A protein engineered to bind uranyl selectively and with femtomolar affinity

Abstract

Uranyl (UO22+), 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.

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Figure 1: Uranyl sequestration strategy.
Figure 2: The main steps in computational screening and design of uranyl-binding proteins.
Figure 3: Uranyl-binding affinity and selectivity of SUP.
Figure 4: Uranyl–SUP crystal structure.
Figure 5: Immobilized SUP provides a useful manifold for a variety of applications.

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Acknowledgements

This work was supported by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the US Department of Energy, under contract number DE-FG02-07ER15865 to C.H., and at Argonne National Laboratory (M.J.) under contract number DE-AC02-06CH11357, the Dreyfus Foundation Postdoctoral Program in Environmental Chemistry to S.O., the Ministry of Science and Technology of China (2009CB918500) and the National Natural Science Foundation of China (21173013, 11021463) to L.L. Use of the Advanced Photon Source for protein crystallography data collection at beamlines LS/CA-CAT (21-ID-F) and NE-CAT (24-ID-C) was supported by the Office of Basic Energy Sciences of the US Department of Energy under contract number DE-AC02-06CH11357. We thank S. F. Reichard for editing the manuscript and C. Yang and L. Lan for experimental support.

Author information

C.H. conceived the project. C.H. and L.L. designed the experiment. C.Z. and L.L. performed the initial screening. W.Z. and C.J.L. performed subcloning of virtual hits. S.O. and C.J.L. expressed, purified and tested all first-generation virtual hits. L.Z., S.O. and M.B. designed second-generation mutants. L.Z., M.B. and J.L. expressed and tested all protein derivatives and designed all later-generation mutants. L.Z., M.B., M.P.J. and C.H. analysed the data and M.B. and L.Z. co-wrote the manuscript. All authors discussed the results and commented on the manuscript.

Correspondence to Luhua Lai or Chuan He.

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Zhou, L., Bosscher, M., Zhang, C. et al. A protein engineered to bind uranyl selectively and with femtomolar affinity. Nature Chem 6, 236–241 (2014). https://doi.org/10.1038/nchem.1856

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