Electron transfer in ruthenium-modified spinach plastocyanin mutants

Catalysis and Electron Transfer in De Novo Designed Metalloproteins

One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.

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.

A QM/MM study of the nature of the entatic state in plastocyanin

Plastocyanin is a copper containing protein that is involved in the electron transfer process in photosynthetic organisms. The active site of plastocyanin is described as an entatic state whereby its structure represents a compromise between the structures favored by the oxidized and reduced forms. In this study, the nature of the entatic state is investigated through density functional theory‐based hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. The strain energy is computed to be 12.8 kcal/mol and 14.5 kcal/mol for the oxidized and reduced forms of the protein, indicating that the active site has an intermediate structure. It is shown that the energy gap between the oxidized and reduced forms varies significantly with the fluctuations in the structure of the active site at room temperature. An accurate determination of the reorganization energy requires averaging over conformation and a large region of the protein around the active site to be treated at the quantum mechanical level. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Electron transfer activity of a de novo designed copper center in a three-helix bundle fold

In this work, we characterized the intermolecular electron transfer (ET) properties of a de novo designed metallopeptide using laser-flash photolysis. α3D-CH3 is three helix bundle peptide that was designed to contain a copper ET site that is found in the β-barrel fold of native cupredoxins. The ET activity of Cuα3D-CH3 was determined using five different photosensitizers. By exhibiting a complete depletion of the photo-oxidant and the successive formation of a Cu(II) species at 400 nm, the transient and generated spectra demonstrated an ET transfer reaction between the photo-oxidant and Cu(I)α3D-CH3. This observation illustrated our success in integrating an ET center within a de novo designed scaffold. From the kinetic traces at 400 nm, first-order and bimolecular rate constants of 10(5) s(-1) and 10(8) M(-1) s(-1) were derived. Moreover, a Marcus equation analysis on the rate versus driving force study produced a reorganization energy of 1.1 eV, demonstrating that the helical fold of α3D requires further structural optimization to efficiently perform ET. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Imidazole and Triazole Coordination Chemistry for Antifouling Coatings

Fouling of marine organisms on the hulls of ships is a severe problem for the shipping industry. Many antifouling agents are based on five-membered nitrogen heterocyclic compounds, in particular imidazoles and triazoles. Moreover, imidazole and triazoles are strong ligands for Cu2+and Cu+, which are both potent antifouling agents. In this review, we summarize a decade of work within our groups concerning imidazole and triazole coordination chemistry for antifouling applications with a particular focus on the very potent antifouling agentmedetomidine. The entry starts by providing a detailed theoretical description of the azole-metal coordination chemistry. Some attention will be given to ways to functionalize polymers with azole ligands. Then, the effect of metal coordination in azole-containing polymers with respect to material properties will be discussed. Our work concerning the controlled release of antifouling agents, in particular medetomidine, using azole coordination chemistry will be reviewed. Finally, an outlook will be given describing the potential for tailoring the azole ligand chemistry in polymers with respect to Cu2+adsorption and Cu2+→Cu+reduction for antifouling coatings without added biocides.

Functional Metalloproteins Integrated with Conductive Substrates: Detecting Single Molecules and Sensing Individual Recognition Events

In the past decade, there has been significant interest in the integration of biomaterials with electronic elements: combining biological functions of biomolecules with nanotechnology offers new perspectives for implementation of ultrasensitive hybrid nanodevices. In particular, great attention has been devoted to redox metalloproteins, since they possess unique characteristics, such as electron-transfer capability, possibility of gating redox activity, and nanometric size, which make them appealing for bioelectronics applications at the nanoscale. The reliable connection of redox proteins to electrodes, aimed at ensuring good electrical contact with the conducting substrate besides preserving protein functionality, is a fundamental step for designing a hybrid nanodevice and calls for a full characterization of the immobilized proteins, possibly at the single-molecule level. Here, we describe how a multitechnique approach, based on several scanning probe microscopy techniques, may provide a comprehensive characterization of different metalloproteins on metal electrodes, disclosing unique information not only about morphological properties of the adsorbed molecules but also about the effectiveness of electrical coupling with the conductive substrate, or even concerning the preserved biorecognition capability upon adsorption. We also show how the success of an immobilization strategy, which is of primary importance for optimal integration of metalloproteins with a metal electrode, can be promptly assessed by means of the proposed approach. Besides the characterization aspect, the complementary employment of the proposed techniques deserves major potentialities for ultrasensitive detection of adsorbed biomolecules. In particular, it is shown how sensing of single metalloproteins may be optimized by monitoring the most appropriate observable. Additionally, we suggest how the combination of several experimental techniques might offer increased versatility, real-time response, and wide applicability as a detection method, once a reproducible correlation among signals coming from different single-molecule techniques is established.

Photo Processes on Self-Associated Cationic Porphyrins and Plastocyanin Complexes 1. Ligation of Plastocyanin Tyrosine 83 onto Metalloporphyrins and Electron-Transfer Fluorescence Quenching

The spectroscopic properties of the self-associated complexes formed between the anionic surface docking site of spinach plastocyanin and the cationic metalloporphyrins, in which the tyrosine 83 (Y83) moiety is placed just below the docking site, tetrakis(N-methyl-4-pyridyl)porphyrin (Pd(II)TMPyP(4+) and Zn(II)TMPyP(4+)), have been studied and reported herein. The fluorescence quenching phenomenon of the self-assembled complex of Zn(II)TMPyP(4+)/plastocyanin has also been discovered. The observed red-shifting of the Soret and Q-bands of the UV-visible spectra, ca. 9 nm for Pd(II)TMPyP(4+)/plastocyanin and ca. 6 nm for the Zn(II)TMPyP(4+)/plastocyanin complexes, was explained in terms of exciton theory coupled with the Gouterman model. Thus, the hydroxyphenyl terminus of the Y83 residue of the self-associated plastocyanin/cationic porphyrin complexes was implicated in the charge-transfer ligation with the central metal atoms of these metalloporphyrins. Moreover, ground-state spectrometric-binding studies between Pd(II)TMPyP(4+) and the Y83 mutant plastocyanin (Y83F-PC) system proved that Y83 moiety of plastocyanin played a critical role in the formation of such ion-pair complexes. Difference absorption spectra and the Job's plots showed that the electrostatic attractions between the cationic porphyrins and the anionic patch of plastocyanin, bearing the nearby Y83 residue, led to the predominant formation of a self-associated 1:1 complex in the ground-state with significantly high binding constants (K = (8.0 +/- 1.1) x 10(5) M(-1) and (2.7 +/- 0.8) x 10(6) M(-1) for Pd(II)TMPyP(4+) and zinc variant, respectively) in low ionic strength buffer, 1 mM KCl and 1 mM phosphate buffer (pH 7.4). Molecular modeling calculations supported the formation of a 1:1 self-associated complex between the porphyrin and plastocyanin with an average distance of ca. 9 A between the centers of mass of the porphyrin and Y83 positioned just behind the anionic surface docking site on the protein surface. The photoexcited singlet state of Zn(II)TMPyP(4+) was quenched by the Y83 residue of the self-associated plastocyanin in a static mechanism as evidenced by steady-state and time-resolved fluorescence experiments. Even when all the porphyrin was complexed (more than 97%), significant residual fluorescence from the complex was observed such that the amplitude of quenching of the singlet state of uncomplexed species was enormously obscured.

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.

A Combined Atomic Force Microscopy and Molecular Dynamics Simulation Study on a Plastocyanin Mutant Chemisorbed on a Gold Surface

A mutant of copper plastocyanin, covalently bound to an Au (111) surface through an engineered disulfide bridge, was investigated in aqueous medium by atomic force microscopy (AFM) and molecular dynamics (MD) simulations. Tapping-mode AFM images revealed adsorption of single molecules which are homogeneously distributed over the substrate and strongly bound to gold and display uniform lateral size. A statistical analysis of the height of the macromolecules on the gold substrate evidenced a distribution around a mean value consistent with that expected from the crystallographic data and with a relatively large standard deviation. A 10-ns classical MD simulation of mutated plastocyanin, hydrated by a layer of water, covalently bound to a gold surface by one or two sulfur atoms, was performed. The simulations indicate that the bound protein retains, in both cases, its overall tertiary structure during the dynamic evolution. Moreover, the macro-molecule can assume different orientations with respect to the gold substrate, which give rise to a distribution of heights on the gold substrate. Experimental and MD simulation results are compared and discussed in connection with the topological and dynamical properties of the protein system.