Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase

Carbonic Anhydrases (CAs) have been a target for de novo protein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes' first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H2O/OH-)]N(TRIL2WL23H)3 n+ that behaves similarly to native Co(II) substituted human-CAs. Like the Zn(II) analogue, the cobalt-derivative at slightly basic pH is incapable of hydrolyzing p-nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH-)]N(TRIL2WL23H)3 + peptide complex. X-ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5-coordinate species by pH 11. UV-vis spectroscopy can monitor this transition, giving a pKa for the conversion of 10.3. We assign this conversion to the formation of a 5-coordinate Co(II)(Nimid)3(OH)(H2O) species. The pH dependent kinetic analysis indicates the maximal rate (kcat), and thus the catalytic efficiency (kcat/Km), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.

Insights on the Structure in Solution of Paramagnetic LnIII/GaIII 12-Metallacrown-4 Complexes Using 1D 1H NMR and Model Structures

The solution structure of Ln^IIINa^I(OBz)₄[12-MC_GaIII(N)Shi-4] complexes was studied through paramagnetic ¹H NMR and DFT models. Although isostructural in the solid state, their ¹H NMR spectra in DMSO-d₆ are extremely different from one another due to the magnetic anisotropy of the lanthanide(III) ions. NMR data were analyzed by the "all-lanthanide" method that were compared to X-ray structures and model structures, allowing to establish the extent of the structural changes that occur from the solid state to the solution phase. Major structural changes involve the phenyl groups of the benzoate ions that, quite surprisingly, in solution present preferential orientations lowering the symmetry of the complex contrary to what observed in the solid state. Overall, DFT methods and 1D NMR data allowed us to clarify aspects related to molecular rearrangement processes in solution that could not be predicted by a simple look at the X-ray structures of these complexes.

Incorporation of a molybdenum atom in a Rubredoxin-type Centre of a de novo-designed α3DIV-L21C three-helical bundle peptide

The rational design and functionalization of small, simple, and stable peptides scaffolds is an attractive avenue to mimic catalytic metal-centres of complex proteins, relevant for the design of metalloenzymes with environmental, biotechnological and health impacts. The de novo designed α₃DIV-L21C framework has a rubredoxin-like metal binding site and was used in this work to incorporate a Mo-atom. Thermostability studies using differential scanning calorimetry showed an increase of 4 °C in the melting temperature of the Mo-α₃DIV-L21C when compared to the apo-α₃DIV-L21C. Circular dichroism in the visible and far-UV regions corroborated these results showing that Mo incorporation provides stability to the peptide even though there were almost no differences observed in the secondary structure. A formal reduction potential of ∼ -408 mV vs. NHE, pH 7.6 was determined. Combining electrochemical results, EPR and UV-visible data we discuss the oxidation state of the molybdenum centre in Mo-α₃DIV-L21C and propose that is mainly in a Mo (VI) oxidation state.

Molecular Rotational Correlation Times and Nanoviscosity Determined by 111m Cd Perturbed Angular Correlation (PAC) of γ-rays Spectroscopy

The nanoviscosity experienced by molecules in solution may be determined through measurement of the molecular rotational correlation time, τ_c , for example, by fluorescence and NMR spectroscopy. With this work, we apply PAC spectroscopy to determine the rate of rotational diffusion, λ=1/τ_c , of a de novo designed protein, TRIL12AL16C, in solutions with viscosities, ξ, from 1.7 to 88 mPa⋅s. TRIL12AL16C was selected as molecular probe because it exhibits minimal effects due to intramolecular dynamics and static line broadening, allowing for exclusive elucidation of molecular rotational diffusion. Diffusion rates determined by PAC data agree well with literature data from fluorescence and NMR spectroscopy, and scales linearly with 1/ξ in agreement with the Stokes-Einstein-Debye model. PAC experiments require only trace amounts (∼10¹¹ ) of probe nuclei and can be conducted over a broad range of sample temperatures and pressures. Moreover, most materials are relatively transparent to γ-rays. Thus, PAC spectroscopy could find applications under circumstances where conventional techniques cannot be applied, spanning from the physics of liquids to in-vivo biochemistry.

Tunable Optical Molecular Thermometers Based on Metallacrowns

The effect of ligands' energy levels on thermal dependence of lanthanide emission was examined to create new molecular nanothermometers. A series of Ln₂Ga₈L₈^'L₈^″ metallacrowns (shorthand Ln₂L₈^'), where Ln = Gd³⁺, Tb³⁺, or Sm³⁺ (H₃L' = salicylhydroxamic acid (H₃shi), 5-methylsalicylhydroxamic acid (H₃mshi), 5-methoxysalicylhydroxamic acid (H₃moshi), and 3-hydroxy-2-naphthohydroxamic acid (H₃nha)) and H₂L″ = isophthalic acid (H₂iph), was synthesized and characterized. Within the series, ligand-centered singlet state (S₁) energy levels ranged from 23,300 to 27,800 cm^-1, while triplet (T₁) energy levels ranged from 18,150 to 21,980 cm^-1. We demonstrated that the difference between T₁ levels and relevant energies of the excited ⁴G_5/2 level of Sm³⁺ (17,800 cm^-1) and ⁵D₄ level of Tb³⁺ (20,400 cm^-1) is the major parameter controlling thermal dependence of the emission intensity via the back energy transfer mechanism. However, when the energy difference between S₁ and T₁ levels is small (below 3760 cm^-1), the S₁ → T₁ intersystem crossing (and its reverse, S₁ ← T₁) mechanism contributes to the thermal behavior of metallacrowns. Both mechanisms affect Ln³⁺-centered room-temperature quantum yields with values ranging from 2.07(6)% to 31.2(2)% for Tb₂L₈^' and from 0.0267(7)% to 2.27(5)% for Sm₂L₈^'. The maximal thermal dependence varies over a wide thermal range (ca. 150-350 K) based on energy gaps between relevant ligand-based and lanthanide-based electronic states. By mixing Tb₂moshi₈^' with Sm₂moshi₈^' in a 1:1 ratio, an optical thermometer with a relative thermal sensitivity larger than 3%/K at 225 K was created. Other temperature ranges are also accessible with this approach.

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.

Cu(I) Binding to Designed Proteins Reveals a Putative Copper Binding Site of the Human Line1 Retrotransposon Protein ORF1p

Long interspersed nuclear elements-1 (L1) are autonomous retrotransposons that encode two proteins in different open reading frames (ORF1 and ORF2). The ORF1p, which may be an RNA binding and chaperone protein, contains a three-stranded coiled coil (3SCC) domain that facilitates the formation of the biologically active homotrimer. This 3SCC domain is composed of seven amino acid (heptad) repeats as found in native and designed peptides and a stammer that modifies the helical structure. Cysteine residues occur at three hydrophobic positions (2 a and 1 d sites) within this domain. We recently showed that the cysteine layers in ORF1p and model de novo designed peptides bind the toxic metalloid lead(II) with high affinities, a feature that had not been previously recognized. However, there is little understanding of how essential metal ions might interact with this metal binding domain. We have, therefore, investigated the copper(I) binding properties of analogous de novo designed 3SCCs that contain cysteine layers within the hydrophobic core. The results from UV-visible and X-ray absorption spectroscopy show that these designed peptides bind Cu(I) with high affinity in a pH-dependent manner. At pH 9, monomeric trigonal planar Cu(I)S3 centers are formed with 1 equiv of metal, while dinuclear centers form with a second equivalent of metal. At physiologic pH conditions, the dinuclear center forms cooperatively. These data suggest that ORF1p is capable of binding two copper ions to its tris(cysteine) layers. This has major implications for ORF1p coiled coil domain stability and dynamics, ultimately potentially impacting the resulting biological activity.

Tuning the photophysical properties of lanthanide(iii)/zinc(ii) ‘encapsulated sandwich’ metallacrowns emitting in the near-infrared range

A family of Zn₁₆Ln(HA)₁₆ metallacrowns (MCs; Ln = Yb^III, Er^III, and Nd^III; HA = picoline- (picHA²⁻), pyrazine- (pyzHA²⁻), and quinaldine- (quinHA²⁻) hydroximates) with an ‘encapsulated sandwich’ structure possesses outstanding luminescence properties in the near-infrared (NIR) and suitability for cell imaging. Here, to decipher which parameters affect their functional and photophysical properties and how the nature of the hydroximate ligands can allow their fine tuning, we have completed this Zn₁₆Ln(HA)₁₆ family by synthesizing MCs with two new ligands, naphthyridine- (napHA²⁻) and quinoxaline- (quinoHA²⁻) hydroximates. Zn₁₆Ln(napHA)₁₆ and Zn₁₆Ln(quinoHA)₁₆ exhibit absorption bands extended into the visible range and efficiently sensitize the NIR emissions of Yb^III, Er^III, and Nd^III upon excitation up to 630 nm. The energies of the lowest singlet (S₁), triplet (T₁) and intra-ligand charge transfer (ILCT) states have been determined. Ln^III-centered total (Q^L_Ln) and intrinsic (Q^Ln_Ln) quantum yields, sensitization efficiencies (η_sens), observed (τ_obs) and radiative (τ_rad) luminescence lifetimes have been recorded and analyzed in the solid state and in CH₃OH and CD₃OD solutions for all Zn₁₆Ln(HA)₁₆. We found that, within the Zn₁₆Ln(HA)₁₆ family, τ_rad values are not constant for a particular Ln^III. The close in energy positions of T₁ and ILCT states in Zn₁₆Ln(picHA)₁₆ and Zn₁₆Ln(quinHA)₁₆ are preferred for the sensitization of Ln^III NIR emission and η_sens values reach 100% for Nd^III. Finally, the highest values of Q^L_Ln are observed for Zn₁₆Ln(quinHA)₁₆ in the solid state or in CD₃OD solutions. With these data at hand, we are now capable of creating MCs with desired properties suitable for NIR optical imaging.

We have created a family of ‘encapsulated sandwich’ Zn₁₆Ln(HA)₁₆ metallacrowns and by detailed quantitative analysis demonstrated how the nature of the hydroximate ligand impacts photophysical properties of these complexes.

Lanthanide Identity Governs Guest-Induced Dimerization in LnIII [15-MC Cu II N(L-pheHA) -5])3+ Metallacrowns

Series of lanthanide-containing metallic coordination complexes are frequently presented as structurally analogous, due to the similar chemical and coordinative properties of the lanthanides. In the case of chiral (Ln^III [15-MC Cu II _N(L-pheHA) -5])³⁺ metallacrowns (MCs), which are well established supramolecular hosts, the formation of dimers templated by a dicarboxylate guest (muconate) in solution of neutral pH is herein shown to have a unique dependence on the identity of the MC's central lanthanide. Calorimetric data and nuclear magnetic resonance diffusion studies demonstrate that MCs containing larger or smaller lanthanides as the central metal only form monomeric host-guest complexes whereas analogues with intermediate lanthanides (for example, Eu, Gd, Dy) participate in formation of dimeric host-guest-host compartments. The driving force for the dimerization event across the series is thought to be a competition between formation of highly stable MCs (larger lanthanides) and optimally linked bridging guests (smaller lanthanides).

Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead

The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.

Nitrite reductase activity within an antiparallel de novo scaffold

Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis₃ binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis₃ binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis₃ binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.

Magnetic properties of two GdIIIFeIII4 metallacrowns and strategies for optimizing the magnetocaloric effect of this topology

Two Gd³⁺ [12-MC_Fe^III_(N)shi-4] metallacrowns are analyzed for magnetic properties, and calculations concerning the magnetic exchange parameters of this topology are considered.

The pH-Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α-Helical Metalloprotein

De Novo metalloprotein design assesses the relationship between metal active site architecture and catalytic reactivity. Herein, we use an α-helical scaffold to control the iron coordination geometry when a heme cofactor is allowed to bind to either histidine or cysteine ligands, within a single artificial protein. Consequently, we uncovered a reversible pH-induced switch of the heme axial ligation within this simplified scaffold. Characterization of the specific heme coordination modes was done by using UV/Vis and Electron Paramagnetic Resonance spectroscopies. The penta- or hexa-coordinate thiolate heme (9≤pH≤11) and the penta-coordinate imidazole heme (6≤pH≤8.5) reproduces well the heme ligation in chloroperoxidases or cyt P450 monooxygenases and peroxidases, respectively. The stability of heme coordination upon ferric/ferrous redox cycling is a crucial property of the construct. At basic pHs, the thiolate mini-heme protein can catalyze O₂ reduction when adsorbed onto a pyrolytic graphite electrode.

Making or Breaking Metal-Dependent Catalytic Activity: The Role of Stammers in Designed Three-Stranded Coiled Coils

While many life-critical reactions would be infeasibly slow without metal cofactors, a detailed understanding of how protein structure can influence catalytic activity remains elusive. Using de novo designed three-stranded coiled coils (TRI and Grand peptides formed using a heptad repeat approach), we examine how the insertion of a three residue discontinuity, known as a stammer insert, directly adjacent to a (His)3 metal binding site alters catalytic activity. The stammer, which locally alters the twist of the helix, significantly increases copper-catalyzed nitrite reductase activity (CuNiR). In contrast, the well-established zinc-catalyzed carbonic anhydrase activity (p-nitrophenyl acetate, pNPA) is effectively ablated. This study illustrates how the perturbation of the protein sequence using non-coordinating and non-acid base residues in the helical core can perturb metalloenzyme activity through the simple expedient of modifying the helical pitch adjacent to the catalytic center.

[Ga3+ 8 Sm3+ 2 , Ga3+ 8 Tb3+ 2 ] Metallacrowns are Highly Promising Ratiometric Luminescent Molecular Nanothermometers Operating at Physiologically Relevant Temperatures

Nanothermometry is the study of temperature at the submicron scale with a broad range of potential applications, such as cellular studies or electronics. Molecular luminescent-based nanothermometers offer a non-contact means to record these temperatures with high spatial resolution and thermal sensitivity. A luminescent-based molecular thermometer comprised of visible-emitting Ga³⁺ /Tb³⁺ and Ga³⁺ /Sm³⁺ metallacrowns (MCs) achieved remarkable relative thermal sensitivity associated with very low temperature uncertainty of S_r =1.9 % K^-1 and δT<0.045 K, respectively, at 328 K, as an aqueous suspension of polystyrene nanobeads loaded with the corresponding MCs. To date, they are the ratiometric molecular nanothermometers offering the highest level of sensitivity in the physiologically relevant temperature range.

Traversing the Red-Green-Blue Color Spectrum in Rationally Designed Cupredoxins

Blue copper proteins have a constrained Cu(II) geometry that has proven difficult to recapitulate outside native cupredoxin folds. Previous work has successfully designed green copper proteins which could be tuned blue using exogenous ligands, but the question of how one can create a self-contained blue copper site within a de novo scaffold, especially one removed from a cupredoxin fold, remained. We have recently reported a red copper protein site within a three helical bundle scaffold which we later revisited and determined to be a nitrosocyanin mimic, with a CuHis₂CysGlu binding site. We now report efforts to rationally design this construct toward either green or blue copper chromophores using mutation strategies that have proven successful in native cupredoxins. By rotating the metal binding site, we created a de novo green copper protein. This in turn was converted to a blue copper protein by removing an axial methionine. Following this rational sequence, we have successfully created red, green, and blue copper proteins within an alpha helical fold, enabling comparisons for the first time of their structure and function disconnected from the overall cupredoxin fold.

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.

Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys)3 template mediated strategy

Three-stranded coiled coils are peptide structures constructed from amphipathic heptad repeats. Here we show that it is possible to form pure heterotrimeric three-stranded coiled coils by combining three distinct characteristics: (1) a cysteine sulfur layer for metal coordination, (2) a thiophilic, trigonal pyramidal metalloid (Pb(II)) that binds to these sulfurs and (3) an adjacent layer of reduced steric bulk generating a cavity where water can hydrogen bond to the cysteine sulfur atoms. Cysteine substitution in an a site yields Pb(II)A₂B heterotrimers, while d sites provide pure Pb(II)C₂D or Pb(II)CD₂ scaffolds. Altering the metal from Pb(II) to Hg(II) or shifting the relative position of the sterically less demanding layer removes heterotrimer specificity. Because only two of the eight or ten hydrophobic layers are perturbed, catalytic sites can be introduced at other regions of the scaffold. A Zn(II)(histidine)₃(H₂O) centre can be incorporated at a remote location without perturbing the heterotrimer selectivity, suggesting a unique strategy to prepare dissymmetric catalytic sites within self-assembling de novo-designed proteins.

Peculiarities of crystal structures and photophysical properties of GaIII/LnIII metallacrowns with a non-planar [12-MC-4] core

The direct synthetic approach can be used to create a series of visible and near-infrared emitting Ga^III/Ln^III metallacrowns with a non-planar [12-MC-4] core.

Derivation of Lanthanide Series Crystal Field Parameters From First Principles

Two series of lanthanide complexes have been chosen to analyze trends in the magnetic properties and crystal field parameters (CFPs) along the two series: The highly symmetric LnZn₁₆ (picHA)₁₆ series (Ln=Tb, Dy, Ho, Er, Yb; picHA=picolinohydroxamic acid) and the [Ln(dpa)₃ ](C₃ H₅ N₂ )₃ ⋅3H₂ O series (Ln=Ce-Yb; dpa=2,6-dipicolinic acid) with approximate three-fold symmetry. The first series presents a compressed coordination sphere of eight oxygen atoms whereas in the second series, the coordination sphere consists of an elongated coordination sphere formed of six oxygen atoms. The CFPs have been deduced from ab initio calculations using two methods: The AILFT (ab initio ligand field theory) method, in which the parameters are determined at the orbital level, and the ITO (irreducible tensor operator) decomposition, in which the problems are treated at the many-electron level. It has been found that the CFPs are transferable from one derivative to another, within a given series, as a first approximation. The sign of the second-order parameter B 0 2 differs in the two series, reflecting the different environments. It has been found that the use of the strength parameter S allows for an easy comparison between complexes. Furthermore, in both series, the parameters have been found to decrease in magnitude along the series, and this decrease is attributed to covalent effects.

Noncoded Amino Acids in de Novo Metalloprotein Design: Controlling Coordination Number and Catalysis

The relationship between structure and function has long been one of the major points of investigation in Biophysics. Understanding how much, or how little, of a protein's often complicated structure is necessary for its function can lead to directed therapeutic strategies and would allow one to design proteins for specific desired functions. Studying protein function by de novo design builds the functionality from the ground up in a completely unrelated and noncoded protein scaffold. Our lab has used this strategy to study heavy and transition metal binding within the TRI family of three stranded coiled coil (3SCC) constructs to understand coordination geometry and metalloenzyme catalytic control within a protein environment. These peptides contain hydrophobic layers within the interior of the 3SCC, which one can mutate to metal binding residues to create a minimal metal binding site, while solid phase synthesis allows our lab to easily incorporate a number of noncoded amino acids including d enantiomers of binding or secondary coordination sphere amino acids, penicillamine, or methylated versions of histidine. Our studies of Cd(II) binding to Cys₃ environments have determined, largely through the use of ¹¹³Cd NMR and ^111mCd PAC, that the coordination environment around a heavy metal can be controlled by incorporating noncoded amino acids in either the primary or secondary coordination spheres. We found mutating the metal binding amino acids to l-Pen can enforce trigonal Cd(II)S₃ geometry exclusively compared to the mixed coordination determined for l-Cys coordination. The same result can be achieved with secondary sphere mutations as well by incorporating d-Leu above a Cys₃. We hypothesize this latter effect is due to the increased steric packing above the metal binding site that occurs when the l-Leu oriented toward the N-terminus of the scaffold is mutated to d-Leu and oriented toward the C-terminus. Mutating the layer below Cys₃ to d-Leu instead formed a mixed 4- and 5-coordinate Cd(II)S₃(H₂O) and Cd(II)S₃(H₂O)₂ construct as steric bulk was decreased below the metal binding site. We have also applied noncoded amino acids to metalloenzyme systems by incorporating His residues that are methylated at the δ- or ε-nitrogen to enforce Cu(I) ligation to the opposite open nitrogen of His and found a 2 orders of magnitude increased catalytic efficiency for nitrite reductase activity with ε-nitrogen coordination compared to δ-nitrogen. These results exemplify the ability to tune coordination environment and catalytic efficiency within a de novo scaffold as well as the utility of noncoded amino acids to increase the chemist's toolbox. By furthering our understanding of metalloprotein design one could envision, through our use of amino acids not normally available to nature, that protein design laboratories will soon be capable of outperforming the native systems previously used as their benchmark of successful design. The ability to design proteins at this level would have far reaching and exciting benefits within various fields including medical and industrial applications.

Methylated Histidines Alter Tautomeric Preferences that Influence the Rates of Cu Nitrite Reductase Catalysis in Designed Peptides

Copper proteins have the capacity to serve as both redox active catalysts and purely electron transfer centers. A longstanding question in this field is how the function of histidine ligated Cu centers are modulated by δ vs ε-nitrogen ligation of the imidazole. Evaluating the impact of these coordination modes on structure and function by comparative analysis of deposited crystal structures is confounded by factors such as differing protein folds and disparate secondary coordination spheres that make direct comparison of these isomers difficult. Here, we present a series of de novo designed proteins using the noncanonical amino acids 1-methyl-histidine and 3-methyl-histidine to create Cu nitrite reductases where δ- or ε-nitrogen ligation is enforced by the opposite nitrogen's methylation as a means of directly comparing these two ligation states in the same protein fold. We find that ε-nitrogen ligation allows for a better nitrite reduction catalyst, displaying 2 orders of magnitude higher activity than the δ-nitrogen ligated construct. Methylation of the δ nitrogen, combined with a secondary sphere mutation we have previously published, has produced a new record for efficiency within a homogeneous aqueous system, improving by 1 order of magnitude the previously published most efficient construct. Furthermore, we have measured Michaelis-Menten kinetics on these highly active constructs, revealing that the remaining barriers to matching the catalytic efficiency ( kcat/ KM) of native Cu nitrite reductase involve both substrate binding ( KM) and catalysis ( kcat).

How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation

A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as HgII , PbII , and AsIII result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that CdII forms three-, four- or five-coordinate CdII S3 (OH2 )x (in which x=0-2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating CdII S3 (OH2 ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming CdII S3 . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding CdII S3 , whereas d-Leu below opens more space, allowing for equal CdII S3 (OH2 ) and CdII S3 (OH2 )2 . These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.

Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein

Cupredoxins are copper-dependent electron-transfer proteins that can be categorized as blue, purple, green, and red depending on the spectroscopic properties of the Cu(II) bound forms. Interestingly, despite significantly different first coordination spheres and nuclearity, all cupredoxins share a common Greek Key β-sheet fold. We have previously reported the design of a red copper protein within a completely distinct three-helical bundle protein, α₃DChC2. (1) While this design demonstrated that a β-barrel fold was not requisite to recapitulate the properties of a native cupredoxin center, the parent peptide α₃D was not sufficiently stable to allow further study through additional mutations. Here we present the design of an elongated protein GRANDα₃D (GRα₃D) with Δ G_u = -11.4 kcal/mol compared to the original design's -5.1 kcal/mol. Diffraction quality crystals were grown of GRα₃D (a first for an α₃D peptide) and solved to a resolution of 1.34 Å. Examination of this structure suggested that Glu41 might interact with the Cu in our previously reported red copper protein. The previous bis(histidine)(cysteine) site (GRα₃DChC2) was designed into this new scaffold and a series of variant constructs were made to explore this hypothesis. Mutation studies around Glu41 not only prove the proposed interaction, but also enabled tuning of the constructs' hyperfine coupling constant from 160 to 127 × 10^-4 cm^-1. X-ray absorption spectroscopy analysis is consistent with these hyperfine coupling differences being the result of variant 4p mixing related to coordination geometry changes. These studies not only prove that an Glu41-Cu interaction leads to the α₃DChC2 construct's red copper protein like spectral properties, but also exemplify the exact control one can have in a de novo construct to tune the properties of an electron-transfer Cu site.

Development of de Novo Copper Nitrite Reductases: Where We Are and Where We Need To Go

The development of redox-active metalloprotein catalysts is a challenging objective of de novo protein design. Within this Perspective we detail our efforts to create a redox-active Cu nitrite reductase (NiR) by incorporating Cu into the hydrophobic interior of well-defined three-stranded coiled coils (3SCCs). The scaffold contains three histidine residues that provide a layer of three nitrogen donors that mimic the type 2 catalytic site of NiR. We have found that this strategy successfully produces an active and stable CuNiR model that functions for over 1000 turnovers. Spectroscopic evidence indicates that the Cu(I) site has a lower coordination number in comparison to the enzyme, whereas the Cu(II) geometry may more faithfully reproduce the NiR type 2 center. Mutations at the helical interface successfully produce a hydrogen bond between an interfacial Glu residue and the Culigating His residue, which allows for the tuning of the redox potential over a 100 mV range. We successfully created constructs with as much as a 120-fold improvement from the original design by modifying the steric bulk above or below the Cu binding site. These systems are now the most active water-soluble and stable artificial NiR catalysts yet produced. Several avenues for improving the catalytic efficiency of later designs are detailed within this Perspective, including adjustment of their resting oxidation state, the use of asymmetric scaffolds to allow for single amino acid mutation within the second coordination sphere, and the design of hydrogen-bonding networks to tune residue orientation and electronics. Through these studies the TRI-H system has given insight into the difficulties that arise in creating a de novo redox active enzyme. Work to improve upon this model will provide strategies by which redox-active de novo enzymes may be tuned and detail how native enzymes accomplish catalytic efficiencies through proton gated redox catalysis.

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

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

Modifying the Steric Properties in the Second Coordination Sphere of Designed Peptides Leads to Enhancement of Nitrite Reductase Activity

Protein design is a useful strategy to interrogate the protein structure-function relationship. We demonstrate using a highly modular 3-stranded coiled coil (TRI-peptide system) that a functional type 2 copper center exhibiting copper nitrite reductase (NiR) activity exhibits the highest homogeneous catalytic efficiency under aqueous conditions for the reduction of nitrite to NO and H₂ O. Modification of the amino acids in the second coordination sphere of the copper center increases the nitrite reductase activity up to 75-fold compared to previously reported systems. We find also that steric bulk can be used to enforce a three-coordinate Cu^I in a site, which tends toward two-coordination with decreased steric bulk. This study demonstrates the importance of the second coordination sphere environment both for controlling metal-center ligation and enhancing the catalytic efficiency of metalloenzymes and their analogues.

Further insights into the metal ion binding abilities and the metalation pathway of a plant metallothionein from Musa acuminata

The superfamily of metallothioneins (MTs) combines a diverse group of metalloproteins, sharing the characteristics of rather low molecular weight and high cysteine content. The latter provides MTs with the capability to coordinate thiophilic metal ions, in particular those with a d 10 electron configuration. The sub-family of plant MT3 proteins is only poorly characterized and there is a complete lack of three-dimensional structure information. Building upon our previous results on the Musa acuminata MT3 (musMT3) protein, the focus of the present work is to understand the metal cluster formation process, the role of the single histidine residue present in musMT3, and the metal ion binding affinity. We concentrate our efforts on the coordination of ZnII and CdII ions, using CoII as a spectroscopic probe for ZnII binding. The overall protein-fold is analysed with a combination of limited proteolytic digestion, mass spectrometry, and dynamic light scattering. Histidine coordination of metal ions is probed with extended X-ray absorption fine structure spectroscopy and CoII titration experiments. Initial experiments with isothermal titration calorimetry provide insights into the thermodynamics of metal ion binding.

Near-infrared luminescent metallacrowns for combined in vitro cell fixation and counter staining

Cell fixation is an essential approach for preserving cell morphology, allowing the targeting and labelling of biomolecules with fluorescent probes. One of the key requirements for more efficient fluorescent labelling is the preservation of cell morphology, which usually requires a combination of several fixation techniques. In addition, the use of a counter stain is often essential to improve the contrast of the fluorescent probes. Current agents possess significant limitations, such as low resistance toward photobleaching and sensitivity to changes in the microenvironment. Luminescent Ln3+ 'encapsulated sandwich' metallacrowns (MCs) overcome these drawbacks and offer complementary advantages. In particular, they emit sharp emission bands, possess a large difference between excitation and emission wavelengths and do not photobleach. Herein, MCs formed with pyrazinehydroxamic acid (Ln3+[Zn(ii)MCpyzHA], Ln3+ = Yb, Nd) were used, combined with near-infrared (NIR) counter staining and fixation agents for HeLa cells upon an initial five minute exposure to UV-A light. The validity and quality of the cell fixation were assessed with Raman spectroscopy. Analysis of the NIR luminescence properties of these MCs was performed under different experimental conditions, including in a suspension of stained cells. Moreover, the high emission intensity of Ln3+[Zn(ii)MCpyzHA] in the NIR region allows these MCs to be used for imaging with standard CCD cameras installed on routine fluorescence microscopes. Finally, the NIR-emitting Ln3+[Zn(ii)MCpyzHA] compounds combine, within a single molecule, features such as cell fixation and staining abilities, good photostability and minimal sensitivity of the emission bands to the local microenvironment, and they are highly promising for establishing the next generation of imaging agents with a single biodistribution.

d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils

Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of Zn^II Cl(CSL16_D C)₃^2- to the published structure of Zn^II (H₂ O)(GRAND-CSL12AL16_L C)₃^- . Moreover, spectroscopic analysis indicates that the Cd^II geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate Cd^II ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.

Anion Encapsulation Drives the Formation of Dimeric GdIII[15-metallacrown-5]3+ Complexes in Aqueous Solution

Metallacrown complexes capable of sequestering dianions, as shown in the solid state, also exist in aqueous solution at neutral pH, as demonstrated by calorimetric and mass spectrometric data. The driving forces for the formation of these dimeric complexes in solution strongly depend on the chain length of the guest rather than its degree of unsaturation.

Lead(II) Binding in Natural and Artificial Proteins

This article describes recent attempts to understand the biological chemistry of lead using a synthetic biology approach. Lead binds to a variety of different biomolecules ranging from enzymes to regulatory and signaling proteins to bone matrix. We have focused on the interactions of this element in thiolate-rich sites that are found in metalloregulatory proteins such as Pbr, Znt, and CadC and in enzymes such as δ-aminolevulinic acid dehydratase (ALAD). In these proteins, Pb(II) is often found as a homoleptic and hemidirectic Pb(II)(SR)3- complex. Using first principles of biophysics, we have developed relatively short peptides that can associate into three-stranded coiled coils (3SCCs), in which a cysteine group is incorporated into the hydrophobic core to generate a (cysteine)3 binding site. We describe how lead may be sequestered into these sites, the characteristic spectral features may be observed for such systems and we provide crystallographic insight on metal binding. The Pb(II)(SR)3- that is revealed within these α-helical assemblies forms a trigonal pyramidal structure (having an endo orientation) with distinct conformations than are also found in natural proteins (having an exo conformation). This structural insight, combined with 207Pb NMR spectroscopy, suggests that while Pb(II) prefers hemidirected Pb(II)(SR)3- scaffolds regardless of the protein fold, the way this is achieved within α-helical systems is different than in β-sheet or loop regions of proteins. These interactions between metal coordination preference and protein structural preference undoubtedly are exploited in natural systems to allow for protein conformation changes that define function. Thus, using a design approach that separates the numerous factors that lead to stable natural proteins allows us to extract fundamental concepts on how metals behave in biological systems.