Mimicking Photosynthesis in a Computationally Designed Synthetic Metalloprotein

What defines biomimetic and bioinspired science and engineering?

Biomimicry, biomimesis and bioinspiration define distinctly different approaches for deepening the understanding of how living systems work and employing this knowledge to meet pressing demands in engineering. Biomimicry involves shear imitation of biological structures that most often do not reproduce the functionality that they have while in the living organisms. Biomimesis aims at reproduction of biological structure-function relationships and advances our knowledge of how different components of complex living systems work. Bioinspiration employs this knowledge in abiotic manners that are optimal for targeted applications. This article introduces and reviews these concepts in a global historic perspective. Representative examples from charge-transfer science and solar-energy engineering illustrate the evolution from biomimetic to bioinspired approaches and show their importance. Bioinspired molecular electrets, aiming at exploration of dipole effects on charge transfer, demonstrate the pintail impacts of biological inspiration that reach beyond its high utilitarian values. The abiotic character of bioinspiration opens doors for the emergence of unprecedented properties and phenomena, beyond what nature can offer.

Multifaceted aspects of charge transfer

Charge transfer and charge transport are by far among the most important processes for sustaining life on Earth and for making our modern ways of living possible. Involving multiple electron-transfer steps, photosynthesis and cellular respiration have been principally responsible for managing the energy flow in the biosphere of our planet since the Great Oxygen Event. It is impossible to imagine living organisms without charge transport mediated by ion channels, or electron and proton transfer mediated by redox enzymes. Concurrently, transfer and transport of electrons and holes drive the functionalities of electronic and photonic devices that are intricate for our lives. While fueling advances in engineering, charge-transfer science has established itself as an important independent field, originating from physical chemistry and chemical physics, focusing on paradigms from biology, and gaining momentum from solar-energy research. Here, we review the fundamental concepts of charge transfer, and outline its core role in a broad range of unrelated fields, such as medicine, environmental science, catalysis, electronics and photonics. The ubiquitous nature of dipoles, for example, sets demands on deepening the understanding of how localized electric fields affect charge transfer. Charge-transfer electrets, thus, prove important for advancing the field and for interfacing fundamental science with engineering. Synergy between the vastly different aspects of charge-transfer science sets the stage for the broad global impacts that the advances in this field have.

Computational approaches for de novo design and redesign of metal-binding sites on proteins

Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.

Computational de novo design and characterization of a protein that selectively binds a highly hyperpolarizable abiological chromophore

This work reports the first example of a single-chain protein computationally designed to contain four α-helical segments and fold to form a four-helix bundle encapsulating a supramolecular abiological chromophore that possesses exceptional nonlinear optical properties. The 109-residue protein, designated SCRPZ-1, binds and disperses an insoluble hyperpolarizable chromophore, ruthenium(II) [5-(4'-ethynyl-(2,2';6',2″-terpyridinyl))-10,20-bis(phenyl)porphinato]zinc(II)-(2,2';6',2″-terpyridine)(2+) (RuPZn) in aqueous buffer solution at a 1:1 stoichiometry. A 1:1 binding stoichiometry of the holoprotein is supported by electronic absorption and circular dichroism spectra, as well as equilibrium analytical ultracentrifugation and size exclusion chromatography. SCRPZ-1 readily dimerizes at micromolar concentrations, and an empirical redesign of the protein exterior produced a stable monomeric protein, SCRPZ-2, that also displayed a 1:1 protein:cofactor stoichiometry. For both proteins in aqueous buffer, the encapsulated cofactor displays photophysical properties resembling those exhibited by the dilute RuPZn cofactor in organic solvent: femtosecond, nanosecond, and microsecond time scale pump-probe transient absorption spectroscopic data evince intensely absorbing holoprotein excited states having large spectral bandwidth that penetrate deep in the near-infrared energy regime; the holoprotein electronically excited triplet state exhibits a microsecond time scale lifetime characteristic of the RuPZn chromophore. Hyper-Rayleigh light scattering measurements carried out at an incident irradiation wavelength of 1340 nm for these holoproteins demonstrate an exceptional dynamic hyperpolarizabilty (β1340 = 3100 × 10(-30) esu). X-ray reflectivity measurements establish that this de novo-designed hyperpolarizable protein can be covalently attached with high surface density to a silicon surface without loss of the cofactor, indicating that these assemblies provide a new approach to bioinspired materials that have unique electro-optic functionality.

Novel proteins: from fold to function

The field of de novo protein design, though only two decades old, has already reached the point where designing and selecting novel proteins that are functionally active has been achieved several times. Here we review recently reported de novo functional proteins that were developed using various approaches, including rational design, computational optimization, and selection from combinatorial libraries. The functions displayed by these proteins range from metal binding to enzymatic catalysis. Some were designed for specific applications in engineering and medicine, and others provide life-sustaining functions in vivo.

Electrostatic docking of a supramolecular host-guest assembly to cytochrome c probed by bidirectional photoinduced electron transfer

A water-soluble octacarboxyhemicarcerand was used as a shuttle to transport redox-active substrates across the aqueous medium and deliver them to the target protein. The results show that weak multivalent interactions and conformational flexibility can be exploited to reversibly bind complex supramolecular assemblies to biological molecules. Hydrophobic electron donors and acceptors were encapsulated within the hemicarcerand, and photoinduced electron transfer (ET) between the Zn-substituted cytochrome c (MW = 12.3 kD) and the host-guest complexes (MW = 2.2 kD) was used to probe the association between the negatively charged hemicarceplex and the positively charged protein. The behavior of the resulting ternary protein-hemicarcerand-guest assembly was investigated in two binding limits: (1) when K(encaps) ≫ K(assoc), the hemicarcerand transports the ligand to the protein while protecting it from the aqueous medium; and (2) when K(assoc) > K(encaps), the hemicarcerand-protein complex is formed first, and the hemicarcerand acts as an artificial receptor site that intercepts ligands from solution and positions them close to the active site of the metalloenzyme. In both cases, ET mediated by the protein-bound hemicarcerand is much faster than that due to diffusional encounters with the respective free donor or acceptor in solution. The measured ET rates suggest that the dominant binding region of the host-guest complex on the surface of the protein is consistent with the docking area of the native redox partner of cytochrome c. The strong association with the protein is attributed to the flexible conformation and adaptable charge distribution of the hemicarcerand, which allow for surface-matching with the cytochrome.

Artificial photoactive proteins

Solar power is the most abundant source of renewable energy. In this respect, the goal of making photoactive proteins is to utilize this energy to generate an electron flow. Photosystems have provided the blueprint for making such systems, since they are capable of converting the energy of light into an electron flow using a series of redox cofactors. Protein tunes the redox potential of the cofactors and arranges them such that their distance and orientation are optimal for the creation of a stable charge separation. The aim of this review is to present an overview of the literature with regard to some elegant functional structures that protein designers have created by introducing cofactors and photoactivity into synthetic proteins.

Conformationally gated photoinduced processes within photosensitizer-acceptor dyads based on osmium(II) complexes with triarylpyridinio-functionalized terpyridyl ligands: insights from experimental study

[(ttpy)Os(tpy-ph-TPH(3)(+))](3+) (2), [(ttpy)Os(tpy-xy-TPH(3)(+))](3+) (3), [(ttpy)Os(tpy-ph-TPH(2)(NO(2))(+))](3+) (4), and [(ttpy)Os(tpy-xy-TPH(2)(NO(2))(+))](3+) (5) are a series of dyads made of an Os(II) bis-tpy complex (tpy = 2,2':6',2"-terpyridine) as the photosensitizer (P) and 2,4,6-triarylpyridinium group (TP(+)) as the electron acceptor (A). These dyads were designed to form charge-separated states (CSS) upon light excitation. Together with analogous Ru(II) complexes (7-10), they have been synthesized and fully characterized. We describe herein how intramolecular photoinduced processes are affected when the electron-accepting strength of A (by nitro-derivatization of TP(+)) and/or the steric hindrance about intercomponent linkage (by replacing a phenyl spacer by a xylyl one) are changed. Electronic absorption and electrochemical behavior revealed that (i) chemical substitution of TP(+) (i.e., TP(+)-NO(2)) has no sizable influence on P-centered electronic features, (ii) reduction processes located on TP(+) depend on the intercomponent tilt angle. Concerning excited-state properties, photophysical investigation evidenced that phosphorescence of P is actually quenched in dyads 4 and 5 only. Ultrafast transient absorption (TA) experiments allowed attributing the quenching in conformationally locked dyad 5 to oxidative electron transfer (ET) from the (3)MLCT level to the TP(+)-NO(2) acceptor (k(el) = 1.1 x 10(9) s(-)(1)). For 4, geometrically unlocked, the (3)MLCT state was shown to first rapidly equilibrate (reversible energy transfer; k(eq) approximately 2 x 10(9) s(-)(1)) with a ligand centered triplet state before undergoing CSS formation. Thus, the pivotal role of conformation in driving excited-state decay pathways is demonstrated. Also, inner P structural planarization as a relaxation mode of the (3)MLCT states has been inferred from TA experiments.

Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up

The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.

Design, folding, and activities of metal-assembled coiled coil proteins

Metal ions serve many purposes in natural proteins, from the stabilization of tertiary structure to the direction of protein folding to crucial roles in electron transfer and catalysis. There is considerable interest in creating metal binding sites in designed proteins to understand the structural role of metal ions and to design new metalloproteins with useful functions. The de novo design of metalloproteins and the role of metals in the folding of designed proteins are reviewed here, with particular focus on the design, folding, and activities of the [M(bpy-peptide)(3)](2+) structure. This maquette is constructed by the covalent attachment of 2,2'-bipyridine to the N-termini of amphiphilic peptides, and it is assembled into a folded trimeric coiled coil by the addition of a six-coordinate transition metal ion and the resulting hydrophobic collapse of the peptides. The [M(bpy-peptide)(3)](2+) structure has been employed in diverse applications, ranging from electron transfer pathway studies to the study of optimal hydrophobic packing in a virtual library to the construction of receptors and biosensors.

From model compounds to protein binding: syntheses, characterizations and fluorescence studies of [RuII(bipy)(terpy)L]2+complexes (bipy = 2,2′-bipyridine; terpy = 2,2′:6′,2″-terpyridine; L = imidazole, pyrazole and derivatives, cytochrome c)

Compounds [RuII(bipy)(terpy)L](PF6)2 with bipy = 2,2'-bipyridine, terpy = 2,2':6',2"-terpyridine, L = H2O, imidazole (imi), 4-methylimidazole, 2-methylimidazole, benzimidazole, 4,5-diphenylimidazole, indazole, pyrazole, 3-methylpyrazole have been synthesized and characterized by 1H NMR, ESI-MS and UV/Vis (in CH3CN and H2O). For L = H2O, imidazole, 4,5-diphenylimidazole and indazole the X-ray structures of the complexes have been determined with the crystal packing featuring only few intermolecular C-H...pi or pi-pi interactions due to the separating action of the PF6-anions. Complexes with L = imidazole and 4-methylimidazole exhibit a fluorescence emission with a maximum at 662 and 667 nm, respectively (lambdaexc= 475 nm, solvent CH3CN or H2O). The substitution of the aqua ligand in [Ru(bipy)(terpy)(H2O)]2+ in aqueous solution by imidazole to give [Ru(bipy)(terpy)(imi)]2+ is fastest at a pH of 8.5 (as followed by the increase in emission intensity). Coupling of the [Ru(bipy)(terpy)]2+ fragment to cytochrome c(Yeast iso-1) starting from the Ru-aqua complex was successful at 35 degrees C and pH 7.0 after 5 d under argon in the dark. The [Ru(bipy)(terpy)(cyt c)]-product was characterized by UV/Vis, emission and mass spectrometry. The location where the [Ru(bipy)(terpy)] complex was coupled to the protein was identified as His44 (corresponding to His39 in other numbering schemes) using digestion of the Ru-coupled protein by trypsin and analysis of the tryptic peptides by HPLC-high resolution MS.