2S] Rieske center. The cluster has a redox potential of +48 mV (25 degrees C and pH 7) and a pK (a) of 10.1 +/- 0.2. These shift to +77 mV and 8.9 +/- 0.3, respectively, upon reduction of the disulfide. RFd2 has a melting temperature near the boiling point of water (T(m) = 99 degrees C, pH 7.0), but it becomes destabilized upon disulfide reduction (DeltaT(m) = -9 degrees C, DeltaC(m) = -0.7 M guanidinium hydrochloride). This example illustrates how the incorporation of an additional structural element such as a disulfide bond in a highly conserved fold such as that of the Rieske domain may fine-tune the protein for a particular function or for increased stability.

On the relative contribution of ionic interactions over iron-sulfur clusters to ferredoxin stability.

Metal centres play an important structural role in maintaining the native conformation of a protein. Here we use biophysical methods to investigate what is the relative contribution of iron-sulfur clusters in respect to ionic interactions in a thermophilic di-cluster ferredoxin model. Changes in protonation affect both the stability and the conformational dynamics of the protein fold. In the pH 5.5-8 interval, the protein has a high melting temperature (T(m) approximately 120 degrees C), which decreases towards pH extremes. Acidification triggers events in two steps: down to the isoelectric point (pH 3.5) the Fe-S clusters remain unchanged, the secondary structure content increases and the single Trp becomes more solvent shielded, denoting a more compact fold. Further acidification down to pH 2 sets off exposure of the hydrophobic core and Fe-S cluster disintegration, yielding a molten globule state. The relative stabilising contribution of the clusters becomes evident when stabilising ionic interactions are switched off as a result of poising the protein at pH 3.5, at an overall null charge: under these conditions, the Fe-S clusters disassemble at T(m)=72 degrees C, whereas the protein unfolds at T(m)=52 degrees C. Overall, this ferredoxin denotes a considerable structural plasticity around its native conformation, a property which appears to depend more on the integrity of its metal clusters rather than on the status of its stabilising electrostatic interactions. The latter however play a relevant role in determining the protein thermal stability.

Comparative architecture of octahedral protein cages. I. Indexed enclosing forms.

The architectural elements of four protein cages (bacterio ferritin, human mitochondrial ferritin, sulfur oxygenase reductase and small heat-shock protein) are compared top-to-bottom. The starting points are polyhedra with octahedral symmetry 432 enclosing the cage and delimiting the central cavity, respectively, which have vertices at points of a species-dependent cubic form lattice. The approach is extended from the whole cage to axial-symmetric clusters down to polyhedral forms of single monomers viewed along the fourfold, the threefold and the twofold axes, respectively. The corresponding projected monomeric forms can be approximated by two-dimensional tiles, 13 enantiomorphic pairs in total. The determination of the cubic indices of the monomeric vertices opens the possibility of the way back analysis, bottom-to-top, as discussed in paper II [Janner (2008). Acta Cryst. A64, 503-512].

Comparative architecture of octahedral protein cages. II. Interplay between structural elements.

In paper I [Janner (2008). Acta Cryst. A64, 494-502], the enclosing forms of the monomers of four octahedral holoenzymes (bacterio and mitochondrial ferritins, small heat-shock protein and sulfur oxygenase reductase) were derived, with vertices at points of a cubic lattice and indexed accordingly. The correspondence between vertices and neighboring residues allows a sequential ordering of the vertices within the polyline defined by the C(alpha) atoms of the primary structure. The alignment of these sequences shows that the form vertices denoted as turning points delimit the elements of the secondary structure (alpha-helices, beta-strands and loops). This relation is analyzed further in a plot of angular changes in orientations of the polyline segments and planes as a function of the residue numbers and of the form vertices, respectively, leading to an alternative characterization of the ternary structure. Finally, two simple connectivity models of monomers, oriented according to the symmetry axes of the octahedral point group 432, suggest possible patterns in the self-assembly process from clusters of monomers to the quaternary structure of the cubic cage.

Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.

Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn(2+) site and the ferredoxin (betaalphabeta)(2) core, which harbours intact clusters I and II, a [3Fe-4S](1+/0) and a [4Fe-4S](2+/1+) centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe-4S](1+/0) centres and poor definition around cluster II.

A spectroscopic study of the temperature induced modifications on ferredoxin folding and iron-sulfur moieties.

Thermal perturbation of the dicluster ferredoxin from Acidianus ambivalens was investigated employing a toolbox of spectroscopic methods. FTIR and visible CD were used for assessing changes of the secondary structure and coarse alterations of the [3Fe4S] and [4Fe4S] cluster moieties, respectively. Fine details of the disassembly of the metal centers were revealed by paramagnetic NMR and resonance Raman spectroscopy. Overall, thermally induced unfolding of AaFd is initiated with the loss of -helical content at relatively low temperatures (T(app)(m) approximately 44 degrees C), followed by the disruption of both iron-sulfur clusters (T(app)(m) approximately 53-60 degrees C). The degradation of the metal centers triggers major structural changes on the protein matrix, including the loss of tertiary contacts (T(app)(m) approximately 58 degrees C) and a change, rather than a significant net loss, of secondary structure (T(app)(m) approximately 60 degrees C). This latter process triggers a secondary structure reorganization that is consistent with the formation of a molten globule state. The combined spectroscopic approach here reported illustrates how changes in the metalloprotein organization are intertwined with disassembly of the iron-sulfur centers, denoting the conformational interplay of the protein backbone with cofactors.

A Rieske ferredoxin typifying a subtype within Rieske proteins: spectroscopic, biochemical and stability studies.

A new subtype of archaeal Rieske ferredoxin (RFd) has been identified in the genome of the thermoacidophilic archaeon Acidianus ambivalens. The gene is inserted in an atypical genomic context in a gene cluster encoding a NiFe hydrogenase. Sequence and phyletic analysis showed that the protein is related to bacterial RFd but not to any of the known archaeal Rieske proteins. The recombinant 14 kDa protein isolated from Escherichia coli behaved as a dimer in solution. It contained approximately 2 Fe/mol and all visible and EPR spectroscopic features typical of Rieske centre-containing proteins. However, its redox potential (+170 mV) was significantly higher than those of canonical RFd. This difference is rationalized in terms of the protein structure environment, as discrete amino acid substitutions in key positions around the metal centre account for the higher potential.