Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer

Journal Article · · Nature (London)

Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number. The natural lanthanide-binding protein lanmodulin (LanM) is a sustainable alternative to conventional solvent-extraction-based separation. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM’s quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM’s greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.

Research Organization:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE National Nuclear Security Administration (NNSA); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Energy Efficiency Office. Advanced Materials & Manufacturing Technologies Office (AMMTO); National Science Foundation (NSF); National Institutes of Health (NIH)
Grant/Contract Number:
AC52-07NA27344; AC02-06CH11357; SC0021007
OSTI ID:
1993554
Report Number(s):
LLNL-JRNL-840467; 1061823
Journal Information:
Nature (London), Journal Name: Nature (London) Journal Issue: 7963 Vol. 618; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

References (68)

Repeated Recovery of Rare Earth Elements Using a Highly Selective and Thermo‐Responsive Genetically Encoded Polypeptide journal December 2021
Electro-kinetic Separation of Rare Earth Elements Using a Redox-Active Ligand journal September 2017
Location‐Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils journal October 2021
Efficient Separation of Light Lanthanides(III) by Using Bis‐Lactam Phenanthroline Ligands journal March 2019
The Earlier the Better: Structural Analysis and Separation of Lanthanides with Pyrroloquinoline Quinone journal July 2020
Aerobic Methylotrophic Prokaryotes book January 2006
Automated Structure Solution with the PHENIX Suite book January 2008
Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C journal August 2018
On the determination of the number of water molecules, q, coordinated to europium(III) ions in solution from luminescence decay lifetimes journal November 2002
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Determination of affinities of lanthanide-binding proteins using chelator-buffered titrations book January 2021
Environmental life cycle assessment on the separation of rare earth oxides through solvent extraction journal December 2017
A critical review on solvent extraction of rare earths from aqueous solutions journal February 2014
Structural Basis for Rare Earth Element Recognition by Methylobacterium extorquens Lanmodulin journal October 2018
The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways journal September 2019
Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags journal February 2016
Selective and Efficient Biomacromolecular Extraction of Rare-Earth Elements using Lanmodulin journal July 2020
Tuning the Separation of Light Lanthanides Using a Reverse-Size Selective Aqueous Complexant journal October 2020
The Lanthanide Contraction Is a Variable journal April 2022
Bridging Hydrometallurgy and Biochemistry: A Protein-Based Process for Recovery and Separation of Rare Earth Elements journal October 2021
Extraction of Lanthanide and Actinide Ions from Aqueous Mixtures Using a Carboxylic Acid-Functionalized Porous Aromatic Framework journal April 2016
Tuning the Equilibrium Ion Affinity and Selectivity of the EF-Hand Calcium Binding Motif:  Substitutions at the Gateway Position journal January 1996
Characterization of Lanthanide Ion Binding to the EF-Hand Protein S100β by Luminescence Spectroscopy journal August 1997
The Lanthanide Contraction Revisited journal September 2007
Macrocyclic Ligands with an Unprecedented Size-Selectivity Pattern for the Lanthanide Ions journal July 2020
Probing Lanmodulin’s Lanthanide Recognition via Sensitized Luminescence Yields a Platform for Quantification of Terbium in Acid Mine Drainage journal August 2021
Characterization of Americium and Curium Complexes with the Protein Lanmodulin: A Potential Macromolecular Mechanism for Actinide Mobility in the Environment journal September 2021
Lanmodulin: A Highly Selective Lanthanide-Binding Protein from a Lanthanide-Utilizing Bacterium journal October 2018
A Selective, Protein-Based Fluorescent Sensor with Picomolar Affinity for Rare Earth Elements journal February 2019
ModelFinder: fast model selection for accurate phylogenetic estimates journal May 2017
Ab initio electron density determination directly from solution scattering data journal January 2018
Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny journal November 2022
Overcoming universal restrictions on metal selectivity by protein design journal March 2022
SignalP 6.0 predicts all five types of signal peptides using protein language models journal January 2022
Two-zone ligand-assisted displacement chromatography for producing high-purity praseodymium, neodymium, and dysprosium with high yield and high productivity from crude mixtures derived from waste magnets journal January 2020
Americium preferred: lanmodulin, a natural lanthanide-binding protein favors an actinide over lanthanides journal January 2021
Engineering lanmodulin's selectivity for actinides over lanthanides by controlling solvent coordination and second-sphere interactions journal January 2022
The coordination (hydration) of rare earth ions in aqueous chloride solutions from x‐ray diffraction. II. LaCl 3 , PrCl 3 , and NdCl 3 a) journal April 1979
Accomplishing simple, solubility-based separations of rare earth elements with complexes bearing size-sensitive molecular apertures journal December 2016
Kinetic control of Ca(II) signaling: tuning the ion dissociation rates of EF-hand Ca(II) binding sites. journal July 1993
Solvent Extraction Separation of Trivalent Americium from Curium and the Lanthanides journal February 2015
Recent Advances in the Chemistry of Hydrometallurgical Methods journal July 2022
Analytical-Scale Separations of the Lanthanides: a Review of Techniques and Fundamentals journal June 2001
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era journal February 2020
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
Hansschlegelia quercus sp. nov., a novel methylotrophic bacterium isolated from oak buds
  • Agafonova, Nadezhda V.; Kaparullina, Elena N.; Grouzdev, Denis S.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 8 https://doi.org/10.1099/ijsem.0.004323
journal August 2020
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal November 2003
PRIMUS: a Windows PC-based system for small-angle scattering data analysis journal September 2003
Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides journal September 1976
Substructure search procedures for macromolecular structures journal October 2003
Simple algorithm for a maximum-likelihood SAD function journal June 2004
Coot model-building tools for molecular graphics journal November 2004
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard journal December 2007
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography journal November 2011
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions journal June 2017
ATSAS 3.0 : expanded functionality and new tools for small-angle scattering data analysis journal February 2021
CheckMyMetal : a macromolecular metal-binding validation tool journal February 2017
Rare earth metals are essential for methanotrophic life in volcanic mudpots: Rare earth metals essential for methanotrophic life journal September 2013
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data journal September 2016
Capturing an elusive but critical element: Natural protein enables actinium chemistry journal October 2021
Rare earth elements: Mendeleev’s bane, modern marvels journal January 2019
Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440 journal June 2017
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis journal April 2019
Protein Identification and Analysis Tools on the ExPASy Server book January 2005
Hyperaccumulation of Gadolinium by Methylorubrum extorquens AM1 Reveals Impacts of Lanthanides on Cellular Processes Beyond Methylotrophy journal March 2022

Similar Records

Characterization of Americium and Curium Complexes with the Protein Lanmodulin: A Potential Macromolecular Mechanism for Actinide Mobility in the Environment
Journal Article · Mon Sep 20 00:00:00 EDT 2021 · Journal of the American Chemical Society · OSTI ID:1823692

Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides
Journal Article · Mon Oct 28 00:00:00 EDT 2024 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:2475197