1
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Liu C, Li Y, Lei M, Liu D, Li B, Fu C, Guo J. Interlayer manipulation of bio-inspired Ti 3C 2T x nanocontainer through intercalation of amino acid molecules to dramatically boosting uranyl hijacking capability from seawater. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134002. [PMID: 38503213 DOI: 10.1016/j.jhazmat.2024.134002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/20/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
More than 4.5 billion tons of unconventional uranium resources [UO2(CO3)3]4- are uniformly dissolved in seawater, providing a sustainable and abundant fuel source for the development of nuclear energy. Herein, we presented a rational design and development of Ti3C2Tx nanocontainer inspired by the exceptional selectivity and affinity exhibited by superb-uranyl proteins through amino acid intercalation. The amino acid intercalation of Ti3C2Tx demonstrated exceptional UO22+ capture capacity (Arg-Ti3C2Tx, His-Ti3C2Tx, and Lys-Ti3C2Tx with qmax values of 594.46, 846.04, and 1030.17 mg/g). Furthermore, these intercalated materials exhibited remarkable sequestration efficiency and selectivity (Uinitial = ∼45.2 ∼7636 μg/L; ∼84.45% ∼98.08%; and ∼2.72 ×104 ∼1.28 ×105 KdU value), despite the presence of an overwhelming surplus of Na+, Ca2+, Mg2+, and Co2+ ions. Significantly, even in the 0.3 M NaHCO3 solution and surpassing 103-fold of the Na3VO4 system, the adsorption efficiency of Lys-Ti3C2Tx still achieved a remarkable 63.73% and 65.05%. Moreover, the Lys-Ti3C2Tx can extract ∼30.23 ∼8664.03 μg/g uranium after 24 h contact in ∼13.3 ∼5000 μg/L concentration from uranium-spiked natural seawater. The mechanism analysis revealed that the high binding capability can be attributed to the chelation of carboxyl and amino groups with uranyl ions. This innovative state-of-the-art approach in regulating uranium harvesting capability through intercalation of amino acid molecules provides novel insights for extracting uranium from seawater.
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Affiliation(s)
- Chang Liu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Ye Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China.
| | - Miao Lei
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Dongxue Liu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Bolin Li
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Chengbin Fu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | - Junpeng Guo
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, People's Republic of China
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2
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Diep P, Stogios PJ, Evdokimova E, Savchenko A, Mahadevan R, Yakunin AF. Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS J 2024. [PMID: 38555564 DOI: 10.1111/febs.17125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Wales, UK
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3
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Shabbir S, Yang N, Wang D. Enhanced uranium extraction from seawater: from the viewpoint of kinetics and thermodynamics. NANOSCALE 2024; 16:4937-4960. [PMID: 38362657 DOI: 10.1039/d3nr05905g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Uranium extraction from seawater (UES) is recognized as one of the seven pivotal chemical separations with the potential to revolutionize global paradigms. The forthcoming decade is anticipated to witness a surge in UES, driven by escalating energy demands. The oceanic reservoirs, possessing uranium quantities approximately 1000-fold higher than terrestrial mines, present a more sustainable and environmentally benign alternative. Empirical evidence from historical research indicates that adsorption emerges as the most efficacious process for uranium recovery from seawater, considering operational feasibility, cost-effectiveness, and selectivity. Over the years, scientific exploration has led to the development of a plethora of adsorbents with superior adsorption capacity. It would be efficient to design materials with a deep understanding of the adsorption from the perspective of kinetics and thermodynamics. Here, we summarize recent advancements in UES technology and the contemporary challenges encountered in this domain. Furthermore, we present our perspectives on the future trajectory of UES and finally offer our insights into this subject.
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Affiliation(s)
- Sania Shabbir
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
| | - Nailiang Yang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
| | - Dan Wang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Preparation and Delivery, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
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4
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Maurya A, Marvaniya K, Dobariya P, Mane MV, Tothadi S, Patel K, Kushwaha S. Biomimetic Helical Hydrogen Bonded Organic Framework Membranes for Efficient Uranium Recovery from Seawater. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2306824. [PMID: 37975153 DOI: 10.1002/smll.202306824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/13/2023] [Indexed: 11/19/2023]
Abstract
Inspired by the uranyl-imidazole interactions via nitrogen's (N's) of histidine residues in single helical protein assemblies with open framework geometry that allows through migration/coordination of metal ions. Here, preliminary components of a stable hydrogen-bonded organic framework (HOF) are designed to mimic the stable single helical open framework with imidazole residues available for Uranium (U) binding. The imidazolate-HOF (CSMCRI HOF2-S) is synthesized with solvent-directed H-bonding in 1D array and tuned hydrophobic CH-π interactions leading to single helix pattern having enhanced hydrolytic stability. De-solvation led CSMCRI HOF2-P with porous helical 1D channels are transformed in a freestanding thin film that showcased improved mass transfer and adsorption of uranyl carbonate. CSMCRI HOF2-P thin film can effectively extract ≈14.8 mg g-1 in 4 weeks period from natural seawater, with > 1.7 U/V (Uranium to Vanadium ratio) selectivity. This strategy can be extended for rational designing of hydrolytically stable, U selective HOFs to realize the massive potential of the blue economy toward sustainable energy.
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Affiliation(s)
- Ashish Maurya
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Karan Marvaniya
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Priyanka Dobariya
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manoj V Mane
- Centre for Nano and Material Sciences, Jain Global Campus, Jain University, Kanakapura, Ramanagaram, Bangalore, 562112, India
| | - Srinu Tothadi
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ketan Patel
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shilpi Kushwaha
- CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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5
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Nasr MA, Martin VJJ, Kwan DH. Divergent directed evolution of a TetR-type repressor towards aromatic molecules. Nucleic Acids Res 2023; 51:7675-7690. [PMID: 37377432 PMCID: PMC10415137 DOI: 10.1093/nar/gkad503] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 06/29/2023] Open
Abstract
Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
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Affiliation(s)
- Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
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6
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Cao K, Li S, Wang Y, Hu H, Xiang S, Zhang Q, Liu Y. Cellular uptake of nickel by NikR is regulated by phase separation. Cell Rep 2023; 42:112518. [PMID: 37210726 DOI: 10.1016/j.celrep.2023.112518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 02/02/2023] [Accepted: 05/01/2023] [Indexed: 05/23/2023] Open
Abstract
Bacterial cells were long thought to be "bags of enzymes" with minimal internal structures. In recent years, membrane-less organelles formed by liquid-liquid phase separation (LLPS) of proteins or nucleic acids have been found to be involved in many important biological processes, although most of them were studied on eukaryotic cells. Here, we report that NikR, a bacterial nickel-responsive regulatory protein, exhibits LLPS both in solution and inside cells. Analyses of cellular nickel uptake and cell growth of E. coli confirm that LLPS enhances the regulatory function of NikR, while disruption of LLPS in cells promotes the expression of nickel transporter (nik) genes, which are negatively regulated by NikR. Mechanistic study shows that Ni(II) ions induces the accumulation of nik promoter DNA into the condensates formed by NikR. This result suggests that the formation of membrane-less compartments can be a regulatory mechanism of metal transporter proteins in bacterial cells.
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Affiliation(s)
- Kaiming Cao
- College of Chemistry and Environmental Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Shixuan Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yu Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Hongze Hu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Sijia Xiang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Qianling Zhang
- College of Chemistry and Environmental Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yangzhong Liu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
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7
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Cao M, Peng Q, Wang Y, Luo G, Feng L, Zhao S, Yuan Y, Wang N. High-efficiency uranium extraction from seawater by low-cost natural protein hydrogel. Int J Biol Macromol 2023; 242:124792. [PMID: 37169051 DOI: 10.1016/j.ijbiomac.2023.124792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
Utilization of uranium resource in seawater are highly possible to meet the growth demands for the sustainable development of nuclear energy industry. Bio-adsorbents exhibit high performance in terms of adsorption selectivity, equilibrium speed, and environmental friendliness, while the high fabrication cost hinders their practical application. In this study, a low-cost soy protein isolate (SPI) is used to fabricate adsorbent named SPI hydrogel for uranium extraction. This is the first report on applying bio-adsorbents derived from low-cost natural proteins for uranium extraction. The SPI hydrogel showed high uranium adsorption capacity of 53.94 mg g-1 in simulated nuclear wastewater and 5.29 mg g-1 is achieved in natural seawater, which is higher than all currently available adsorbents based on non-modified natural biomolecules. The amino and oxygen-containing groups are identified as the functional groups for uranyl binding by providing four oxygen and two nitrogen atoms to form equatorial coordination with uranyl, which guarantees the high binding selectivity and affinity to uranyl ions. The low cost for accessing the raw material together with the environmental friendliness, high salt tolerance, high uranium adsorption ability, and high selectivity to uranium, make SPI hydrogel a promising adsorbent for uranium extraction from seawater and nuclear wastewater.
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Affiliation(s)
- Meng Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Qin Peng
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Yue Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Guangsheng Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Shilei Zhao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.
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8
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Platts JA, Tolbatov I. Simulation of Uranyl-Biomolecule Interaction using a Cationic Dummy Atom Model. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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9
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Vallet A, Martin-Laffon J, Favier A, Revel B, Bonnot T, Vidaud C, Armengaud J, Gaillard JC, Delangle P, Devime F, Figuet S, Serre NBC, Erba EB, Brutscher B, Ravanel S, Bourguignon J, Alban C. The plasma membrane-associated cation-binding protein PCaP1 of Arabidopsis thaliana is a uranyl-binding protein. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130668. [PMID: 36608581 DOI: 10.1016/j.jhazmat.2022.130668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) is a naturally-occurring radionuclide that is toxic to living organisms. Given that proteins are primary targets of U(VI), their identification is an essential step towards understanding the mechanisms of radionuclide toxicity, and possibly detoxification. Here, we implemented a chromatographic strategy including immobilized metal affinity chromatography to trap protein targets of uranyl in Arabidopsis thaliana. This procedure allowed the identification of 38 uranyl-binding proteins (UraBPs) from root and shoot extracts. Among them, UraBP25, previously identified as plasma membrane-associated cation-binding protein 1 (PCaP1), was further characterized as a protein interacting in vitro with U(VI) and other metals using spectroscopic and structural approaches, and in planta through analyses of the fate of U(VI) in Arabidopsis lines with altered PCaP1 gene expression. Our results showed that recombinant PCaP1 binds U(VI) in vitro with affinity in the nM range, as well as Cu(II) and Fe(III) in high proportions, and that Ca(II) competes with U(VI) for binding. U(VI) induces PCaP1 oligomerization through binding at the monomer interface, at both the N-terminal structured domain and the C-terminal flexible region. Finally, U(VI) translocation in Arabidopsis shoots was affected in pcap1 null-mutant, suggesting a role for this protein in ion trafficking in planta.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, 38000 Grenoble, France
| | | | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, IBS, 38000 Grenoble, France
| | - Benoît Revel
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Titouan Bonnot
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Claude Vidaud
- BIAM, CEA, CNRS, Univ. Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-F-30200 Bagnols-sur-Cèze, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-F-30200 Bagnols-sur-Cèze, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, GRE-INP, IRIG, SyMMES, 38000 Grenoble, France
| | - Fabienne Devime
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Sylvie Figuet
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | - Nelson B C Serre
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | | | | | - Stéphane Ravanel
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France
| | | | - Claude Alban
- Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, 38000 Grenoble, France.
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10
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Trypsin-modified amidoxime improves the adsorption selectivity of uranium. J Radioanal Nucl Chem 2023. [DOI: 10.1007/s10967-023-08770-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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11
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Xie Y, Liu Z, Geng Y, Li H, Wang N, Song Y, Wang X, Chen J, Wang J, Ma S, Ye G. Uranium extraction from seawater: material design, emerging technologies and marine engineering. Chem Soc Rev 2023; 52:97-162. [PMID: 36448270 DOI: 10.1039/d2cs00595f] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Uranium extraction from seawater (UES), a potential approach to securing the long-term uranium supply and sustainability of nuclear energy, has experienced significant progress in the past decade. Promising adsorbents with record-high capacities have been developed by diverse innovative synthetic strategies, and scale-up marine field tests have been put forward by several countries. However, significant challenges remain in terms of the adsorbents' properties in complex marine environments, deployment methods, and the economic viability of current UES systems. This review presents an up-to-date overview of the latest advancements in the UES field, highlighting new insights into the mechanistic basis of UES and the methodologies towards the function-oriented development of uranium adsorbents with high adsorption capacity, selectivity, biofouling resistance, and durability. A distinctive emphasis is placed on emerging electrochemical and photochemical strategies that have been employed to develop efficient UES systems. The most recent achievements in marine tests by the major countries are summarized. Challenges and perspectives related to the fundamental, technical, and engineering aspects of UES are discussed. This review is envisaged to inspire innovative ideas and bring technical solutions towards the development of technically and economically viable UES systems.
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Affiliation(s)
- Yi Xie
- Collaborative Innovation Center of Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China.
| | - Zeyu Liu
- AVIC Manufacturing Technology Institute, Beijing 100024, China
| | - Yiyun Geng
- Collaborative Innovation Center of Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China.
| | - Hao Li
- Collaborative Innovation Center of Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China. .,China Academy of Engineering Physics, Mianyang 621900, China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yanpei Song
- Department of Chemistry, University of North Texas, Denton, TX, 76201, USA
| | - Xiaolin Wang
- China Academy of Engineering Physics, Mianyang 621900, China
| | - Jing Chen
- Collaborative Innovation Center of Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China.
| | - Jianchen Wang
- Collaborative Innovation Center of Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China.
| | - Shengqian Ma
- Department of Chemistry, University of North Texas, Denton, TX, 76201, USA
| | - Gang Ye
- Collaborative Innovation Center of Advanced Nuclear Energy Technology, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, China.
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12
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Pardoux R, Sauge-Merle S, Bremond N, Beccia MR, Lemaire D, Battesti C, Delangle P, Solari PL, Guilbaud P, Berthomieu C. Optimized Coordination of Uranyl in Engineered Calmodulin Site 1 Provides a Subnanomolar Affinity for Uranyl and a Strong Uranyl versus Calcium Selectivity. Inorg Chem 2022; 61:20480-20492. [DOI: 10.1021/acs.inorgchem.2c03185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Romain Pardoux
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Sandrine Sauge-Merle
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Nicolas Bremond
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Maria Rosa Beccia
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - David Lemaire
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Christine Battesti
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000Grenoble, France
| | - Pier Lorenzo Solari
- MARS beamline, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192Gif-sur-Yvette Cedex, France
| | | | - Catherine Berthomieu
- Aix Marseille Univ, CEA, CNRS, UMR 7265, BIAM, Interactions Protéine Métal, 13108Saint Paul-Lez-Durance, France
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13
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Zuo L, Peng W, Xu Z, Guo H, Luo M. Selective adsorption of uranyl by glutamic acid-modified amidoxime fiber. REACT FUNCT POLYM 2022. [DOI: 10.1016/j.reactfunctpolym.2022.105376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Liu C, Yu H, Zhang B, Liu S, Liu CG, Li F, Song H. Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol Adv 2022; 60:108019. [PMID: 35853551 DOI: 10.1016/j.biotechadv.2022.108019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg2+, Zn2+, Pb2+, Au3+, Cd2+, As3+, Ni2+, Cu2+, and UO22+) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.
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Affiliation(s)
- Changjiang Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shilin Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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15
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Uehara A, Matsumura D, Tsuji T, Yakumaru H, Tanaka I, Shiro A, Saitoh H, Ishihara H, Homma-Takeda S. Uranium chelating ability of decorporation agents in serum evaluated by X-ray absorption spectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2439-2445. [PMID: 35694955 DOI: 10.1039/d2ay00565d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Internal exposure to actinides such as uranium and plutonium has been reduced using chelating agents for decorporation because of their potential to induce both radiological and chemical toxicities. This study measures uranium chemical forms in serum in the presence and absence of chelating agents based on X-ray absorption spectroscopy (XAS). The chelating agents used were 1-hydroxyethane 1,1-bisphosphonate (EHBP), inositol hexaphosphate (IP6), deferoxamine B (DFO), and diethylenetriaminepentaacetate (DTPA). Percentages of uranium-chelating agents and uranium-bioligands (bioligands: inorganic and organic ligands coordinating with uranium) dissolving in the serum were successfully evaluated based on principal component analysis of XAS spectra. The main ligands forming complexes with uranium in the serum were estimated as follows: IP6 > EHBP > bioligands > DFO ≫ DTPA when the concentration ratio of the chelating agent to uranium was 10. Measurements of uranium chemical forms and their concentrations in the serum would be useful for the appropriate treatment using chelating agents for the decorporation of uranium.
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Affiliation(s)
- Akihiro Uehara
- National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Japan.
| | - Daiju Matsumura
- Materials Sciences Research Center, Japan Atomic Energy Agency, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takuya Tsuji
- Materials Sciences Research Center, Japan Atomic Energy Agency, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Haruko Yakumaru
- National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Japan.
| | - Izumi Tanaka
- National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Japan.
| | - Ayumi Shiro
- Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroyuki Saitoh
- Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Ishihara
- National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Japan.
| | - Shino Homma-Takeda
- National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage, Chiba 263-8555, Japan.
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16
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Choi TS, Tezcan FA. Overcoming universal restrictions on metal selectivity by protein design. Nature 2022; 603:522-527. [PMID: 35236987 PMCID: PMC9157509 DOI: 10.1038/s41586-022-04469-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Selective metal coordination is central to the functions of metalloproteins:1,2 each metalloprotein must pair with its cognate metallocofactor to fulfil its biological role3. However, achieving metal selectivity solely through a three-dimensional protein structure is a great challenge, because there is a limited set of metal-coordinating amino acid functionalities and proteins are inherently flexible, which impedes steric selection of metals3,4. Metal-binding affinities of natural proteins are primarily dictated by the electronic properties of metal ions and follow the Irving-Williams series5 (Mn2+ < Fe2+ < Co2+ < Ni2+ < Cu2+ > Zn2+) with few exceptions6,7. Accordingly, metalloproteins overwhelmingly bind Cu2+ and Zn2+ in isolation, regardless of the nature of their active sites and their cognate metal ions1,3,8. This led organisms to evolve complex homeostatic machinery and non-equilibrium strategies to achieve correct metal speciation1,3,8-10. Here we report an artificial dimeric protein, (AB)2, that thermodynamically overcomes the Irving-Williams restrictions in vitro and in cells, favouring the binding of lower-Irving-Williams transition metals over Cu2+, the most dominant ion in the Irving-Williams series. Counter to the convention in molecular design of achieving specificity through structural preorganization, (AB)2 was deliberately designed to be flexible. This flexibility enabled (AB)2 to adopt mutually exclusive, metal-dependent conformational states, which led to the discovery of structurally coupled coordination sites that disfavour Cu2+ ions by enforcing an unfavourable coordination geometry. Aside from highlighting flexibility as a valuable element in protein design, our results illustrate design principles for constructing selective metal sequestration agents.
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Affiliation(s)
- Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - F Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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17
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Mattocks JA, Cotruvo JA. Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides. Chem Soc Rev 2020; 49:8315-8334. [PMID: 33057507 DOI: 10.1039/d0cs00653j] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lanthanides and actinides are elements of ever-increasing technological importance in the modern world. However, the similar chemical and physical properties within these groups make purification of individual elements a challenge. Current industrial standards for the extraction, separation, and purification of these metals from natural sources, recycled materials, and industrial waste are inefficient, relying upon harsh conditions, repetitive steps, and ligands with only modest selectivity. Biological, biomolecular, and bio-inspired strategies towards improving these separations and making them more environmentally sustainable have been researched for many years; however, these methods often have insufficient selectivity for practical application. Recent developments in the understanding of how lanthanides are selectively acquired and used by certain bacteria offer the opportunity for a newer, more efficient take on these designs, as well as the possibility for fundamentally new designs and strategies. Herein, we review current cell-based and biomolecular (primarily small-molecule and protein-based) methods for detection, extraction, and separations of f-block elements. We discuss how the increasing knowledge regarding the selective recognition, uptake, trafficking, and storage of these elements in biological systems has informed and will continue to promote development of novel approaches to achieve these ends.
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Affiliation(s)
- Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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18
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Lin YW. Uranyl Binding to Proteins and Structural-Functional Impacts. Biomolecules 2020; 10:biom10030457. [PMID: 32187982 PMCID: PMC7175365 DOI: 10.3390/biom10030457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/08/2020] [Accepted: 03/13/2020] [Indexed: 01/29/2023] Open
Abstract
The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO22+). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; ; Tel.: +86-734-8578079
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China
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19
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Yuan Y, Feng S, Feng L, Yu Q, Liu T, Wang N. A Bio‐inspired Nano‐pocket Spatial Structure for Targeting Uranyl Capture. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Shiwei Feng
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Tingting Liu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
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20
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Engineering uranyl-chelating peptides from NikR for electrochemical peptide-based sensing applications. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2019.113698] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Yuan Y, Feng S, Feng L, Yu Q, Liu T, Wang N. A Bio‐inspired Nano‐pocket Spatial Structure for Targeting Uranyl Capture. Angew Chem Int Ed Engl 2020; 59:4262-4268. [DOI: 10.1002/anie.201916450] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Shiwei Feng
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Tingting Liu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan University Haikou 570228 P. R. China
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22
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Garai A, Delangle P. Recent advances in uranyl binding in proteins thanks to biomimetic peptides. J Inorg Biochem 2019; 203:110936. [PMID: 31864150 DOI: 10.1016/j.jinorgbio.2019.110936] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/05/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022]
Abstract
Uranium is an element belonging to the actinide series. It is ubiquitous in rock, soil, and water. Uranium is found in the ecosystem due to mining and milling industrial activities and processing to nuclear fuel, but also to the extensive use of phosphate fertilizers. Understanding uranium binding in vivo is critical, first to deepen our knowledge of molecular events leading to chemical toxicity, but also to provide new mechanistic information useful for the development of efficient decorporation treatments to be applied in case of intoxication. The most stable form in physiological conditions is the uranyl cation (UO22+), in which uranium oxidation state is +VI. This short review presents uranyl coordination properties and chelation, and what is currently known about uranium binding to proteins. Although several target proteins have been identified, the UO22+ binding sites have barely been identified. Biomimetic approaches using model peptides are good options to shed light on high affinity uranyl binding sites in proteins. A strategy based on constrained cyclodecapeptides allowed recently to propose a tetraphosphate binding site for uranyl that provides an affinity similar to the one measured with the phosphoprotein osteopontin.
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Affiliation(s)
- Aditya Garai
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France
| | - Pascale Delangle
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France.
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23
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Hoarau M, Koebke KJ, Chen Z, Marsh ENG. Probing Metal Ion Discrimination in a Protein Designed to Bind Uranyl Cation With Femtomolar Affinity. Front Mol Biosci 2019; 6:73. [PMID: 31552264 PMCID: PMC6736553 DOI: 10.3389/fmolb.2019.00073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022] Open
Abstract
The design of metal-binding sites in proteins that combine high affinity with high selectivity for the desired metal ion remains a challenging goal. Recently, a protein designed to display femtomolar affinity for UO22+, dubbed “Super Uranyl-binding Protein” (SUP), was described, with potential applications for removing UO22+ in water. Although it discriminated most metal ions present in seawater, the protein showed a surprisingly high affinity for Cu2+ ions. Here, we have investigated Cu2+ binding to SUP using a combination of electron paramagnetic resonance, fluorescence and circular dichroism spectroscopies. Our results provide evidence for two Cu2+ binding sites on SUP that are distinct from the UO22+ binding site, but one of which interferes with UO22+ binding. They further suggest that in solution the protein's secondary structure changes significantly in response to binding UO22+; in contrast, the crystal structures of the apo- and holo-protein are almost superimposable. These results provide insights for further improving the selectivity of SUP for UO22+, paving the way toward protein-based biomaterials for decontamination and/or recovery of uranium.
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Affiliation(s)
- Marie Hoarau
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Zhan Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
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24
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Park DM, Taffet MJ. Combinatorial Sensor Design in Caulobacter crescentus for Selective Environmental Uranium Detection. ACS Synth Biol 2019; 8:807-817. [PMID: 30897331 DOI: 10.1021/acssynbio.8b00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to detect uranium (U) through environmental monitoring is of critical importance for informing water resource protection and nonproliferation efforts. While technologies exist for environmental U detection, wide-area environmental monitoring, i.e. sampling coverage over large areas not known to possess U contamination, remains a challenging prospect that necessitates the development of novel detection approaches. Herein, we describe the development of a whole-cell U sensor by integrating two functionally independent, native U-responsive two-component signaling systems (TCS), UzcRS and UrpRS, within an AND gate circuit in the bacterium Caulobacter crescentus. Through leverage of the distinct but imperfect selectivity profiles of both TCS, this combinatorial approach enabled greater selectivity relative to a prior biosensor developed with UzcRS alone; no cross-reactivity was observed with most common environmental metals (e.g, Fe, As, Cu, Ca, Mg, Cd, Cr, Al) or the U decay-chain product Th, and the selectivity against Zn and Pb was significantly improved. In addition, integration of the UzcRS signal amplifier protein UzcY within the AND gate circuit further enhanced overall sensitivity and selectivity for U. The functionality of the sensor in an environmental context was confirmed by detection of U concentrations as low as 1 μM in groundwater samples. The results highlight the value of a combinatorial approach for constructing whole-cell sensors for the selective detection of analytes for which there are no known evolved regulators.
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Affiliation(s)
- Dan M. Park
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Michael J. Taffet
- Environmental Restoration Department (ERD), Operations and Business Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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25
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Carugo O. Structural features of uranium-protein complexes. J Inorg Biochem 2018; 189:1-6. [PMID: 30149122 DOI: 10.1016/j.jinorgbio.2018.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/19/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
Uranium toxicity depends on its chemical properties rather than on its radioactivity and involves its interaction with macromolecules. Here, a systematic survey of the structural features of the uranyl sites observed in protein crystal structures deposited in the Protein Data Bank is reported. Beside the two uranyl oxygens, which occupy the axial positions, uranium tends to be coordinated by five other oxygen atoms, which occupy the equatorial vertices of a pentagonal bipyramid. Even if one or more of these equatorial positions are sometime empty, they can be occupied only by oxygen atoms that belong to the carboxylate groups of Glu and Asp side-chains, usually acting as monodentate ligands, to water molecules, or to acetate anions. Although several uranium sites appear undefined or unrefined, with a single uranium atom that lacks the two uranyl oxygen atoms, this problem seems to become less frequent in recent years. However, it is clear that the crystallographic refinements of the uranyl sites are not always well restrained and a better parametrization of these restraints seems to be necessary.
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Affiliation(s)
- Oliviero Carugo
- Chemistry Department, University of Pavia, Italy; Department of Structural and Computational Biology, University of Vienna, Austria.
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26
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Padkina MV, Sambuk EV. Prospects for the Application of Yeast Display in Biotechnology and Cell Biology (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818040105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Kolhe N, Zinjarde S, Acharya C. Responses exhibited by various microbial groups relevant to uranium exposure. Biotechnol Adv 2018; 36:1828-1846. [PMID: 30017503 DOI: 10.1016/j.biotechadv.2018.07.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.
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Affiliation(s)
- Nilesh Kolhe
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India.
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Trombay, Mumbai 400094, India.
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28
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Bio-inspired nano-traps for uranium extraction from seawater and recovery from nuclear waste. Nat Commun 2018; 9:1644. [PMID: 29691403 PMCID: PMC5915388 DOI: 10.1038/s41467-018-04032-y] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/28/2018] [Indexed: 11/26/2022] Open
Abstract
Nature can efficiently recognize specific ions by exerting second-sphere interactions onto well-folded protein scaffolds. However, a considerable challenge remains to artificially manipulate such affinity, while being cost-effective in managing immense amounts of water samples. Here, we propose an effective approach to regulate uranyl capture performance by creating bio-inspired nano-traps, illustrated by constructing chelating moieties into porous frameworks, where the binding motif’s coordinative interaction towards uranyl is enhanced by introducing an assistant group, reminiscent of biological systems. Representatively, the porous framework bearing 2-aminobenzamidoxime is exceptional in sequestering high uranium concentrations with sufficient capacities (530 mg g−1) and trace quantities, including uranium in real seawater (4.36 mg g−1, triple the benchmark). Using a combination of spectroscopic, crystallographic, and theory calculation studies, it is revealed that the amino substituent assists in lowering the charge on uranyl in the complex and serves as a hydrogen bond acceptor, boosting the overall uranyl affinity of amidoxime. Uranium extraction is important for both uranium recovery and nuclear waste management. Here, inspired by the high sensitivity of proteins towards specific metal ions, Ma and colleagues demonstrate that introducing secondary coordination spheres into amidoxime-functionalized porous polymers can enhance their uranyl chelating abilities.
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29
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Wei X, Liu Q, Zhang H, Lu Z, Liu J, Chen R, Li R, Li Z, Liu P, Wang J. Efficient removal of uranium(vi) from simulated seawater using amidoximated polyacrylonitrile/FeOOH composites. Dalton Trans 2018; 46:15746-15756. [PMID: 29095447 DOI: 10.1039/c7dt02164j] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The ability to recover uranium, an important nuclear fuel, from seawater provides the potential for long-term sustainable fuel supply for nuclear energy. In this work, novel amidoximated polyacrylonitrile/FeOOH (FeOOH-APAN) composites were synthesized and characterized by CHN analysis, Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), scanning electron microscopy (SEM), N2 adsorption-desorption, and X-ray photoelectron spectroscopy (XPS). In batch adsorption experiments, a variety of parameters were investigated in detail. The FeOOH-APAN composites exhibit high adsorption capacities (qL = 980.39 mg g-1, T = 298 K), superior to many other materials. In addition, they possess large Kd values (>104 mL g-1 at 25-400 mg L-1 U concentration), high removal rates (∼95% at 25-300 mg L-1, and ∼90% for ppb level simulated seawater), excellent selectivity and rapid capturing rates for uranium. XPS analysis shows that the removal of uranium is mainly related to amidoxime groups, involving the interaction with oxime oxygen and oxime nitrogen. In this paper, a more dominant binding mode is proposed, namely η2 coordination.
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Affiliation(s)
- Xintao Wei
- Key Laboratory of Superlight Material and Surface Technology, Ministry of Education, Harbin Engineering University, 150001, P. R. China.
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Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
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Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
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31
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Vats BG, Das D, Sadhu B, Kannan S, Pius IC, Noronha DM, Sundararajan M, Kumar M. Selective recognition of uranyl ions from bulk of thorium(iv) and lanthanide(iii) ions by tetraalkyl urea: a combined experimental and quantum chemical study. Dalton Trans 2018; 45:10319-25. [PMID: 27241102 DOI: 10.1039/c6dt01191h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The selective separation of uranyl ions from an aqueous solution is one of the most important criteria for sustainable nuclear energy production. We report herein a known, but unexplored extractant, tetraalkyl urea, which shows supreme selectivity for uranium in the presence of interfering thorium and other lanthanide ions from a nitric acid medium. The structural characterization of the uranyl complex (UO2X2·2L, where X = NO3(-), Cl(-) and Br(-)) by IR, NMR and single crystal X-ray diffraction provides insight into the strong interaction between the uranyl ion and the ligand. The origin of this supreme selectivity for uranyl ions is further supported by electronic structure calculations. Uranyl binding with the extractant is thermodynamically more favourable when compared to thorium and the selectivity is achieved through a combination of electronic and steric effects.
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Affiliation(s)
- Bal Govind Vats
- Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
| | - Debasish Das
- Fuel Reprocessing Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Biswajit Sadhu
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - S Kannan
- Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
| | - I C Pius
- Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
| | - D M Noronha
- Fuel Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
| | - Mahesh Sundararajan
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
| | - Mukesh Kumar
- Solid state physics division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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Sauge-Merle S, Brulfert F, Pardoux R, Solari PL, Lemaire D, Safi S, Guilbaud P, Simoni E, Merroun ML, Berthomieu C. Structural Analysis of Uranyl Complexation by the EF-Hand Motif of Calmodulin: Effect of Phosphorylation. Chemistry 2017; 23:15505-15517. [DOI: 10.1002/chem.201703484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Sandrine Sauge-Merle
- CEA; CNRS; Aix-Marseille Université; UMR 7265 Biologie Végétale et Microbiologie Environnementales; Laboratoire des Interactions Protéine Métal; 13108 Saint-Paul-lez-Durance France
| | - Florian Brulfert
- Institut de Physique Nucléaire d'Orsay, CNRS-IN2P3; Univ. Paris-Sud, Univ. Paris-Saclay; 91405 Orsay France
| | - Romain Pardoux
- CEA; CNRS; Aix-Marseille Université; UMR 7265 Biologie Végétale et Microbiologie Environnementales; Laboratoire des Interactions Protéine Métal; 13108 Saint-Paul-lez-Durance France
| | - Pier Lorenzo Solari
- MARS beamline; Synchrotron SOLEIL; L'Orme des Merisiers, Saint-Aubin; 91192 Gif-sur-Yvette Cedex France
| | - David Lemaire
- CEA; CNRS; Aix-Marseille Université; UMR 7265 Biologie Végétale et Microbiologie Environnementales; Laboratoire des Interactions Protéine Métal; 13108 Saint-Paul-lez-Durance France
| | - Samir Safi
- Institut de Physique Nucléaire d'Orsay, CNRS-IN2P3; Univ. Paris-Sud, Univ. Paris-Saclay; 91405 Orsay France
| | - Philippe Guilbaud
- CEA, Nuclear Energy Division; Research Department on Mining and fuel Recycling Processes (LILA); BP17171 30207 Bagnols-sur-Cèze France
| | - Eric Simoni
- Institut de Physique Nucléaire d'Orsay, CNRS-IN2P3; Univ. Paris-Sud, Univ. Paris-Saclay; 91405 Orsay France
| | | | - Catherine Berthomieu
- CEA; CNRS; Aix-Marseille Université; UMR 7265 Biologie Végétale et Microbiologie Environnementales; Laboratoire des Interactions Protéine Métal; 13108 Saint-Paul-lez-Durance France
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Kou S, Yang Z, Sun F. Protein Hydrogel Microbeads for Selective Uranium Mining from Seawater. ACS APPLIED MATERIALS & INTERFACES 2017; 9:2035-2039. [PMID: 28059497 DOI: 10.1021/acsami.6b15968] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Practical methods for oceanic uranium extraction have yet to be developed in order to tap into the vast uranium reserve in the ocean as an alternative energy. Here we present a protein hydrogel system containing a network of recently engineered super uranyl binding proteins (SUPs) that is assembled through thiol-maleimide click chemistry under mild conditions. Monodisperse SUP hydrogel microbeads fabricated by a microfluidic device further enable uranyl (UO22+) enrichment from natural seawater with great efficiency (enrichment index, K = 2.5 × 103) and selectivity. Our results demonstrate the feasibility of using protein hydrogels to extract uranium from the ocean.
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Affiliation(s)
- Songzi Kou
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong
| | - Zhongguang Yang
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong
| | - Fei Sun
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong
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Kannan S, Kumar M, Sadhu B, Jaccob M, Sundararajan M. Unusual intramolecular CH⋯O hydrogen bonding interaction between a sterically bulky amide and uranyl oxygen. Dalton Trans 2017; 46:16939-16946. [DOI: 10.1039/c7dt02760e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unusual intramolecular CH⋯O hydrogen bonding interaction between a sterically bulky amide and uranyl oxygen is found to selectively extract uranyl.
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Affiliation(s)
| | - Mukesh Kumar
- Solid State Physics Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | - Biswajit Sadhu
- Radiation Safety and Systems Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | | | - Mahesh Sundararajan
- Theoretical Chemistry Section
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
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35
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Selective adsorption of uranium(VI) onto prismatic sulfides from aqueous solution. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2015.11.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Burbank KA, Walker RA, Peyton BM. A molecular level mechanism for uranium (VI) toxicity through Ca2+ displacement in pyrroloquinoline quinone-dependent bacterial dehydrogenase. J Inorg Biochem 2015; 149:59-67. [DOI: 10.1016/j.jinorgbio.2014.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/30/2022]
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Huynh TNS, Bourgeois D, Basset C, Vidaud C, Hagège A. Assessment of CE-ICP/MS hyphenation for the study of uranyl/protein interactions. Electrophoresis 2015; 36:1374-82. [PMID: 25630637 DOI: 10.1002/elps.201400471] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 12/27/2014] [Accepted: 01/11/2015] [Indexed: 11/06/2022]
Abstract
Identification of uranyl transport proteins is key to develop efficient detoxification approaches. Therefore, analytical approaches have to be developed to cope with the complexity of biological media and allow the analysis of metal speciation. CE-ICP/MS was used to combine the less-intrusive character and high separation efficiency of CE with the sensitive detection of ICP/MS. The method was based on the incubation of samples with uranyl prior to the separation. Electrophoretic buffers were compared to select a 10 mM Tris to 15 mM NaCl buffer, which enabled analyses at pH 7.4 and limited dissociation. This method was applied to the analysis of a serum. Two main fractions were observed. By comparison with synthetic mixtures of proteins, the first one was attributed to fetuin and in a lesser extent to HSA, and the second one to uranyl unbound to proteins. The analysis showed that fetuin was likely to be the main target of uranyl. CE-ICP/MS was also used to investigate the behavior of the fetuin-uranyl complex, in the presence of carbonate, an abundant complexing agent of uranyl in blood. This method enabled association constants determination, suggesting the occurrence of both FETUA(UO2(2+)) and FETUA(UO2(2+))(CO3(2-)) complexes, depending on the carbonate concentration.
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Affiliation(s)
- Thi-Ngoc Suong Huynh
- CEA/DSV/iBEB/SBTN, Laboratoire d'Etude des Protéines Cibles, Bagnols sur Cèze Cedex, France
| | - Damien Bourgeois
- Institut de Chimie Séparative de Marcoule, Laboratoire de Chimie et Physico-chimie des Actinides, Bagnols-sur-Cèze cedex, France
| | - Christian Basset
- CEA/DSV/iBEB/SBTN, Laboratoire d'Etude des Protéines Cibles, Bagnols sur Cèze Cedex, France
| | - Claude Vidaud
- CEA/DSV/iBEB/SBTN, Laboratoire d'Etude des Protéines Cibles, Bagnols sur Cèze Cedex, France
| | - Agnès Hagège
- CEA/DSV/iBEB/SBTN, Laboratoire d'Etude des Protéines Cibles, Bagnols sur Cèze Cedex, France.,CNRS, UMR 7265, CEA/DSV/iBEB, St. Paul Les Durance, France
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Zhang D, Chen Z, Omar H, Deng L, Khashab NM. Colorimetric peroxidase mimetic assay for uranyl detection in sea water. ACS APPLIED MATERIALS & INTERFACES 2015; 7:4589-4594. [PMID: 25658750 DOI: 10.1021/am507361x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Uranyl (UO2(2+)) is a form of uranium in aqueous solution that represents the greatest risk to human health because of its bioavailability. Different sensing techniques have been used with very sensitive detection limits especially the recently reported uranyl-specific DNAzymes systems. However, to the best of our knowledge, few efficient detection methods have been reported for uranyl sensing in seawater. Herein, gold nanoclusters (AuNCs) are employed in an efficient spectroscopic method to detect uranyl ion (UO2(2+)) with a detection limit of 1.86 μM. In the absence of UO2(2+), the BSA-stabilized AuNCs (BSA-AuNCs) showed an intrinsic peroxidase-like activity. In the presence of UO2(2+), this activity can be efficiently restrained. The preliminary quenching mechanism and selectivity of UO2(2+) was also investigated and compared with other ions. This design strategy could be useful in understanding the binding affinity of protein-stabilized AuNCs to UO2(2+) and consequently prompt the recycling of UO2(2+) from seawater.
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Affiliation(s)
- Dingyuan Zhang
- Controlled Release and Delivery Lab, Advanced Membranes and Porous Materials Center, King Abdullah University of Science and Technology , Thuwal 23955-6900, Kingdom of Saudi Arabia
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40
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Yang CT, Han J, Gu M, Liu J, Li Y, Huang Z, Yu HZ, Hu S, Wang X. Fluorescent recognition of uranyl ions by a phosphorylated cyclic peptide. Chem Commun (Camb) 2015; 51:11769-72. [DOI: 10.1039/c5cc04112k] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Fluorescent recognition of uranyl ions was achieved using a phosphorylated cyclic peptide, which can be used as a fluorescent sensor.
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Affiliation(s)
- Chu-Ting Yang
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Jun Han
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Mei Gu
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Jun Liu
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Yi Li
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Zeng Huang
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Hai-Zhu Yu
- Department of Chemistry and Center for Atomic Engineering of Advanced Materials
- Anhui University
- Hefei
- P. R. China
| | - Sheng Hu
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
| | - Xiaolin Wang
- Institute of Nuclear Physics and Chemistry
- China Academy of Engineering Physics
- Mianyang
- P. R. China
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Odoh SO, Bondarevsky GD, Karpus J, Cui Q, He C, Spezia R, Gagliardi L. UO22+ Uptake by Proteins: Understanding the Binding Features of the Super Uranyl Binding Protein and Design of a Protein with Higher Affinity. J Am Chem Soc 2014; 136:17484-94. [DOI: 10.1021/ja5087563] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel O. Odoh
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Gary D. Bondarevsky
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Jason Karpus
- Department
of Chemistry and Institute of Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Qiang Cui
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chuan He
- Department
of Chemistry and Institute of Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Riccardo Spezia
- CNRS,
Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement,
UMR 8587, Université d’Evry-Val-d’Essonne, 91025, Every Cedex, France
| | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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42
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Duan L, Du L, Jia Y, Liu W, Liu Z, Li J. High Impact of Uranyl Ions on Carrying-Releasing Oxygen Capability of Hemoglobin-Based Blood Substitutes. Chemistry 2014; 21:520-5. [DOI: 10.1002/chem.201405439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Indexed: 11/12/2022]
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43
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Lebrun C, Starck M, Gathu V, Chenavier Y, Delangle P. Engineering Short Peptide Sequences for Uranyl Binding. Chemistry 2014; 20:16566-73. [DOI: 10.1002/chem.201404546] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Indexed: 01/16/2023]
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Kuroda K, Ebisutani K, Iida K, Nishitani T, Ueda M. Enhanced adsorption and recovery of uranyl ions by NikR mutant-displaying yeast. Biomolecules 2014; 4:390-401. [PMID: 24970221 PMCID: PMC4101488 DOI: 10.3390/biom4020390] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/12/2014] [Accepted: 03/14/2014] [Indexed: 11/25/2022] Open
Abstract
Uranium is one of the most important metal resources, and the technology for the recovery of uranyl ions (UO22+) from aqueous solutions is required to ensure a semi-permanent supply of uranium. The NikR protein is a Ni2+-dependent transcriptional repressor of the nickel-ion uptake system in Escherichia coli, but its mutant protein (NikRm) is able to selectively bind uranyl ions in the interface of the two monomers. In this study, NikRm protein with ability to adsorb uranyl ions was displayed on the cell surface of Saccharomyces cerevisiae. To perform the binding of metal ions in the interface of the two monomers, two metal-binding domains (MBDs) of NikRm were tandemly fused via linker peptides and displayed on the yeast cell surface by fusion with the cell wall-anchoring domain of yeast α-agglutinin. The NikRm-MBD-displaying yeast cells with particular linker lengths showed the enhanced adsorption of uranyl ions in comparison to the control strain. By treating cells with citrate buffer (pH 4.3), the uranyl ions adsorbed on the cell surface were recovered. Our results indicate that the adsorption system by yeast cells displaying tandemly fused MBDs of NikRm is effective for simple and concentrated recovery of uranyl ions, as well as adsorption of uranyl ions.
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Affiliation(s)
- Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Kazuki Ebisutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Katsuya Iida
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Takashi Nishitani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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45
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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46
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Zhou L, Bosscher M, Zhang C, Özçubukçu S, Zhang L, Zhang W, Li CJ, Liu J, Jensen MP, Lai L, He C. A protein engineered to bind uranyl selectively and with femtomolar affinity. Nat Chem 2014; 6:236-41. [DOI: 10.1038/nchem.1856] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/17/2013] [Indexed: 12/24/2022]
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Liang H, Deng X, Bosscher M, Ji Q, Jensen MP, He C. Engineering Bacterial Two-Component System PmrA/PmrB to Sense Lanthanide Ions. J Am Chem Soc 2013; 135:2037-9. [DOI: 10.1021/ja312032c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Haihua Liang
- Department of Chemistry and
Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Xin Deng
- Department of Chemistry and
Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Mike Bosscher
- Department of Chemistry and
Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Quanjiang Ji
- Department of Chemistry and
Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Mark P. Jensen
- Chemical Science and Engineering
Division, Argonne National Laboratory,
Argonne, Illinois, 60439, United States United States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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Schleuter D, Günther A, Paasch S, Ehrlich H, Kljajić Z, Hanke T, Bernhard G, Brunner E. Chitin-based renewable materials from marine sponges for uranium adsorption. Carbohydr Polym 2013; 92:712-8. [DOI: 10.1016/j.carbpol.2012.08.090] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/17/2012] [Accepted: 08/17/2012] [Indexed: 11/29/2022]
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Krishnaji ST, Kaplan DL. Bioengineered chimeric spider silk-uranium binding proteins. Macromol Biosci 2012; 13:256-64. [PMID: 23212989 DOI: 10.1002/mabi.201200272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 08/30/2012] [Indexed: 11/06/2022]
Abstract
Heavy metals constitute a source of environmental pollution. Here, novel functional hybrid biomaterials for specific interactions with heavy metals are designed by bioengineering consensus sequence repeats from spider silk of Nephila clavipes with repeats of a uranium peptide recognition motif from a mutated 33-residue of calmodulin protein from Paramecium tetraurelia. The self-assembly features of the silk to control nanoscale organic/inorganic material interfaces provides new biomaterials for uranium recovery. With subsequent enzymatic digestion of the silk to concentrate the sequestered metals, options can be envisaged to use these new chimeric protein systems in environmental engineering, including to remediate environments contaminated by uranium.
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Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression. Curr Opin Biotechnol 2012; 23:689-94. [DOI: 10.1016/j.copbio.2011.12.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 01/06/2023]
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