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A Protein Engineered to Bind Uranyl Selectively and with Femtomolar Affinity

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A Protein Engineered to Bind Uranyl Selectively and with Femtomolar Affinity ARTICLES PUBLISHED ONLINE: 26 JANUARY 2014 | DOI: 10.1038/NCHEM.1856 A protein engineered to bind uranyl selectively and with femtomolar affinity Lu Zhou1†, Mike Bosscher1†, Changsheng Zhang2,3†,SalihO¨ zc¸ubukc¸u1, Liang Zhang1, Wen Zhang1, Charles J. Li1, Jianzhao Liu1, Mark P. Jensen4, Luhua Lai2,3* and Chuan He1* 21 ∼ Uranyl (UO2 ), the predominant aerobic form of uranium, is present in the ocean at a concentration of 3.2 parts per 109 (13.7 nM); however, the successful enrichment of uranyl from this vast resource has been limited by the high concentrations of metal ions of similar size and charge, which makes it difficult to design a binding motif that is selective for uranyl. Here we report the design and rational development of a uranyl-binding protein using a computational screening process in the initial search for potential uranyl-binding sites. The engineered protein is thermally stable and offers very high affinity and selectivity for uranyl with a Kd of 7.4 femtomolar (fM) and >10,000-fold selectivity over other metal ions. We also demonstrated that the uranyl-binding protein can repeatedly sequester 30–60% of the uranyl in synthetic sea water. The chemical strategy employed here may be applied to engineer other selective metal-binding proteins for biotechnology and remediation applications. ranium is the key element for nuclear-energy production and Through billions of years of evolution nature has produced is important in many other applications. The most stable and strategies to recognize beneficial or toxic metal ions with high Urelevant uranium ion in aerobic environments is the uranyl sensitivity and selectivity. In many cases, with the help of a well- 2þ cation, UO2 . As a consequence of its solubility the concentration folded protein scaffold and the assistance of second-sphere of uranyl in sea water is surprisingly high at 3.2 mg per tonne of sea interactions, metal ions can be recognized in the femtomolar to water (13.7 nM)1. Based on this concentration the ocean is esti- zeptomolar (10221) range with extremely high selectivity14–16.Ifa mated to contain 1,000 times more uranium than land contains, correct and robust scaffold can be developed for the metal of inter- and so offers an enormous resource that, unlike land resources, est, such affinities are sufficient for economic mining of uranium or may be tapped at minimal environmental cost. other elements from sea water or to remediate polluted environ- Functionalized polymers with amidoxime-type ligands have mental sites. Additionally, proteins may be displayed on the surfaces been used to sequester uranyl in sea water since the 1980s2,3. of living organisms17, thus allowing for the biological regeneration However, the low binding affinity and selectivity of the ligands of these systems for recovery and/or remediation purposes at very used limited the utility of the approach. Other approaches based low costs. on functional groups or small-molecule chelates have been pro- Uranyl-binding motifs are well known and offer distinctive posed, with limited success4,5. Sea water is slightly basic and con- handholds for the rational design of proteins that selectively bind tains 2.2 mM total carbonate, which chelates uranyl strongly uranyl7,8. Uranium prefers to oxidize to the þ6 state with two and leaves a free uranium concentration of only 2 × 10217 M axial oxo ligands and form the linear triatomic uranyl ion with (Supplementary Tables 1 and 2, and Supplementary Fig. 1). To an overall charge of þ2. The ability to afford five or six equatorial compete with this high concentration of dissolved carbonate ligands in pentagonal or hexagonal bipyramidal geometry separates under practical conditions, a ligand that can bind uranyl with uranyl from most of the alkali, alkaline and transition metals. The close to femtomolar (fM, 10215) affinity is required (see presence of the axial oxo ligands as potential hydrogen-bond Supplementary Information). In addition, calcium(II) is present at acceptors also distinguishes uranyl from most known lanthanide 10 mM in sea water and prefers an oxygen-rich environment and actinide species in the environment7. Although some uranyl- similar to that which typically binds uranyl. Therefore, a daunting binding motifs have been designed in organic ligands, in DNA selectivity of 106-fold for uranyl over calcium is desired. and in proteins6–11, none have been able to cross the affinity Sophisticated chelating ligands6–11 have been developed for other threshold to compete with carbonate (2.2 mM in ocean) and useful applications, but high synthetic costs limit their utilization achieve the selectivity requirements over other metals in sea when dealing with vast amounts of sea water. A layered solid-state water. Our strategy was to use computational screening and ion exchanger, K2MnSn2S6, has been shown to have high affinity design to develop a stable protein with sufficient binding affinity for uranium in addition to many other metals12. Very recently, for uranyl and selectivity over other metals. The protein can be metal–organic frameworks (MOFs) have also been employed as immobilized on a solid support or displayed on the cell surface novel sorbents to extract uranyl from aqueous media13. Biological for repeated use and sequestration (Fig. 1). This approach can be systems, which can be self-regenerated, offer an opportunity to applied to both engineered systems (resin immobilization) and achieve economically both the required affinity and high selectivity. biological systems (cell-surface display). 1Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA, 2BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering and Center for Quantitative Biology, Peking University, Beijing 100871, China, 3Center for Life Sciences, Peking University, Beijing 100871, China, 4Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, USA, †These authors contributed equally to this work. *e-mail: [email protected]; [email protected] 236 NATURE CHEMISTRY | VOL 6 | MARCH 2014 | www.nature.com/naturechemistry © 2014 Macmillan Publishers Limited. All rights reserved. NATURE CHEMISTRY DOI: 10.1038/NCHEM.1856 ARTICLES Pible et al. designed an algorithm to identify native uranyl- 2+ 2+ 19 UO2 VO binding proteins and the corresponding binding sites . However, Zn2+ Ni2+ the Amber force-field-based scoring and optimizing algorithm Ca2+ Fe3+ used in their study was not suitable for searching the vast 2+ 2+ Cu Mg numbers of mutations shown in our de novo design. The scoring function (see Supplementary Information) used in our program Adsorption not only predicts correct uranyl coordination geometry, but also Recovery helps to establish potential hydrogen-bonding interactions between uranyl oxo and residues from the binding protein. Structures of uranyl complexes with inorganic or organic ligands8, as well as Solid support Solid support crystal structures of proteins in which uranyl was used as a source 2+ UO2 of anomalous signal (Supplementary Table 3), provided a basis for the screening and uranyl-binding protein designs. Figure 1 | Uranyl sequestration strategy. Immobilization of a high-affinity Using URANTEIN we searched the PDB for pockets that could and selective uranyl-binding protein on a solid support allows for the accommodate hexagonal bipyramid or pentagonal bipyramid enrichment of uranium over other metals. The protein was de novo designed uranyl-binding geometries, either natively or through mutation of by computational screening based on the known scaffolds in the PDB. potential ligand residues to aspartate/asparagine or glutamate/gluta- Immobilized on resin or displayed on the cell surface by chemical or mine (see Supplementary Figs 2–4 and Supplementary Table 3). We biological means, the protein could effectively sequester uranyl from sea set the optimum distance between the oxygen-based ligand from the water or uranyl-containing groundwater. protein to the central uranium ion at 2.46 Å. In addition, we also incorporated a search method for potential hydrogen bonding Results between the oxo groups of the uranyl with the scaffold protein in Computational screening for potential uranyl-binding sites. We our screening process to maximize potential uranyl-binding affinity developed a large-scale computational screening algorithm, and selectivity (see Supplementary Information). From this initial named URANTEIN, to search the Protein Data Bank (PDB) for screen we identified over 5,000 hits. Hits were further selected pockets that may accommodate uranyl (Fig. 2). A total of 12,173 based on their potential stability, potential steric clashes in the pre- protein structures in the PDB were considered as scaffolds, on dicted coordination site and accessibility of the binding site. The which every residue could be mutated to Asp, Glu, Asn or Gln carboxylate side-chain ligand can be bidentate or monodentate, using the corresponding rotamers in silico. Based on an algorithm and therefore the fivefold or sixfold planar coordination around modified from Automatch18, URANTEIN can search efficiently the central uranyl can be flexible and affected by surrounding for uranyl-binding sites from these mutated pseudo-proteins. protein residues. Ten promising candidates were selected, of Step 1 Step 2 Step 3 Coordination features Pick a scaffold Build oxygen library and hydrogen library Step 5 Step 4 Go back to step 2 if there is no hit Scoring and sorting Top solutions library Search for uranyl-binding sites Figure 2 | The main steps in computational screening and design of uranyl-binding proteins. In step 1, three uranyl-coordination features were designed. In step 2, protein scaffolds were prepared by PDB query (version 2010). All entries that contained protein chains of length 60–200 amino acids (12,173 in total) were employed as scaffolds. Then, one scaffold in the library was picked for further screening (for example, the green one shown here). In step 3, the oxygen library of possible mutations and the hydrogen library of native protein were built (Supplementary Fig.
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