Determination of affinities of lanthanide-binding proteins using chelator-buffered titrations

Mattocks, Joseph A.; Tirsch, Jonathan L.; Cotruvo, Jr., Joseph A.

doi:10.1016/bs.mie.2021.01.044

Determination of affinities of lanthanide-binding proteins using chelator-buffered titrations

Journal Article · Tue Mar 02 23:00:00 EST 2021 · Methods in Enzymology

DOI:https://doi.org/10.1016/bs.mie.2021.01.044· OSTI ID:1781338

^[1]; Tirsch, Jonathan L. ^[2]; ^[2]

Pennsylvania State Univ., University Park, PA (United States); The Pennsylvania State University
Pennsylvania State Univ., University Park, PA (United States)

The recent discoveries of the first proteins that bind lanthanides as part of their biological function not only are relevant to the emerging field of lanthanide-dependent biology, but also hold promise to revolutionize the technologically critical rare earths industry. Although protocols to assess the thermodynamics of metal–protein interactions are well established for “traditional” metal ions in biology, the characterization of lanthanide-binding proteins presents a challenge to biochemists due to the lanthanides' Lewis acidity, propensity for hydrolysis, and high-affinity complexes with biological ligands. These properties necessitate the preparation of metal stock solutions with very low buffered “free” metal concentrations (e.g., femtomolar to nanomolar) for such determinations. Here in this paper we describe several protocols to overcome these challenges. First, we present standardization methods for the preparation of chelator-buffered solutions of lanthanide ions with easily calculated free metal concentrations. We also describe how these solutions can be used in concert with analytical methods including UV–visible spectrophotometry, circular dichroism spectroscopy, Förster resonance energy transfer (FRET), and sensitized terbium luminescence, in order to accurately determine dissociation constants (K_ds) of lanthanide–protein complexes. Finally, we highlight how application of these methods to lanthanide-binding proteins, such as lanmodulin, has yielded insights into selective recognition of lanthanides in biology. We anticipate that these protocols will facilitate discovery and characterization of additional native lanthanide-binding proteins, will motivate the understanding of their biological context, and will prompt their applications in biotechnology.

View Accepted Manuscript (DOE)

Research Organization:: Pennsylvania State Univ., University Park, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0021007

OSTI ID:: 1781338

Journal Information:: Methods in Enzymology, Journal Name: Methods in Enzymology Vol. 651; ISSN 0076-6879

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (69)

Structural Origin of the High Affinity of a Chemically Evolved Lanthanide-Binding Peptide Nitz, Mark; Sherawat, Manashi; Franz, Katherine J. Angewandte Chemie International Edition, Vol. 43, Issue 28 https://doi.org/10.1002/anie.200460028	journal	July 2004
Essential and Ubiquitous: The Emergence of Lanthanide Metallobiochemistry Daumann, Lena J. Angewandte Chemie International Edition, Vol. 58, Issue 37 https://doi.org/10.1002/anie.201904090	journal	August 2019
Determination of Iron in Solutions with the Ferric–Xylenol Orange Complex Gay, Craig; Collins, James; Gebicki, Janusz M. Analytical Biochemistry, Vol. 273, Issue 2 https://doi.org/10.1006/abio.1999.4207	journal	September 1999
Absorptiometric study of the chelates formed between the lanthanoids and xylenol orange Munshi, Kailash N.; Dey, Arun K. Microchimica Acta, Vol. 56, Issue 5 https://doi.org/10.1007/BF01221178	journal	September 1968
PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference Keltjens, Jan T.; Pol, Arjan; Reimann, Joachim Applied Microbiology and Biotechnology, Vol. 98, Issue 14 https://doi.org/10.1007/s00253-014-5766-8	journal	May 2014
Rare earth elements in soil and plant systems - A review Tyler, Germund Plant and Soil, Vol. 267, Issue 1-2 https://doi.org/10.1007/s11104-005-4888-2	journal	December 2004
Lanthanides: New life metals? Chistoserdova, Ludmila World Journal of Microbiology and Biotechnology, Vol. 32, Issue 8 https://doi.org/10.1007/s11274-016-2088-2	journal	June 2016
Differential ultraviolet spectra of insulin Laskowski, Michael; Widom, Joanne M.; McFadden, Mary L. Biochimica et Biophysica Acta, Vol. 19 https://doi.org/10.1016/0006-3002(56)90502-9	journal	January 1956
Tyrosyl-carboxylate ion hydrogen bonding in ribonuclease Scheraga, Harold A. Biochimica et Biophysica Acta, Vol. 23 https://doi.org/10.1016/0006-3002(57)90304-9	journal	January 1957
Complexometric titration of yttrium and the lanthanons—IA comparison of direct methods Lyle, S. J.; Rahman, Md. M. Talanta, Vol. 10, Issue 11 https://doi.org/10.1016/0039-9140(63)80170-8	journal	November 1963
Investigation of equilibria in solution. Determination of equilibrium constants with the HYPERQUAD suite of programs Gans, P.; Sabatini, A.; Vacca, A. Talanta, Vol. 43, Issue 10 https://doi.org/10.1016/0039-9140(96)01958-3	journal	October 1996
Hyperquad simulation and speciation (HySS): a utility program for the investigation of equilibria involving soluble and partially soluble species Alderighi, Lucia; Gans, Peter; Ienco, Andrea Coordination Chemistry Reviews, Vol. 184, Issue 1 https://doi.org/10.1016/S0010-8545(98)00260-4	journal	April 1999
Techniques for measuring cellular zinc Carpenter, Margaret C.; Lo, Maria N.; Palmer, Amy E. Archives of Biochemistry and Biophysics, Vol. 611 https://doi.org/10.1016/j.abb.2016.08.018	journal	December 2016
The biochemistry of lanthanide acquisition, trafficking, and utilization Featherston, Emily R.; Cotruvo, Joseph A. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1868, Issue 1 https://doi.org/10.1016/j.bbamcr.2020.118864	journal	January 2021
How to study proteins by circular dichroism Kelly, Sharon M.; Jess, Thomas J.; Price, Nicholas C. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1751, Issue 2 https://doi.org/10.1016/j.bbapap.2005.06.005	journal	August 2005
Molecular structure of La3+-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans Hibi, Yoshihisa; Asai, Kentaro; Arafuka, Hiroshi Journal of Bioscience and Bioengineering, Vol. 111, Issue 5 https://doi.org/10.1016/j.jbiosc.2010.12.017	journal	May 2011
Molecular structure and gene analysis of Ce3+-induced methanol dehydrogenase of Bradyrhizobium sp. MAFF211645 Fitriyanto, Nanung Agus; Fushimi, Mako; Matsunaga, Mika Journal of Bioscience and Bioengineering, Vol. 111, Issue 6 https://doi.org/10.1016/j.jbiosc.2011.01.015	journal	June 2011
Method for Accurate Determination of Dissociation Constants of Optical Ratiometric Systems: Chemical Probes, Genetically Encoded Sensors, and Interacting Molecules Pomorski, Adam; Kochańczyk, Tomasz; Miłoch, Anna Analytical Chemistry, Vol. 85, Issue 23 https://doi.org/10.1021/ac402637h	journal	November 2013
Structural Basis for Rare Earth Element Recognition by Methylobacterium extorquens Lanmodulin Cook, Erik C.; Featherston, Emily R.; Showalter, Scott A. Biochemistry, Vol. 58, Issue 2 https://doi.org/10.1021/acs.biochem.8b01019	journal	October 2018
Bioadsorption of Rare Earth Elements through Cell Surface Display of Lanthanide Binding Tags Park, Dan M.; Reed, David W.; Yung, Mimi C. Environmental Science & Technology, Vol. 50, Issue 5 https://doi.org/10.1021/acs.est.5b06129	journal	February 2016
Selective and Efficient Biomacromolecular Extraction of Rare-Earth Elements using Lanmodulin Deblonde, Gauthier J. -P.; Mattocks, Joseph A.; Park, Dan M. Inorganic Chemistry, Vol. 59, Issue 17 https://doi.org/10.1021/acs.inorgchem.0c01303	journal	July 2020
Influence of a Heterocyclic Nitrogen-Donor Group on the Coordination of Trivalent Actinides and Lanthanides by Aminopolycarboxylate Complexants Grimes, Travis S.; Heathman, Colt R.; Jansone-Popova, Santa Inorganic Chemistry, Vol. 57, Issue 3 https://doi.org/10.1021/acs.inorgchem.7b02792	journal	January 2018
Implementing f-Block Metal Ions in Medicine: Tuning the Size Selectivity of Expanded Macrocycles Thiele, Nikki A.; Woods, Joshua J.; Wilson, Justin J. Inorganic Chemistry, Vol. 58, Issue 16 https://doi.org/10.1021/acs.inorgchem.9b01277	journal	June 2019
Engineered PQQ-Dependent Alcohol Dehydrogenase for the Oxidation of 5-(Hydroxymethyl)furoic Acid Wehrmann, Matthias; Elsayed, Eslam M.; Köbbing, Sebastian ACS Catalysis, Vol. 10, Issue 14 https://doi.org/10.1021/acscatal.0c01789	journal	June 2020
The Chemistry of Lanthanides in Biology: Recent Discoveries, Emerging Principles, and Technological Applications Cotruvo, Joseph A. ACS Central Science, Vol. 5, Issue 9 https://doi.org/10.1021/acscentsci.9b00642	journal	August 2019
From Antenna to Assay: Lessons Learned in Lanthanide Luminescence Moore, Evan G.; Samuel, Amanda P. S.; Raymond, Kenneth N. Accounts of Chemical Research, Vol. 42, Issue 4 https://doi.org/10.1021/ar800211j	journal	April 2009
Tyrosine and tyrosinate fluorescence of bovine testes calmodulin: calcium and pH dependence Pundak, Shlomo; Roche, Rodney S. Biochemistry, Vol. 23, Issue 7 https://doi.org/10.1021/bi00302a032	journal	March 1984
Kinetic studies show that calcium and terbium have different binding preferences toward the four calcium-binding sites of calmodulin Wang, Chih Lueh A.; Leavis, Paul C.; Gergely, John Biochemistry, Vol. 23, Issue 26 https://doi.org/10.1021/bi00321a020	journal	December 1984
Characterization of lanthanide(III) ion binding to calmodulin using luminescence spectroscopy Mulqueen, Paul; Tingey, Joel M.; Horrocks, William D. Biochemistry, Vol. 24, Issue 23 https://doi.org/10.1021/bi00344a051	journal	November 1985
Solution Structure of the Paramagnetic Complex of the N-Terminal Domain of Calmodulin with Two Ce³⁺ Ions by ¹H NMR^, Bentrop, Detlef; Bertini, Ivano; Cremonini, Mauro A. Biochemistry, Vol. 36, Issue 39 https://doi.org/10.1021/bi971022+	journal	September 1997
Fluorescent Sensors for Measuring Metal Ions in Living Systems Carter, Kyle P.; Young, Alexandra M.; Palmer, Amy E. Chemical Reviews, Vol. 114, Issue 8 https://doi.org/10.1021/cr400546e	journal	March 2014
Binding constants for neodymium(III) and samarium(III) with human serum transferrin Harris, Wesley R. Inorganic Chemistry, Vol. 25, Issue 12 https://doi.org/10.1021/ic00232a026	journal	June 1986
Fluorescence quenching of the indole ring system by lanthanide ions Ricci, Robert W.; Kilichowski, Kurt B. The Journal of Physical Chemistry, Vol. 78, Issue 19 https://doi.org/10.1021/j100612a017	journal	September 1974
On the Mechanism of Fluorescence Quenching. Tyrosine and Similar Compounds Feitelson, Jehuda The Journal of Physical Chemistry, Vol. 68, Issue 2 https://doi.org/10.1021/j100784a033	journal	February 1964
Lanthanide ion probes of structure in biology. Laser-induced luminescence decay constants provide a direct measure of the number of metal-coordinated water molecules Horrocks, William DeW.; Sudnick, Daniel R. Journal of the American Chemical Society, Vol. 101, Issue 2 https://doi.org/10.1021/ja00496a010	journal	January 1979
Probing Site-Specific Calmodulin Calcium and Lanthanide Affinity by Grafting Ye, Yiming; Lee, Hsiau-Wei; Yang, Wei Journal of the American Chemical Society, Vol. 127, Issue 11 https://doi.org/10.1021/ja042786x	journal	March 2005
Calcium Ion Gradients Modulate the Zinc Affinity and Antibacterial Activity of Human Calprotectin Brophy, Megan Brunjes; Hayden, Joshua A.; Nolan, Elizabeth M. Journal of the American Chemical Society, Vol. 134, Issue 43 https://doi.org/10.1021/ja307974e	journal	October 2012
Functional Synthetic Model for the Lanthanide-Dependent Quinoid Alcohol Dehydrogenase Active Site McSkimming, Alex; Cheisson, Thibault; Carroll, Patrick J. Journal of the American Chemical Society, Vol. 140, Issue 4 https://doi.org/10.1021/jacs.7b12318	journal	January 2018
Lanmodulin: A Highly Selective Lanthanide-Binding Protein from a Lanthanide-Utilizing Bacterium Cotruvo, Joseph A.; Featherston, Emily R.; Mattocks, Joseph A. Journal of the American Chemical Society, Vol. 140, Issue 44 https://doi.org/10.1021/jacs.8b09842	journal	October 2018
A Selective, Protein-Based Fluorescent Sensor with Picomolar Affinity for Rare Earth Elements Mattocks, Joseph A.; Ho, Jackson V.; Cotruvo, Joseph A. Journal of the American Chemical Society, Vol. 141, Issue 7 https://doi.org/10.1021/jacs.8b12155	journal	February 2019
Affinity gradients drive copper to cellular destinations Banci, Lucia; Bertini, Ivano; Ciofi-Baffoni, Simone Nature, Vol. 465, Issue 7298 https://doi.org/10.1038/nature09018	journal	May 2010
Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes Thestrup, Thomas; Litzlbauer, Julia; Bartholomäus, Ingo Nature Methods, Vol. 11, Issue 2 https://doi.org/10.1038/nmeth.2773	journal	January 2014
Measuring calcium signaling using genetically targetable fluorescent indicators Palmer, Amy E.; Tsien, Roger Y. Nature Protocols, Vol. 1, Issue 3 https://doi.org/10.1038/nprot.2006.172	journal	August 2006
Rare earth element alcohol dehydrogenases widely occur among globally distributed, numerically abundant and environmentally important microbes Huang, Jing; Yu, Zheng; Groom, Joseph The ISME Journal, Vol. 13, Issue 8 https://doi.org/10.1038/s41396-019-0414-z	journal	April 2019
Gene products and processes contributing to lanthanide homeostasis and methanol metabolism in Methylorubrum extorquens AM1 Roszczenko-Jasińska, Paula; Vu, Huong N.; Subuyuj, Gabriel A. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-69401-4	journal	July 2020
Open questions on the environmental chemistry of radionuclides Deblonde, Gauthier J. -P.; Kersting, Annie B.; Zavarin, Mavrik Communications Chemistry, Vol. 3, Issue 1 https://doi.org/10.1038/s42004-020-00418-6	journal	November 2020
Challenges to achievement of metal sustainability in our high-tech society Izatt, Reed M.; Izatt, Steven R.; Bruening, Ronald L. Chem. Soc. Rev., Vol. 43, Issue 8 https://doi.org/10.1039/C3CS60440C	journal	January 2014
Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides Mattocks, Joseph A.; Cotruvo, Joseph A. Chemical Society Reviews, Vol. 49, Issue 22 https://doi.org/10.1039/D0CS00653J	journal	January 2020
Taking advantage of luminescent lanthanide ions Bünzli, Jean-Claude G.; Piguet, Claude Chemical Society Reviews, Vol. 34, Issue 12 https://doi.org/10.1039/b406082m	journal	January 2005
The challenges of determining metal–protein affinities Xiao, Zhiguang; Wedd, Anthony G. Natural Product Reports, Vol. 27, Issue 5 https://doi.org/10.1039/b906690j	journal	January 2010
Circularly permuted green fluorescent proteins engineered to sense Ca²⁺ Nagai, T.; Sawano, A.; Park, E. S. Proceedings of the National Academy of Sciences, Vol. 98, Issue 6, p. 3197-3202 https://doi.org/10.1073/pnas.051636098	journal	March 2001
Siderocalin-mediated recognition, sensitization, and cellular uptake of actinides Allred, Benjamin E.; Rupert, Peter B.; Gauny, Stacey S. Proceedings of the National Academy of Sciences, Vol. 112, Issue 33 https://doi.org/10.1073/pnas.1508902112	journal	August 2015
Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion Caldwell, Shane J.; Haydon, Ian C.; Piperidou, Nikoletta Proceedings of the National Academy of Sciences, Vol. 117, Issue 48 https://doi.org/10.1073/pnas.2008535117	journal	November 2020
Uptake and effect of rare earth elements on gene expression in Methylosinus trichosporium OB3b Gu, Wenyu; Farhan Ul Haque, Muhammad; DiSpirito, Alan A. FEMS Microbiology Letters, Vol. 363, Issue 13 https://doi.org/10.1093/femsle/fnw129	journal	May 2016
The Hill equation revisited: uses and misuses. Weiss, J. N. The FASEB Journal, Vol. 11, Issue 11 https://doi.org/10.1096/fasebj.11.11.9285481	journal	September 1997
Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides Shannon, R. D. Acta Crystallographica Section A, Vol. 32, Issue 5, p. 751-767 https://doi.org/10.1107/S0567739476001551	journal	September 1976
Rare earth metals are essential for methanotrophic life in volcanic mudpots: Rare earth metals essential for methanotrophic life Pol, Arjan; Barends, Thomas R. M.; Dietl, Andreas Environmental Microbiology, Vol. 16, Issue 1 https://doi.org/10.1111/1462-2920.12249	journal	September 2013
Metal-Binding Properties of Calmodulin Wang, Chih-Lueh A.; Aquaron, Robert R.; Leavis, Paul C. European Journal of Biochemistry, Vol. 124, Issue 1 https://doi.org/10.1111/j.1432-1033.1982.tb05900.x	journal	May 1982
Use of rare‐earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1 Ochsner, Andrea M.; Hemmerle, Lucas; Vonderach, Thomas Molecular Microbiology, Vol. 111, Issue 5 https://doi.org/10.1111/mmi.14208	journal	February 2019
Rare earth elements: Mendeleev’s bane, modern marvels Cheisson, Thibault; Schelter, Eric J. Science, Vol. 363, Issue 6426 https://doi.org/10.1126/science.aau7628	journal	January 2019
Metals and Methanotrophy Semrau, Jeremy D.; DiSpirito, Alan A.; Gu, Wenyu Applied and Environmental Microbiology, Vol. 84, Issue 6 https://doi.org/10.1128/AEM.02289-17	journal	January 2018
Pyrroloquinoline Quinone Ethanol Dehydrogenase in Methylobacterium extorquens AM1 Extends Lanthanide-Dependent Metabolism to Multicarbon Substrates Good, Nathan M.; Vu, Huong N.; Suriano, Carly J. Journal of Bacteriology, Vol. 198, Issue 22 https://doi.org/10.1128/JB.00478-16	journal	August 2016
Lanthanide-Dependent Regulation of Methanol Oxidation Systems in Methylobacterium extorquens AM1 and Their Contribution to Methanol Growth Vu, Huong N.; Subuyuj, Gabriel A.; Vijayakumar, Srividhya Journal of Bacteriology, Vol. 198, Issue 8 https://doi.org/10.1128/JB.00937-15	journal	February 2016
Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440 Wehrmann, Matthias; Billard, Patrick; Martin-Meriadec, Audrey mBio, Vol. 8, Issue 3 https://doi.org/10.1128/mBio.00570-17	journal	June 2017
The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in Pseudomonas putida KT2440 Wehrmann, Matthias; Berthelot, Charlotte; Billard, Patrick mSphere, Vol. 3, Issue 4 https://doi.org/10.1128/mSphere.00376-18	journal	August 2018
Spectrophotometric Determination of Cerium(III) and Some Rare Earths with Xylenol Orange Tonosaki, Kôichi; Otomo, Makoto Bulletin of the Chemical Society of Japan, Vol. 35, Issue 10 https://doi.org/10.1246/bcsj.35.1683	journal	October 1962
A Catalytic Role of XoxF1 as La3+-Dependent Methanol Dehydrogenase in Methylobacterium extorquens Strain AM1 Nakagawa, Tomoyuki; Mitsui, Ryoji; Tani, Akio PLoS ONE, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pone.0050480	journal	November 2012
Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties Huang, Jing; Yu, Zheng; Chistoserdova, Ludmila Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01366	journal	June 2018
MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense Chu, Frances; Beck, David A. C.; Lidstrom, Mary E. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2435	journal	January 2016

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
Bioinorganic chemistry
Circular dichroism
Dissociation constant
Lanthanide biochemistry
Lanthanide luminescence
Metal affinity
Metalloprotein
Rare earth elements

Determination of affinities of lanthanide-binding proteins using chelator-buffered titrations

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