Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light

Designing metal sites into de novo proteins has significantly improved, recently. However, identifying the minimal coordination spheres, able to encompass the necessary information for metal binding and activity, still represents a great challenge, today. Here, we test our understanding with a benchmark, nevertheless difficult, case. We assemble into a miniature 28-residue protein, the quintessential elements required to fold properly around a FeCys4 redox center, and to function efficiently in electron-transfer. This study addresses a challenge in de novo protein design, as it reports the crystal structure of a designed tetra-thiolate metal-binding protein in sub-Å agreement with the intended design. This allows us to well correlate structure to spectroscopic and electrochemical properties. Given its high reduction potential compared to natural and designed FeCys4-containing proteins, we exploit it as terminal electron acceptor of a fully artificial chain triggered by visible light.

Electronic Structure of Tetrahedral, S = 2, [Fe{(EPiPr2)2N}2], E = S, Se, Complexes: Investigation by High-Frequency and -Field Electron Paramagnetic Resonance, 57Fe Mössbauer Spectroscopy, and Quantum Chemical Studies

In this work, we assessed the electronic structures of two pseudotetrahedral complexes of FeII, [Fe{(SPiPr2)2N}2] (1) and [Fe{(SePiPr2)2N}2] (2), using high-frequency and -field EPR (HFEPR) and field-dependent 57Fe Mössbauer spectroscopies. This investigation revealed S = 2 ground states characterized by moderate, negative zero-field splitting (zfs) parameters D. The crystal-field (CF) theory analysis of the spin Hamiltonian (sH) and hyperfine structure parameters revealed that the orbital ground states of 1 and 2 have a predominant dx2-y2 character, which is admixed with dz2 (∼10%). Although replacing the S-containing ligands of 1 by their Se-containing analogues in 2 leads to a smaller |D| value, our theoretical analysis, which relied on extensive ab initio CASSCF calculations, suggests that the ligand spin-orbit coupling (SOC) plays a marginal role in determining the magnetic anisotropy of these compounds. Instead, the dx2-y2β → dxyβ excitations yield a large negative contribution, which dominates the zfs of both 1 and 2, while the different energies of the dx2-y2β → dxzβ transitions are the predominant factor responsible for the difference in zfs between 1 and 2. The electronic structures of these compounds are contrasted with those of other [FeS4] sites, including reduced rubredoxin by considering a D2-type distortion of the [Fe(E-X)4] cores, where E = S, Se; X = C, P. Our combined CASSCF/DFT calculations indicate that while the character of the orbital ground state and the quintet excited states' contribution to the zfs of 1 and 2 are modulated by the magnitude of the D2 distortion, this structural change does not impact the contribution of the excited triplet states.

A new twist of rubredoxin function in M. tuberculosis

Electron transfer mediated by metalloproteins drives many biological processes. Rubredoxins are a ubiquitous [1Fe-0S] class of electron carriers that play an important role in bacterial adaptation to changing environmental conditions. In Mycobacterium tuberculosis, oxidative and acidic stresses as well as iron starvation induce rubredoxins expression. However, their functions during M. tuberculosis infection are unknown. In the present work, we show that rubredoxin B (RubB) is able to efficiently shuttle electrons from cognate reductases, FprA and FdR to support catalytic activity of cytochrome P450s, CYP124, CYP125, and CYP142, which are important for bacterial viability and pathogenicity. We solved the crystal structure of RubB and characterized the interaction between RubB and CYPs using site-directed mutagenesis. Mutations that not only neutralize single charge but also change the specific residues on the surface of RubB did not dramatically decrease activity of studied CYPs. Together with isothermal calorimetry (ITC) experiments, the obtained results suggest that interactions are transient and not highly specific. The redox potential of RubB is -264 mV vs. Ag/AgCl and the measured extinction coefficients are 9931 M^-1cm^-1 and 8371 M^-1cm^-1 at 380 nm and 490 nm, respectively. Characteristic parameters of RubB along with the discovered function might be useful for biotechnological applications. Our findings suggest that a switch from ferredoxins to rubredoxins might be crucial for M. tuberculosis to support CYPs activity during the infection.

Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds

The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.

Development of a Rubredoxin-Type Center Embedded in a de Dovo-Designed Three-Helix Bundle

Protein design is a powerful tool for interrogating the basic requirements for the function of a metal site in a way that allows for the selective incorporation of elements that are important for function. Rubredoxins are small electron transfer proteins with a reduction potential centered near 0 mV (vs normal hydrogen electrode). All previous attempts to design a rubredoxin site have focused on incorporating the canonical CXXC motifs in addition to reproducing the peptide fold or using flexible loop regions to define the morphology of the site. We have produced a rubredoxin site in an utterly different fold, a three-helix bundle. The spectra of this construct mimic the ultraviolet-visible, Mössbauer, electron paramagnetic resonance, and magnetic circular dichroism spectra of native rubredoxin. Furthermore, the measured reduction potential suggests that this rubredoxin analogue could function similarly. Thus, we have shown that an α-helical scaffold sustains a rubredoxin site that can cycle with the desired potential between the Fe(II) and Fe(III) states and reproduces the spectroscopic characteristics of this electron transport protein without requiring the classic rubredoxin protein fold.

Design of Redox-Active Peptides: Towards Functional Materials

In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.

A flexible iron(ii) complex in which zero-field splitting is resistant to structural variation

The zero-field splitting parameters D and E in the iron(ii) complex [Fe(C₃S₅)₂]^2– are shown to be remarkably resistant to a twist of the inter-ligand dihedral angle (θ_d) from 90 to 70°.

The relationship between electronic structure and zero-field splitting dictates key design parameters for magnetic molecules. In particular, to enable the directed synthesis of new electronic spin based qubits, developing complexes where zero-field splitting energies are invariant to structural changes is a critical challenge. Toward those ends, we report three salts of a new compound, a four-coordinate iron(ii) complex [Fe(C₃S₅)₂]^2– ([(18-crown-6)K]⁺ (1), Ph₄P⁺ (2), Bu₄N⁺ (3)) with a continuous structural variation in a single parameter, the dihedral angle (θ_d) between the two C₃S₅^2– ligands, as a function of counterion (θ_d = 89.98(4)° for 1 to 72.41(2)° for 3). Electron paramagnetic resonance data for 1–3 reveal zero-field splitting parameters that are unusually robust to the structural variation. Mössbauer spectroscopic measurements indicate that the structural variation in θ_d primarily affects the highest-energy 3d-orbitals (d_xz and d_yz) of the iron(ii) ion. These orbitals have the smallest impact on the zero-field splitting parameters, thus the distortion has a minor effect on D and E. These results represent the first part of a directed effort to understand how spin state energies may be fortified against structural distortions for future applications of qubits in non-crystalline environments.