Design of a single protein that spans the entire 2-V range of physiological redox potentials

Contrasting secondary coordination sphere effects on spin density distribution in Red vs. Blue Cu azurin

Metalloproteins tune the electronic properties of metal active sites through a combination of primary and secondary coordination sphere effects (PCS and SCS) to efficiently perform an array of redox chemistry, including electron transfer (ET) and catalysis. A major influence of these effects is the anisotropic spatial distribution of redox-active molecular orbitals (RAMOs), which in turn dictates redox chemistry of the metalloproteins. While much progress has been made in understanding the SCS effects on RAMOs in individual native metalloproteins, it has been difficult to experimentally examine the influence of the same SCS effects on RAMOs with different spatial distributions. Taking advantage of our recent studies of SCS effect on blue copper azurin from Pseudomonas aeruginosa (Blue CuAz) and its M121H/H46E variant that closely mimic the red copper protein (Red CuAz), in which their RAMOs are dominated by either Cu-Sπ or Cu-Sσ interactions, respectively, we herein compare and contrast how the same SCS modifications impact the electronic and geometric structures of blue and red Cu center in the same protein scaffold. Specifically, we expand our understanding of unpaired electron distribution at the Cu-binding site of Red CuAz and its SCS N47S, F114P, and F114N mutations using 1H and 14N electron-nuclear double resonance (ENDOR) spectroscopy, and then further combine these data sets with recent studies and DFT calculations to provide insight into how these mutations differentially (or similarly) impact electronic structure in Red vs. Blue CuAz. We find that electrostatics produce similar effects in both Red and Blue CuAz, where the introduction of dipole moments in the vicinity of Cu and S produces changes in spin density distribution and of the same sign and comparable magnitude. However, disruption of H-bonding with S through the F114P mutation leads to opposing effects in Red vs. Blue CuAz, which we propose arise from differences in the conformation of Cys112 sidechain adapted in the absence the stabilizing SC112⋯H-N backbone interaction.

Azurin: A Model to Study a Metal Coordination Sphere or Electron Transfer in Metalloproteins

Azurin is a small blue copper protein that participates in redox reactions during anaerobic respiration in Pseudomonas aeruginosa, and there are a significant number of studies employing this model to investigate the electron transfer (ET) processes or coordination sphere of metal ion in metalloproteins. Azurin naturally contains Cu(II/I) as a central ion and is redox-active for a single electron ET. Moreover, azurin with no central ion (apo-azurin) is capable of binding other metal cofactors-e.g., Zn(II)-forming redox-inactive Zn-form and many others impacting the redox potential and structural variation in the active site's arrangement. Also, mutations of amino acid residues in the immediate vicinity of the metal ion can influence the structure and functionality of a particular metalloprotein. Therefore, this review aims to summarize the abundant information about selected topics related to redox reactions and blue copper proteins, particularly azurin, and is structured as follows: (i) introduction to the structure, properties, and physiological role of this group of metalloproteins, (ii) the role of the equatorial and axial ligands of the central metal ions, or metal species, in the active site on the metal coordination sphere's structure and related determination of the particular azurin form's redox potentials, and (iii) the effects of the particular amino acid's moiety (Phe, Tyr and Trp residues together with acceleration employing Trp-Trp π-π stacking interactions contrary to ET distance dependence) on the preferable type of long-range ET mechanism in an azurin-mediated model biomolecule. We assume that azurin is a suitable model to study the structural functionality of a particular central metal ion or individual amino acid residues in the central ion coordination sphere for studying the redox potential and ET reactions in metalloproteins.

Protein Electronic Energy Transport Levels Derived from High-Sensitivity Near-UV and Constant Final State Yield Photoemission Spectroscopy

Proteins are attractive as functional components in molecular junctions. However, controlling the electronic charge transport via proteins, held between two electrodes, requires information on their frontier orbital energy level alignment relative to the electrodes' Fermi level (EF), which normally requires studies of UV Photoemission Spectroscopy (UPS) with HeI excitation. Such excitation is problematic for proteins, which can denature under standard measuring conditions. Here high-sensitivity soft UV photoemission spectroscopy (HS-UPS) combined with Constant Final State Yield Spectroscopy (CFS-YS) is used to get this information for electrode/protein contacts. Monolayers of the redox protein Azurin, (Az) and its Apo-form on Au substrates, have HOMO onset energies, obtained from CFS-YS, differ by ≈0.2 eV, showing the crucial role of the Cu redox centre in the electron transport process. It is found that combined HS-UPS/CFS-YS measurements agree with the Photoelectron Yield Spectroscopy (PYS), showing potential of the HS-UPS + CFS-YS as a powerful tool to characterize and map the energetics of a protein-electrode interfaces, which will aid optimizing design of devices with targeted electronic properties, as well as for novel applications.

Electronic structures of blue copper centers of amicyanin and azurin in the solution state

X-ray absorption near edge structure (XANES) spectra of blue copper proteins, amicyanin and azurin, in the solution state were measured in the copper L3-edge energy region. The absorption peak energies were quite similar for both proteins, while the main edge region for azurin was broader than that for amicyanin, owing to more pronounced shoulder spectral features in the former. Ab initio calculations at the whole protein level qualitatively reproduced the experimental spectra well. The relative X-ray absorption intensities suggest that the degree of covalency of the copper-ligand bond at the active site was weaker for amicyanin than that for azurin.

Single-step purification and characterization of Pseudomonas aeruginosa azurin

Azurin is a small periplasmic blue copper protein found in bacterial strains such as Pseudomonas and Alcaligenes where it facilitates denitrification. Azurin is extensively studied for its ability to mediate electron-transfer processes, but it has also sparked interest of the pharmaceutical community as a potential antimicrobial or anticancer agent. Here we offer a novel approach for expression and single-step purification of azurin in Escherichia coli with high yields and optimal metalation. A fusion tag strategy using an N-terminal GST tag was employed to obtain pure protein without requiring any additional purification steps. After the on-column cleavage by HRV 3C Protease, azurin is collected and additionally incubated with copper sulphate to ensure sufficient metalation. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect azurin structure. In addition, the biological activity of azurin was tested in HeLa cells.

Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis

This review aims to provide an overview of the progress in protein-based artificial photosystem design and their potential to uncover the underlying principles governing light-harvesting in photosynthesis. While significant advances have been made in this area, a gap persists in reviewing these advances. This review provides a perspective of the field, pinpointing knowledge gaps and unresolved challenges that warrant further inquiry. In particular, it delves into the key considerations when designing photosystems based on the chromophore and protein scaffold characteristics, presents the established strategies for artificial photosystems engineering with their advantages and disadvantages, and underscores the recent breakthroughs in understanding the molecular mechanisms governing light-harvesting, charge separation, and the role of the protein motions in the chromophore's excited state relaxation. By disseminating this knowledge, this article provides a foundational resource for defining the field of bio-hybrid photosystems and aims to inspire the continued exploration of artificial photosystems using protein design.

Oxygen-resistant [FeFe]hydrogenases: new biocatalysis tools for clean energy and cascade reactions

The use of enzymes to generate hydrogen, instead of using rare metal catalysts, is an exciting area of study in modern biochemistry and biotechnology, as well as biocatalysis driven by sustainable hydrogen. Thus far, the oxygen sensitivity of the fastest hydrogen-producing/exploiting enzymes, [FeFe]hydrogenases, has hindered their practical application, thereby restricting innovations mainly to their [NiFe]-based, albeit slower, counterparts. Recent exploration of the biodiversity of clostridial hydrogen-producing enzymes has yielded the isolation of representatives from a relatively understudied group. These enzymes possess an inherent defense mechanism against oxygen-induced damage. This discovery unveils fresh opportunities for applications such as electrode interfacing, biofuel cells, immobilization, and entrapment for enhanced stability in practical uses. Furthermore, it suggests potential combinations with cascade reactions for CO2 conversion or cofactor regeneration, like NADPH, facilitating product separation in biotechnological processes. This work provides an overview of this new class of biocatalysts, incorporating unpublished protein engineering strategies to further investigate the dynamic mechanism of oxygen protection and to address crucial details remaining elusive such as still unidentified switching hot-spots and their effects. Variants with improved kcat as well as chimeric versions with promising features to attain gain-of-function variants and applications in various biotechnological processes are also presented.

57Fe nuclear resonance vibrational spectroscopic studies of tetranuclear iron clusters bearing terminal iron(iii)-oxido/hydroxido moieties

57Fe nuclear resonance vibrational spectroscopy (NRVS) has been applied to study a series of tetranuclear iron ([Fe4]) clusters based on a multidentate ligand platform (L3-) anchored by a 1,3,5-triarylbenzene linker and pyrazolate or (tertbutylamino)pyrazolate ligand (PzNH t Bu-). These clusters bear a terminal Fe(iii)-O/OH moiety at the apical position and three additional iron centers forming the basal positions. The three basal irons are connected with the apical iron center via a μ4-oxido ligand. Detailed vibrational analysis via density functional theory calculations revealed that strong NRVS spectral features below 400 cm-1 can be used as an oxidation state marker for the overall [Fe4] cluster core. The terminal Fe(iii)-O/OH stretching frequencies, which were observed in the range of 500-700 cm-1, can be strongly modulated (energy shifts of 20-40 cm-1 were observed) upon redox events at the three remote basal iron centers of the [Fe4] cluster without the change of the terminal Fe(iii) oxidation state and its coordination environment. Therefore, the current study provides a quantitative vibrational analysis of how the remote iron centers within the same iron cluster exert exquisite control of the chemical reactivities and thermodynamic properties of the specific iron site that is responsible for small molecule activation.

HYSCORE and QM/MM Studies of Second Sphere Variants of the Type 1 Copper Site in Azurin: Influence of Mutations on the Hyperfine Couplings of Remote Nitrogens

Secondary coordination sphere (SCS) interactions have been shown to play important roles in tuning reduction potentials and electron transfer (ET) properties of the Type 1 copper proteins, but the precise roles of these interactions are not fully understood. In this work, we examined the influence of F114P, F114N, and N47S mutations in the SCS on the electronic structure of the T1 copper center in azurin (Az) by studying the hyperfine couplings of (i) histidine remote Nε nitrogens and (ii) the amide Np using the two-dimensional (2D) pulsed electron paramagnetic resonance (EPR) technique HYSCORE (hyperfine sublevel correlation) combined with quantum mechanics/molecular mechanics (QM/MM) and DLPNO-CCSD calculations. Our data show that some components of hyperfine tensor and isotropic coupling in N47SAz and F114PAz (but not F114NAz) deviate by up to ∼±20% from WTAz, indicating that these mutations significantly influence the spin density distribution between the CuII site and coordinating ligands. Furthermore, our calculations support the assignment of Np to the backbone amide of residue 47 (both in Asn and Ser variants). Since the spin density distributions play an important role in tuning the covalency of the Cu-Scys bond of Type 1 copper center that has been shown to be crucial in controlling the reduction potentials, this study provides additional insights into the electron spin factor in tuning the reduction potentials and ET properties.

Electrochemical and structural characterization of recombinant respiratory proteins of the acidophilic iron oxidizer Ferrovum sp. PN-J47-F6 suggests adaptations to the acidic pH at protein level

The tendency of the periplasmic redox proteins in acidophiles to have more positive redox potentials (Em) than their homologous counterparts in neutrophiles suggests an adaptation to acidic pH at protein level, since thermodynamics of electron transfer processes are also affected by acidic pH. Since this conclusion is mainly based on the electrochemical characterization of redox proteins from extreme acidophiles of the genus Acidithiobacillus, we aimed to characterize three recombinant redox proteins of the more moderate acidophile Ferrovum sp. PN-J47-F6. We applied protein film voltammetry and linear sweep voltammetry coupled to UV/Vis spectroscopy to characterize the redox behavior of HiPIP-41, CytC-18, and CytC-78, respectively. The Em-values of HiPIP-41 (571 ± 16 mV), CytC-18 (276 ± 8 mV, 416 ± 2 mV), and CytC-78 (308 ± 7 mV, 399 ± 7 mV) were indeed more positive than those of homologous redox proteins in neutrophiles. Moreover, our findings suggest that the adaptation of redox proteins with respect to their Em occurs more gradually in response to the pH, since there are also differences between moderate and more extreme acidophiles. In order to address structure function correlations in these redox proteins with respect to structural features affecting the Em, we conducted a comparative structural analysis of the Ferrovum-derived redox proteins and homologs of Acidithiobacillus spp. and neutrophilic proteobacteria. Hydrophobic contacts in the redox cofactor binding pockets resulting in a low solvent accessibility appear to be the major factor contributing to the more positive Em-values in acidophile-derived redox proteins. While additional cysteines in HiPIPs of acidophiles might increase the effective shielding of the [4Fe-4S]-cofactor, the tight shielding of the heme centers in acidophile-derived cytochromes is achieved by a drastic increase in hydrophobic contacts (A.f. Cyc41), and by a larger fraction of aromatic residues in the binding pockets (CytC-18, CytC-78).

Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features

Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.

The energetics and evolution of oxidoreductases in deep time

The core metabolic reactions of life drive electrons through a class of redox protein enzymes, the oxidoreductases. The energetics of electron flow is determined by the redox potentials of organic and inorganic cofactors as tuned by the protein environment. Understanding how protein structure affects oxidation-reduction energetics is crucial for studying metabolism, creating bioelectronic systems, and tracing the history of biological energy utilization on Earth. We constructed ProtReDox (https://protein-redox-potential.web.app), a manually curated database of experimentally determined redox potentials. With over 500 measurements, we can begin to identify how proteins modulate oxidation-reduction energetics across the tree of life. By mapping redox potentials onto networks of oxidoreductase fold evolution, we can infer the evolution of electron transfer energetics over deep time. ProtReDox is designed to include user-contributed submissions with the intention of making it a valuable resource for researchers in this field.

Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase from Streptomyces coelicolor through Secondary Coordination Sphere Mutations

The key to type 1 copper (T1Cu) function lies in the fine tuning of the CuII/I reduction potential (E°'T1Cu ) to match those of its redox partners, enabling efficient electron transfer in a wide range of biological systems. While the secondary coordination sphere (SCS) effects have been used to tune E°'T1Cu in azurin over a wide range, these principles are yet to be generalized to other T1Cu-containing proteins to tune catalytic properties. To this end, we have examined the effects of Y229F, V290N and S292F mutations around the T1Cu of small laccase (SLAC) from Streptomyces coelicolor to match the high E°'T1Cu of fungal laccases. Using ultraviolet-visible absorption and electron paramagnetic resonance spectroscopies, together with X-ray crystallography and redox titrations, we have probed the influence of SCS mutations on the T1Cu and corresponding E°'T1Cu . While minimal and small E°'T1Cu increases are observed in Y229F- and S292F-SLAC, the V290N mutant exhibits a major E°'T1Cu increase. Moreover, the influence of these mutations on E°'T1Cu is additive, culminating in a triple mutant Y229F/V290N/S292F-SLAC with the highest E°'T1Cu of 556 mV vs. SHE reported to date. Further activity assays indicate that all mutants retain oxygen reduction reaction activity, and display improved catalytic efficiencies (kcat /KM ) relative to WT-SLAC.

Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)

Per and polyfluoroalkyl substances (PFAS) present a unique challenge to remediation techniques because their strong carbon-fluorine bonds make them difficult to degrade. This review explores the use of in silico enzymatic design as a potential PFAS degradation technique. The scope of the enzymes included is based on currently known PFAS degradation techniques, including chemical redox systems that have been studied for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) defluorination, such as those that incorporate hydrated electrons, sulfate, peroxide, and metal catalysts. Bioremediation techniques are also discussed, namely the laccase and horseradish peroxidase systems. The redox potential of known reactants and enzymatic radicals/metal-complexes are then considered and compared to potential enzymes for degrading PFAS. The molecular structure and reaction cycle of prospective enzymes are explored. Current knowledge and techniques of enzyme design, particularly radical-generating enzymes, and application are also discussed. Finally, potential routes for bioengineering enzymes to enable or enhance PFAS remediation are considered as well as the future outlook for computational exploration of enzymatic in situ bioremediation routes for these highly persistent and globally distributed contaminants.

Surface Charge Deposition by Moving Drops Reduces Contact Angles

Slide electrification-the spontaneous charge separation by sliding aqueous drops-can lead to an electrostatic potential in the order of 1 kV and change drop motion substantially. To find out how slide electrification influences the contact angles of moving drops, we analyzed the dynamic contact angles of aqueous drops sliding down tilted plates with insulated surfaces, grounded surfaces, and while grounding the drop. The observed decrease in dynamic contact angles at different salt concentrations is attributed to two effects: An electrocapillary reduction of contact angles caused by drop charging and a change in the free surface energy of the solid due to surface charging.

A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase

The "Histidine-brace" (His-brace) copper-binding site, composed of Cu(His)2 with a backbone amine, is found in metalloproteins with diverse functions. A primary example is lytic polysaccharide monooxygenase (LPMO), a class of enzymes that catalyze the oxidative depolymerization of polysaccharides, providing not only an energy source for native microorganisms but also a route to more effective industrial biomass conversion. Despite its importance, how the Cu His-brace site performs this unique and challenging oxidative depolymerization reaction remains to be understood. To answer this question, we have designed a biosynthetic model of LPMO by incorporating the Cu His-brace motif into azurin, an electron transfer protein. Spectroscopic studies, including ultraviolet-visible (UV-Vis) absorption and electron paramagnetic resonance, confirm copper binding at the designed His-brace site. Moreover, the designed protein is catalytically active towards both cellulose and starch, the native substrates of LPMO, generating degraded oligosaccharides with multiturnovers by C1 oxidation. It also performs oxidative cleavage of the model substrate 4-nitrophenyl-D-glucopyranoside, achieving a turnover number ~9% of that of a native LPMO assayed under identical conditions. This work presents a rationally designed artificial metalloenzyme that acts as a structural and functional mimic of LPMO, which provides a promising system for understanding the role of the Cu His-brace site in LPMO activity and potential application in polysaccharide degradation.

The Mechanism of Inhibition of Pyruvate Formate Lyase by Methacrylate

Pyruvate Formate Lyase (PFL) catalyzes acetyl transfer from pyruvate to coenzyme a by a mechanism involving multiple amino acid radicals. A post-translationally installed glycyl radical (G734· in Escherichia coli) is essential for enzyme activity and two cysteines (C418 and C419) are proposed to form thiyl radicals during turnover, yet their unique roles in catalysis have not been directly demonstrated with both structural and electronic resolution. Methacrylate is an isostructural analog of pyruvate and an informative irreversible inhibitor of pfl. Here we demonstrate the mechanism of inhibition of pfl by methacrylate. Treatment of activated pfl with methacrylate results in the conversion of the G734· to a new radical species, concomitant with enzyme inhibition, centered at g = 2.0033. Spectral simulations, reactions with methacrylate isotopologues, and Density Functional Theory (DFT) calculations support our assignment of the radical to a C2 tertiary methacryl radical. The reaction is specific for C418, as evidenced by mass spectrometry. The methacryl radical decays over time, reforming G734·, and the decay exhibits a H/D solvent isotope effect of 3.4, consistent with H-atom transfer from an ionizable donor, presumably the C419 sulfhydryl group. Acrylate also inhibits PFL irreversibly, and alkylates C418, but we did not observe an acryl secondary radical in H2O or in D2O within 10 s, consistent with our DFT calculations and the expected reactivity of a secondary versus tertiary carbon-centered radical. Together, the results support unique roles of the two active site cysteines of PFL and a C419 S-H bond dissociation energy between that of a secondary and tertiary C-H bond.

Primary and Secondary Coordination Sphere Effects on the Structure and Function of S-Nitrosylating Azurin

Much progress has been made in understanding the roles of the secondary coordination sphere (SCS) in tuning redox potentials of metalloproteins. In contrast, the impact of SCS on reactivity is much less understood. A primary example is how copper proteins can promote S-nitrosylation (SNO), which is one of the most important dynamic post-translational modifications, and is crucial in regulating nitric oxide storage and transportation. Specifically, the factors that instill CuII with S-nitrosylating capabilities and modulate activity are not well understood. To address this issue, we investigated the influence of the primary and secondary coordination sphere on CuII-catalyzed S-nitrosylation by developing a series of azurin variants with varying catalytic capabilities. We have employed a multidimensional approach involving electronic absorption, S and Cu K-edge XAS, EPR, and resonance Raman spectroscopies together with QM/MM computational analysis to examine the relationships between structure and molecular mechanism in this reaction. Our findings have revealed that kinetic competency is correlated with three balancing factors, namely Cu-S bond strength, Cu spin localization, and relative S(ps) vs S(pp) contributions to the ground state. Together, these results support a reaction pathway that proceeds through the attack of the Cu-S bond rather than electrophilic addition to CuII or radical attack of SCys. The insights gained from this work provide not only a deeper understanding of SNO in biology but also a basis for designing artificial and tunable SNO enzymes to regulate NO and prevent diseases due to SNO dysregulation.

Charge Regulation in a Rieske Proton Pump Pinpoints Zero, One, and Two Proton-Coupled Electron Transfer

The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZET) remains undetermined due to difficulties in measuring the net charge of solvated proteins. Values of ΔZET can reflect reorganization energies or redox potentials associated with ET and can be used to distinguish ET from proton(s)-coupled electron transfer (PCET). Here, we synthesized protein "charge ladders" of a Rieske [2Fe-2S] subunit from Thermus thermophilus (truncTtRp) and made 120 electrostatic measurements of ΔZET across pH. Across pH 5-10, truncTtRp is suspected of transitioning from ET to PCET, and then to two proton-coupled ET (2PCET). Upon reduction, we found that truncTtRp became more negative at pH 6.0 by one unit (ΔZET = -1.01 ± 0.14), consistent with single ET; was isoelectric at pH 8.8 (ΔZET = -0.01 ± 0.45), consistent with PCET; and became more positive at pH 10.6 (ΔZET = +1.37 ± 0.60), consistent with 2PCET. These ΔZET values are attributed to protonation of H154 and H134. Across pH, redox potentials of TtRp (measured previously) correlated with protonation energies of H154 and H134 and ΔZET for truncTtRp, supporting a discrete proton pumping mechanism for Rieske proteins at the Fe-coordinating histidines.

AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies

Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as pKa shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM (r = 0.88) and the FTLS (r = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.

Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands

In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O₂ is reduced to H₂O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. This study focused on the ∼350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255-285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90-150 mV for anionic charge and ∼100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.

Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases

Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.

Classifying metal-binding sites with neural networks

To advance our ability to predict impacts of the protein scaffold on catalysis, robust classification schemes to define features of proteins that will influence reactivity are needed. One of these features is a protein's metal-binding ability, as metals are critical to catalytic conversion by metalloenzymes. As a step toward realizing this goal, we used convolutional neural networks (CNNs) to enable the classification of a metal cofactor binding pocket within a protein scaffold. CNNs enable images to be classified based on multiple levels of detail in the image, from edges and corners to entire objects, and can provide rapid classification. First, six CNN models were fine-tuned to classify the 20 standard amino acids to choose a performant model for amino acid classification. This model was then trained in two parallel efforts: to classify a 2D image of the environment within a given radius of the central metal binding site, either an Fe ion or a [2Fe-2S] cofactor, with the metal visible (effort 1) or the metal hidden (effort 2). We further used two sub-classifications of the [2Fe-2S] cofactor: (1) a standard [2Fe-2S] cofactor and (2) a Rieske [2Fe-2S] cofactor. The accuracy for the model correctly identifying all three defined features was >95%, despite our perception of the increased challenge of the metalloenzyme identification. This demonstrates that machine learning methodology to classify and distinguish similar metal-binding sites, even in the absence of a visible cofactor, is indeed possible and offers an additional tool for metal-binding site identification in proteins.

AMOEBA Force Field Trajectories Improve Predictions of Accurate pKa Values of the GFP Fluorophore: The Importance of Polarizability and Water Interactions

Precisely quantifying the magnitude, direction, and biological functions of electric fields in proteins has long been an outstanding challenge in the field. The most widely implemented experimental method to measure such electric fields at a particular residue in a protein has been through changes in pKa of titratable residues. While many computational strategies exist to predict these values, it has been difficult to do this accurately or connect predicted results to key structural or mechanistic features of the molecule. Here, we used experimentally determined pKa values of the fluorophore in superfolder green fluorescent protein (GFP) with amino acid mutations made at position Thr 203 to evaluate the pKa prediction ability of molecular dynamics (MD) simulations using a polarizable force field, AMOEBA. Structure ensembles from AMOEBA were used to calculate pKa values of the GFP fluorophore. The calculated pKa values were then compared to trajectories using a conventional fixed charge force field (Amber03 ff). We found that the position of water molecules included in the pKa calculation had opposite effects on the pKa values between the trajectories from AMOEBA and Amber03 force fields. In AMOEBA trajectories, the inclusion of water molecules within 35 Å of the fluorophore decreased the difference between the predicted and experimental values, resulting in calculated pKa values that were within an average of 0.8 pKa unit from the experimental results. On the other hand, in Amber03 trajectories, including water molecules that were more than 5 Å from the fluorophore increased the differences between the calculated and experimental pKa values. The inaccuracy of pKa predictions determined from Amber03 trajectories was caused by a significant stabilization of the deprotonated chromophore's free energy compared to the result in AMOEBA. We rationalize the cutoffs for explicit water molecules when calculating pKa to better predict the electrostatic environment surrounding the fluorophore buried in GFP. We discuss how the results from this work will assist the prospective prediction of pKa values or other electrostatic effects in a wide variety of folded proteins.

On the roles of methionine and the importance of its microenvironments in redox metalloproteins

The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.

Fine-tuning of FeS proteins monitored via pulsed EPR redox potentiometry at Q-band

As essential electron translocating proteins in photosynthetic organisms, multiple plant-type ferredoxin (Fdx) isoforms are involved in a high number of reductive metabolic processes in the chloroplast. To allow quick cellular responses under changing environmental conditions, different plant-type Fdxs in Chlamydomonas reinhardtii were suggested to have adapted their midpoint potentials to a wide range of interaction partners. We performed pulsed electron paramagnetic resonance (EPR) monitored redox potentiometry at Q-band on three Fdx isoforms for a straightforward determination of their midpoint potentials. Additionally, site-directed mutagenesis was used to tune the midpoint potential of CrFdx1 in a range of approximately -338 to -511 mV, confirming the importance of single positions in the protein environment surrounding the [2Fe2S] cluster. Our results present a new target for future studies aiming to modify the catalytic activity of CrFdx1 that plays an essential role either as electron acceptor of photosystem I or as electron donor to hydrogenases under certain conditions. Additionally, the precisely determined redox potentials in this work using pulsed EPR demonstrate an alternative method that provides additional advantages compared with the well-established continuous wave EPR technique.

Recent advances in tuning redox properties of electron transfer centers in metalloenzymes catalyzing oxygen reduction reaction and H2 oxidation important for fuel cells design

Current fuel-cell catalysts for oxygen reduction reaction (ORR) and H₂ oxidation use precious metals and, for ORR, require high overpotentials. In contrast, metalloenzymes perform their respective reaction at low overpotentials using earth-abundant metals, making metalloenzymes ideal candidates for inspiring electrocatalytic design. Critical to the success of these enzymes are redox-active metal centers surrounding the enzyme active sites that ensure fast electron transfer (ET) to or away from the active site, by tuning the catalytic potential of the reaction as observed in multicopper oxidases but also in dictating the catalytic bias of the reaction as realized in hydrogenases. This review summarizes recent advances in studying these ET centers in multicopper oxidases and heme-copper oxidases that perform ORR and hydrogenases in carrying out H₂ oxidation. Insights gained from understanding how the reduction potential of the ET centers effects reactivity at the active site in both the enzymes and their models are provided.

1.3 V Inorganic Sequential Redox Chain with an All-Anionic Couple 1-/2- in a Single Framework

The relatively low symmetry of [3,3′-Co(1,2-C₂B₉H₁₁)₂]⁻ ([1]⁻), along with the high number of available substitution sites, 18 on the boron atoms and 4 on the carbon atoms, allows a fairly regioselective and stepwise chlorination of the platform and therefore a very controlled tuning of the electrochemical potential tuning. This is not so easily found in other systems, e.g., ferrocene. In this work, we show how a single platform with boron and carbon in the ligand, and only cobalt can produce a tuning of potentials in a stepwise manner in the 1.3 V range. The platform used is made of two icosahedra sharing one vertex. The E_1/2 tuning has been achieved from [1]⁻ by sequential chlorination, which has given potentials whose values increase sequentially and linearly with the number of chloro groups in the platform. [Cl₈-1]⁻, [Cl₁₀-1]⁻, and [Cl₁₂-1]⁻ have been obtained, which are added to the existing [Cl-1]⁻, [Cl₂-1]⁻, [Cl₄-1]⁻, and [Cl₆-1]⁻ described earlier to give the 1.3 V range. It is envisaged to extend this range also sequentially by changing the metal from cobalt to iron. The last successful synthesis of the highest chlorinated derivatives of cobaltabis(dicarbollide) dates back to 1982, and since then, no more advances have occurred toward more substituted metallacarborane chlorinated compounds. [Cl₈-1]⁻, [Cl₁₀-1]⁻, and [Cl₁₂-1]⁻ are made with an easy and fast method. The key point of the reaction is the use of the protonated form of [Co(C₂B₉H₁₁)₂]⁻, as a starting material, and the use of sulfuryl chloride, a less hazardous and easier to use chlorinating agent. In addition, we present a complete, spectroscopic, crystallographic, and electrochemical characterization, together with a study of the influence of the chlorination position in the electrochemical properties.

By sequential halogenation of [Co(C₂B₉H₁₁)₂]⁻ ([1]⁻) with chlorine, the [Cl₈-1]⁻, [Cl₁₀-1]⁻, and [Cl₁₂-1]⁻ derivatives of [1]⁻ have been prepared and isolated. The E_1/2 values increase sequentially and linearly with the number of chloro groups in the platform. If these potentials are added to the existing E_1/2 values due to [Cl-1]⁻, [Cl₂-1]⁻, [Cl₄-1]⁻, and [Cl₆-1]⁻ described earlier, a 1.3 V range is obtained. This allows tuning of the desired potentials for the purposes of nature.

Overview of Methods for Purification and Characterization of Metalloproteins

Metalloproteins make up one third of all proteins and perform some of the most essential reactions on earth. The unique properties of the metal ions within these proteins, and in particular of redox-active metal ions, enables the use of a number of characterization techniques. It also necessitates unique considerations in terms of purification and characterization. In this overview, we describe the considerations and methods used for metalloprotein purification and characterization. © 2021 Wiley Periodicals LLC.

Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis

Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.

Cu(II) nonspecifically binding chromate reductase NfoR promotes Cr(VI) reduction

Cu(II)-enhanced microbial Cr(VI) reduction is common in the environment, yet its mechanism is unknown. The specific activity of chromate reductase, NfoR, from Staphylococcus aureus sp. LZ-01 was augmented 1.5-fold by Cu(II). Isothermal titration calorimetry and spectral data show that Cu(II) binds to NfoR nonspecifically. Further, Cu(II) stimulates the nitrobenzene reduction of NfoR, indicating that Cu(II) promotes electron transfer. The crystal structure of NfoR in complex with CuSO₄ (1.46 Å) was determined. The overall structure of NfoR-Cu(II) complex is a dimer that covalently binds with FMN and Cu(II)-binding pocket is located at the interface of the NfoR dimer. Structural superposition revealed that NfoR resembles the structure of class II chromate reductase. Site-directed mutagenesis revealed that Leu⁴⁶ and Phe¹²³ were involved in NADH binding, whereas Trp⁷⁰ and Ser⁴⁵ were the key residues for nitrobenzene binding. Furthermore, His¹⁰⁰ and Asp¹⁷¹ were preferential affinity sites for Cu(II) and that Cys¹⁶³ is an active site for FMN binding. Attenuation reductase activity in C163S can be partially restored to 54% wild type by increasing Cu(II) concentration. Partial restoration indicates dual-channel electron transfer of NfoR via Cu(II) and FMN. We propose a catalytic mechanism for Cu(II)-enhanced NfoR activity in which Cu(I) is formed transiently. Together, the current results provide an insight on Cu (II)-induced enhancement and benefit of Cr(VI) bioremediation.

A Binuclear CuA Center Designed in an All α-Helical Protein Scaffold

The primary and secondary coordination spheres of metal binding sites in metalloproteins have been investigated extensively, leading to the creation of high-performing functional metalloproteins; however, the impact of the overall structure of the protein scaffold on the unique properties of metalloproteins has rarely been studied. A primary example is the binuclear Cu_A center, an electron transfer cupredoxin domain of photosynthetic and respiratory complexes and, recently, a protein coregulated with particulate methane and ammonia monooxygenases. The redox potential, Cu-Cu spectroscopic features, and a valence delocalized state of Cu_A are difficult to reproduce in synthetic models, and every artificial protein Cu_A center to-date has used a modified cupredoxin. Here, we present a fully functional Cu_A center designed in a structurally nonhomologous protein, cytochrome c peroxidase (CcP), by only two mutations (Cu_ACcP). We demonstrate with UV-visible absorption, resonance Raman, and magnetic circular dichroism spectroscopy that Cu_ACcP is valence delocalized. Continuous wave and pulsed (HYSCORE) X-band EPR show it has a highly compact g_z area and small A_z hyperfine principal value with g and A tensors that resemble axially perturbed Cu_A. Stopped-flow kinetics found that Cu_A formation proceeds through a single T2Cu intermediate. The reduction potential of Cu_ACcP is comparable to native Cu_A and can transfer electrons to a physiological redox partner. We built a structural model of the designed Cu binding site from extended X-ray absorption fine structure spectroscopy and validated it by mutation of coordinating Cys and His residues, revealing that a triad of residues (R48C, W51C, and His52) rigidly arranged on one α-helix is responsible for chelating the first Cu(II) and that His175 stabilizes the binuclear complex by rearrangement of the CcP heme-coordinating helix. This design is a demonstration that a highly conserved protein fold is not uniquely necessary to induce certain characteristic physical and chemical properties in a metal redox center.

Structural Basis for a Quadratic Relationship between Electronic Absorption and Electronic Paramagnetic Resonance Parameters of Type 1 Copper Proteins

Type 1 copper (T1Cu) proteins play important roles in electron transfer in biology, largely due to the unique structure of the T1Cu center, which is reflected by its spectroscopic properties. Previous reports have suggested a correlation between a high ratio of electronic absorbance at ∼450 nm to that at ∼600 nm (R = A₄₅₀/A₆₀₀) and a large copper(II) hyperfine coupling in the z direction (A_z) in electron paramagnetic resonance (EPR). However, this correlation does not have a clear physical meaning, nor does it hold for many proteins with a perturbed T1Cu center. To address this issue, a new parameter of R' [A₄₅₀/(A₄₅₀ + A₆₀₀)] with a better physical meaning of a fractional S_Cys pseudo-σ to Cu(II) charge transfer transition intensity is defined and a quadratic relationship between R' and A_z is found on the basis of a comprehensive analysis of ultraviolet-visible absorption, EPR, and structural parameters of T1Cu proteins. We are able to find good correlations between R' and the displacement of copper from the trigonal plane defined by the His₂Cys ligands and the angle between the N_His1-Cu-N_His2 plane and the S_Cys-Cu-axial ligand plane, providing a structural basis for the observed correlation. These findings and analyses provide a new framework for a deeper understanding of the spectroscopic and electronic properties of T1Cu proteins, which may allow better design and applications of this important class of proteins for redox and electron transfer functions.

Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry

Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.

The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha - a minimal hydrogenase?

Chemically synthesized compounds that are capable of facilitating the reversible splitting of dihydrogen into protons and electrons are rare in chemists' portfolio. The corresponding biocatalysts – hydrogenases – are, however, abundant in the microbial world. [NiFe]-hydrogenases represent a major subclass and display a bipartite architecture, composed of a large subunit, hosting the catalytic NiFe(CO)(CN)₂ cofactor, and a small subunit whose iron–sulfur clusters are responsible for electron transfer. To analyze in detail the catalytic competence of the large subunit without its smaller counterpart, we purified the large subunit HoxC of the regulatory [NiFe]-hydrogenase of the model H₂ oxidizer Ralstonia eutropha to homogeneity. Metal determination and infrared spectroscopy revealed a stoichiometric loading of the metal cofactor. This enabled for the first time the determination of the UV-visible extinction coefficient of the NiFe(CO)(CN)₂ cofactor. Moreover, the absence of disturbing iron–sulfur clusters allowed an unbiased look into the low-spin Fe²⁺ of the active site by Mössbauer spectroscopy. Isolated HoxC was active in catalytic hydrogen–deuterium exchange, demonstrating its capacity to activate H₂. Its catalytic activity was drastically lower than that of the bipartite holoenzyme. This was consistent with infrared and electron paramagnetic resonance spectroscopic observations, suggesting that the bridging position between the active site nickel and iron ions is predominantly occupied by water-derived ligands, even under reducing conditions. In fact, the presence of water-derived ligands bound to low-spin Ni²⁺ was reflected by the absorption bands occurring in the corresponding UV-vis spectra, as revealed by time-dependent density functional theory calculations conducted on appropriate in silico models. Thus, the isolated large subunits indeed represent simple [NiFe]-hydrogenase models, which could serve as blueprints for chemically synthesized mimics. Furthermore, our data point to a fundamental role of the small subunit in preventing water access to the catalytic center, which significantly increases the H₂ splitting capacity of the enzyme.

Spectroscopic investigation of an isolated [NiFe]-hydrogenase large subunit enables a unique view of the NiFe(CO)(CN)₂ cofactor.

Inhibition in multicopper oxidases: a critical review

This review critiques the literature on inhibition of O₂-reduction catalysis in multicopper oxidases like laccase and bilirubin oxidase and provide recommendations for best practice when carrying out experiments and interpreting published data.

Catalytic M Center of Copper Monooxygenases Probed by Rational Design. Effects of Selenomethionine and Histidine Substitution on Structure and Reactivity

The M centers of the mononuclear monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase bind and activate dioxygen en route to substrate hydroxylation. Recently, we reported the rational design of a protein-based model in which the CusF metallochaperone was repurposed via a His to Met mutation to act as a structural and spectroscopic biomimic. The PHM M site exhibits a number of unusual attributes, including a His₂Met ligand set, a fluxional Cu(I)-S(Met) bond, tight binding of exogenous ligands CO and N₃^-, and complete coupling of oxygen reduction to substrate hydroxylation even at extremely low turnover rates. In particular, mutation of the Met ligand to His completely eliminates the catalytic activity despite the propensity of Cu^I-His₃ centers to bind and activate dioxygen in other metalloenzyme systems. Here, we further develop the CusF-based model to explore methionine variants in which Met is replaced by selenomethionine (SeM) and histidine. We examine the effects on coordinate structure and exogenous ligand binding via X-ray absorption spectroscopy and electron paramagnetic resonance and probe the consequences of mutations on redox chemistry via studies of the reduction by ascorbate and oxidation via molecular oxygen. The M-site model is three-coordinate in the Cu(I) state and binds CO to form a four-coordinate carbonyl. In the oxidized forms, the coordination changes to tetragonal five-coordinate with a long axial Met ligand that like the enzymes is undetectable at either the Cu or Se K edges. The EXAFS data at the Se K edge of the SeM variant provide unique information about the nature of the Cu-methionine bond that is likewise weak and fluxional. Kinetic studies document the sluggish reactivity of the Cu(I) complexes with molecular oxygen and rapid rates of reduction of the Cu(II) complexes by ascorbate, indicating a remarkable stability of the Cu(I) state in all three derivatives. The results show little difference between the Met ligand and its SeM and His congeners and suggest that the Met contributes to catalysis in ways that are more complex than simple perturbation of the redox chemistry. Overall, the results stimulate a critical re-examination of the canonical reaction mechanisms of the mononuclear copper monooxygenases.

Shift from Entropic Cu2+ Binding to Enthalpic Cu+ Binding Determines the Reduction Thermodynamics of Blue Copper Proteins

The enthalpic and entropic components of Cu²⁺ and Cu⁺ binding to the blue copper protein azurin have been quantified with isothermal titration calorimetry (ITC) measurements and analysis, providing the first such experimental values for Cu⁺ binding to a protein. The high affinity of azurin for Cu²⁺ is entirely due to a very favorable binding entropy, while its even higher affinity for Cu⁺ is due to a favorable binding enthalpy and entropy. The binding thermodynamics provide insight into bond enthalpies at the blue copper site and entropic contributions from desolvation and proton displacement. These values were used in thermodynamic cycles to determine the enthalpic and entropic contributions to the free energy of reduction and thus the reduction potential. The reduction thermodynamics obtained with this method are in good agreement with previous results from temperature-dependent electrochemical measurements. The calorimetry method, however, provides new insight into contributions from the initial (oxidized) and final (reduced) states of the reduction. Since ITC measurements quantify the protons that are displaced upon metal binding, the proton transfer that is coupled with electron transfer is also determined with this method. Preliminary results for Cu²⁺ and Cu⁺ binding to the Phe114Pro variant of azurin demonstrate the insight about protein tuning of the reduction potential that is provided by the binding thermodynamics of each metal oxidation state.

Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters

Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.

Understanding and Modulating Metalloenzymes with Unnatural Amino Acids, Non-Native Metal Ions, and Non-Native Metallocofactors

Metalloproteins set the gold standard for performing important functions, including catalyzing demanding reactions under mild conditions. Designing artificial metalloenzymes (ArMs) to catalyze abiological reactions has been a major endeavor for many years, but most ArM activities are far below those of native enzymes, making them unsuitable for most pratical applications. A critical step to advance the field is to fundamentally understand what it takes to not only confer but also fine-tune ArM activities so they match those of native enzymes. Indeed, only once we can freely modulate ArM activity to rival (or surpass!) natural enzymes can the potential of ArMs be fully realized. A key to unlocking ArM potential is the observation that one metal primary coordination sphere can display a range of functions and levels of activity, leading to the realization that secondary coordination sphere (SCS) interactions are critically important. However, SCS interactions are numerous, long-range, and weak, making them very difficult to reproduce in ArMs. Furthermore, natural enzymes are tied to a small set of biologically available functional moieties from canonical amino acids and physiologically available metal ions and metallocofactors, severely limiting the chemical space available to probe and tune ArMs. In this Account, we summarize the use of unnatural amino acids (UAAs) and non-native metal ions and metallocofactors by our group and our collaborators to probe and modulate ArM functions. We incorporated isostructural UAAs in a type 1 copper (T1Cu) protein azurin to provide conclusive evidence that axial ligand hydrophobicity is a major determinant of T1Cu redunction potential ( E°'). Closely related work from other groups are also discussed. We also probed the role of protein backbone interactions that cannot be altered by standard mutagenesis by replacing the peptide bond with an ester linkage. We used insight gained from these studies to tune the E°' of azurin across the entire physiological range, the broadest range ever achieved in a single metalloprotein. Introducing UAA analogues of Tyr into ArM models of heme-copper oxidase (HCO) revealed a linear relationship between p K_a, E°', and activity. We also substituted non-native hemes and non-native metal ions for their native equivalents in these models to resolve several issues that were intractable in native HCOs and the closely related nitric oxide reductases, such as their roles in modulating substrate affinity, electron transfer rate, and activity. We incorporated abiological cofactors such as ferrocene and Mn(salen) into azurin and myoglobin, respectively, to stabilize these inorganic and organometallic compounds in water, confer abiological functions, tune their E°' and activity through SCS interactions, and show that the approach to metallocofactor anchoring and orientation can tune enantioselectivity and alter function. Replacing Cu in azurin with non-native Fe or Ni can impart novel activities, such as superoxide reduction and C-C bond formation. While progress was made, we have identified only a small fraction of the interactions that can be generally applied to ArMs to fine-tune their functions. Because SCS interactions are subtle and heavily interconnected, it has been difficult to characterize their effects quantitatively. It is vital to develop spectroscopic and computational techniques to detect and quantify their effects in both resting states and catalytic intermediates.

What Are We Missing by Not Measuring the Net Charge of Proteins?

The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pK_a . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pK_a values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔG_z ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔG_z contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.