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 LnIIINaI(OBz)4[12-MCGaIII(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.

Lower Energy Excitation of Water Soluble Near-Infrared Emitting Mixed-Ligand Metallacrowns.

By combining advantages of two series of lanthanide(III)/zinc(II) metallacrowns (MCs) assembled using pyrazine- (pyzHA2- ) and quinoxaline- (quinoHA2- ) hydroximate building blocks ligands, we created here water-soluble mixed-ligand MCs with extended absorption to the visible range. The YbIII analogue demonstrated improved photophysical properties in the near-infrared (NIR) range in cell culture media, facilitating its application for NIR optical imaging in living HeLa cells.

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, τc , for example, by fluorescence and NMR spectroscopy. With this work, we apply PAC spectroscopy to determine the rate of rotational diffusion, λ=1/τc , 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 4G5/2 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.

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 = YbIII, ErIII, and NdIII; 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 YbIII, ErIII, and NdIII 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. LnIII-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 LnIII. The close in energy positions of T1 and ILCT states in Zn16Ln(picHA)16 and Zn16Ln(quinHA)16 are preferred for the sensitization of LnIII NIR emission and η sens values reach 100% for NdIII. 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.

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.

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 (LnIII [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).

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.

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.

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.

Visible, Near-Infrared, and Dual-Range Luminescence Spanning the 4f Series Sensitized by a Gallium(III)/Lanthanide(III) Metallacrown Structure.

Lanthanide(III) ions (Ln3+) in coordination compounds exhibit unique luminescence properties with narrow and characteristic f-f transitions throughout the visible and near-infrared (NIR) ranges. In addition, some Ln3+ such as Pr3+, Sm3+, Dy3+, Ho3+, Er3+, and Tm3+ possess an exceptional ability, although less explored, to exhibit dual-range emissions. Such remarkable features allow highly specific use in materials science and biology, for example, for the creation of sophisticated barcode modules or for the next generation of optical imaging applications. Herein, a series of Ga3+/Ln3+ metallacrowns (MCs) with the general composition [LnGa8(shi)8(OH)4]Na·xCH3OH·yH2O (Ln-1, Ln = Pr3+, Nd3+, Sm3+-Yb3+ and analogue Y3+; H3shi = salicylhydroxamic acid) is presented. Ln-1 were obtained by reacting Ga3+ and Ln3+ nitrate salts with the H3shi ligand. X-ray single crystal unit cell analysis confirmed that all MCs are isostructural. The crystal structure was solved for the Nd3+ analogue and revealed that Nd3+ is centered between two [12-MCGaIIIN(shi)-4] MC rings and bound to eight hydroximate oxygen ions (four from each ring) in a pseudosquare antiprismatic fashion adopting a pseudo-D4h symmetry. Pulsed gradient spin echo diffusion ordered 1H NMR spectroscopy and electrospray ionization mass spectrometry confirmed that the structure of Ln-1 remains intact in methanol solutions while mass spectrometry suggests that four OH- bridges are exchanged with CH3O-/CD3O-. An exceptional ability of this series of MCs to sensitize the characteristic emission of Ln3+ was confirmed with the observation of bright red and green emission signals of Eu-1 and Tb-1, NIR emissions of Yb-1 and Nd-1, and dual-range emissions of Pr-1, Sm-1, Dy-1, Ho-1, Er-1, and Tm-1 in the solid state upon excitation into ligand-centered bands at 340 nm. The luminescence properties of Ln-1 (Ln = Nd3+, Sm3+, Eu3+, Tb3+, Dy3+, and Yb3+) were also investigated in CH3OH and CD3OD solutions. For Eu-1 and Yb-1 MCs, more extensive analyses of the photophysical properties were performed, which included the determination of radiative lifetimes, intrinsic quantum yields, and sensitization efficiencies. The absolute quantum yields (QLnL) of Ln-1 in the visible and NIR ranges have been determined. In the case of Sm-1, the values of QLnL in CH3OH and CD3OD solutions are exceptionally high, that is, 10.1(5) and 83(1) %. Values obtained for Yb-1, that is, 0.78(4) % in CH3OH and 8.4(1)% in CD3OD, are among the highest ones reported today for Yb3+ complexes formed with nondeuterated and nonhalogenated ligands.

Dy3+ White Light Emission Can Be Finely Controlled by Tuning the First Coordination Sphere of Ga3+/Dy3+ Metallacrown Complexes.

Single lanthanide(III) ion white light emission is in high demand since it provides the advantage of requiring only one chromophore for the control of the color. Herein, a series of Ga3+/Dy3+ metallacrowns (MCs) is presented, demonstrating outstanding white light colorimetric properties with CIE chromaticity coordinates of (0.309, 0.334) and correlated color temperature (CCT) equal to 6670 K for the MC emitting the closest to the standard white color. Experimental data reveal that the CIE coordinates within the studied series of MCs are controlled mainly by the Dy3+-centered emission rather than by the ligand-centered bands, implying that Dy3+ can be tuned as a single ionic white light emitter by a simple modification of the coordination environment.

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.

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.

[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 Sr =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.

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.

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.