Near-adjacent heavy lanthanide separation and sensing using dimerizing lanmodulins
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A family portrait of lanmodulin selectivity for enhanced rare-earth separations
Proteins offer a molecular design space to create bespoke ligands for the separation of critical metals like rare earth elements (REs). However, data-intensive approaches to tune metalloprotein selectivity are constrained by the low-throughput nature of existing characterization methods. Here we invented an assay called ‘SpyTag-Catcher Immobilization of Lanmodulin for Assaying Metal-Binding Selectivity’ (SpyCI-LAMBS) to measure metalloprotein selectivity en masse. This 96-format workflow was used to study the selectivity of 621 lanmodulin (LanM) orthologs for 15 REs, revealing eight distinct selectivity profiles based on sequence-to-function analyses. We discovered >200 LanMs with stronger selectivity against low-value LaIII relative to the prototypical LanM. This includes a LanM that can perform a challenging one-stage separation of PrIII from LaIII with up to >99.9 mol% purity and 83% yield. SpyCI-LAMBS is a powerful tool that can rapidly collect high-fidelity selectivity data to inform metal ion separations and machine-learning-assisted metalloprotein design.
59 BASIC BIOLOGICAL SCIENCES↗
EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin
The lanmodulin (LanM) protein has emerged as an effective means for rare earth element (REE) extraction and separation from complex feedstocks without the use of organic solvents. Whereas the binding of LanM to individual REEs has been well characterized, little is known about the thermodynamics of mixed metal binding complexes (i.e., heterogeneous ion complexes), which limits the ability to accurately predict separation performance for a given metal ion mixture. In this paper, we employ the law of mass action to establish a theory of perfect cooperativity for LanM-REE complexation at the two highest-affinity binding sites. The theory is then used to derive an equation that explains the nonintuitive REE binding behavior of LanM, where separation factors for binary pairs of ions vary widely based on the ratio of ions in the aqueous phase, a phenomenon that is distinct from single-ion-binding chemical chelators. We then experimentally validate this theory and perform the first quantitative characterization of LanM complexation with heterogeneous ion pairs using resin-immobilized LanM. Importantly, the resulting homogeneous and heterogeneous constants enable accurate prediction of the equilibrium state of LanM in the presence of mixtures of up to 10 REEs, confirming that the perfect cooperativity model is an accurate mechanistic description of REE complexation by LanM. We further employ the model to simulate separation performance over a range of homogeneous and heterogeneous binding constants, revealing important insights into how mixed binding differentially impacts REE separations based on the relative positioning of the ion pairs within the lanthanide series. In addition to informing REE separation process optimization, these results provide mathematical and experimental insight into competition dynamics in other ubiquitous and medically relevant, cooperative binding proteins, such as calmodulin.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Mechanically and Chemically Robust Lanmodulin-Functionalized Silk Sponges for Rare Earth Element Sequestration
The extraction of rare-earth elements (REEs) from low-grade sources like electronic waste (E-waste) could supplement current unsustainable mining practices. REEs are crucial for various industries, but supply struggles to meet growing demand. Herein, we present an environmentally friendly method for REE extraction using silk protein sponges functionalized with lanmodulin (LanM), a protein that selectively binds REEs. These sponges are relatively facile to fabricate and scale, while offering highly selective REE binding. The REEs can then be recovered via simple acid leaching, allowing sponge reuse for multiple cycles as well as specific desorption of different REEs by changing the pH of the desorption buffer. Finally, this method avoids harmful solvents used in traditional extraction and enables recycling of REEs from industrial and E-waste.
REEs↗
X-ray absorption spectroscopy of lanmodulin-derived peptides bound to rare earth elements
A sustainable and robust supply chain of rare earth elements (REEs) is necessary to meet our consumer, national security and clean energy goals. However, current intra-REE separation technologies (e.g. solvent extraction) are costly and carry a heavy environmental burden. Therefore, the development of new aqueous based ligands that are selective for individual REEs will be integral in future REE production systems. To develop these ligands, an understanding of how ligand coordination structure relates to selectivity is imperative. We used X-ray absorption spectroscopy (XAS) to observe the local structure around four lanthanide (Ln) ions (La, Ce, Pr and Nd) complexed by water and several relevant chelating ligands [lanmodulin EF-hand 1 peptides (LanM1), ethylenediaminetetraacetic acid (EDTA), aminotris(methylenephosphonic acid) (ATMP) and citric acid]. To collect these liquid-phase XAS spectra, we developed a new flow cell that prevents bubble interference and beam damage to the samples. In the X-ray absorption near-edge structure (XANES), we observed energy shifts in the white line, white line broadening and differences in the white line intensity of different Ln–ligand complexes between ligands. In the extended X-ray absorption fine structure (EXAFS), we distinguished differences in peak intensity and distance between coordinating ligands. Differences in the local coordination structure between Ln–LanM1 peptide complexes were more subtle compared with the other ligands (La–water, La–EDTA, La–ATMP and La–citric acid complexes). Further XANES and EXAFS studies, in combination with modelling and other techniques, could greatly improve our structural knowledge of how these aqueous ligands bind Ln ions and how they can be used to design more selective ligands for more efficient and sustainable REE separations.
EDTA↗
Probing lanmodulin's mechanisms of rare-earth selectivity for protein-based bioseparations
Our BES Separation Science program project, DE-SC0021007, supported our efforts to begin to understand the mechanisms underlying selectivity of a novel class of lanthanide-binding proteins discovered by our laboratory, called lanmodulin (LanM), and to leverage these proteins for recovery and separations of trivalent rare earth elements (REEs) as well as of trivalent actinides. Overall, our work provides important insights into how higher-order (e.g., secondary, tertiary, and quaternary) protein structure modulates selectivity profiles of proteins that bind f-elements highly selectively. These results are important for advancing the concept of protein-based separations of REEs and, perhaps, of other critical minerals.
Lanmodulin, rare earth elements, protein-based met↗
Rational Design of Lanmodulin Variants for Size-Based Selectivity of Individual Rare Earth Elements
Rare earth elements (REEs) are essential to modern technologies, yet their high physical and chemical similarity makes separation of individual REEs difficult and environmentally taxing. Metalloproteins offer a promising alternative for selective REE binding, as they tend to have high metal ion affinity and specificity. Lanmodulin (LanM), in particular, has arisen as a potential candidate for REE separation as it exhibits picomolar affinity for elements in the REE family. Prior work has shown that the single point mutation D9N can shift LanM’s preference away from lanthanides toward actinides, motivating efforts to tune selectivity of LanM through targeted mutagenesis. Here, we tested the hypothesis that introducing selective aspartic acid to glutamic acid substitutions in the metal coordinating EF hands of LanM would impose steric constraints that would drive LanM affinity away from larger ions, such as La3+, to smaller ions, such as Y3+. To test this hypothesis, a combination of computational and experimental approaches were employed to evaluate the signal mutations LanM D5E and LanM D3E and the double mutants LanM D1ED5E and LanM D3ED9E. Surprisingly, increasing the number of mutations within the metal center did not enhance affinity for smaller REEs, or decrease affinity for larger ions. Only the single point mutation LanM D5E weakened La3+ binding by one order of magnitude relative to LanM wild type (WT), and pairing it with a second mutation to produce LanM D1ED5E drove La3+ affinity to be stronger than that seen for LanM WT. The D3E mutation alone prevented proper expression and folding, but paring it with D9E to produce LanM D3ED9E rescued expression and yielded La3+ affinities comparable to LanM WT. All variants that expressed (LanM D5E, LanM D1ED5E, LanM D3ED9E) displayed Y3+ affinities comparable to LanM WT. Overall, these results highlight the tunability of LanM’s metal-binding environment but also expose current limitations in predicting structural responses to point mutations within a protein sequence. This work establishes a foundation that can be used for refining computational and experimental strategies to engineer metalloproteins with tailored REE selectivity.
Close, Emily [Pacific Northwest National Laborator↗
Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides
Elucidating details of biology’s selective uptake and trafficking of rare earth elements, particularly the lanthanides, has the potential to inspire sustainable biomolecular separations of these essential metals for myriad modern technologies. Here, we biochemically and structurally characterize Methylobacterium (Methylorubrum) extorquens LanD, a periplasmic protein from a bacterial gene cluster for lanthanide uptake. This protein provides only four ligands at its surface-exposed lanthanide-binding site, allowing for metal-centered protein dimerization that favors the largest lanthanide, La III . However, the monomer prefers Nd III and Sm III , which are disfavored lanthanides for cellular utilization. Structure-guided mutagenesis of a metal-ligand and an outer-sphere residue weakens metal binding to the LanD monomer and enhances dimerization for Pr III and Nd III by 100-fold. Selective dimerization enriches high-value Pr III and Nd III relative to low-value La III and Ce III in an all-aqueous process, achieving higher separation factors than lanmodulins and comparable or better separation factors than common industrial extractants. Finally, we show that LanD interacts with lanmodulin (LanM), a previously characterized periplasmic protein that shares LanD’s preference for Nd III and Sm III . Our results suggest that LanD’s unusual metal-binding site transfers less-desirable lanthanides to LanM to siphon them away from the pathway for cytosolic import. The properties of LanD show how relatively weak chelators can achieve high selectivity, and they form the basis for the design of protein dimers for separation of adjacent lanthanide pairs and other metal ions.
lanthanide biochemistry↗
QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models
Here, conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln 3+ ) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln 3+ interaction with representatives of solvent (water, H 2 O) and protein binding sites (acetate, CH 3 COO – ), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln 3+ with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln 3+ interactions with (H 2 O) 9 and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu 3+ , which bound less favorably than the preceding element, Yb 3+ . Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln 3+ interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln 3+ interactions with biomolecules and presents an effective computational platform for designing specific single-site REM binding peptides more efficiently.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗