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Double-lanthanide-binding tags for macromolecular crystallographic structure determination.

Silvaggi NR, Martin LJ, Schwalbe H, Imperiali B, Allen KN
J Am Chem Soc 129 7114-20 (2007)
Cited: 39 times
EuropePMC logo PMID: 17497863

Abstract

A double-lanthanide-binding tag (dLBT), a small peptide sequence engineered to bind two lanthanide ions (e.g., Tb3+) with high affinity, was used to solve the phase problem for the structure determination of ubiquitin by the single-wavelength anomalous diffraction (SAD) method. Since the dLBT is comprised exclusively of encoded amino acids, the necessity for the incorporation of unnatural amino acids or chemical modification of the protein as a prerequisite for X-ray structure determination is eliminated. A construct encoding the dLBT as an N-terminal fusion with ubiquitin provides for facile expression and purification using standard methods. Phasing of the single-wavelength X-ray data (at 2.6 A resolution) using only the anomalous signal from the two tightly bound Tb3+ ions in the dLBT led to clear electron-density maps. Nearly 75% of the ubiquitin structure was built using automated model-building software without user intervention. It is anticipated that this technique will be broadly applicable, complementing existing macromolecular phasing methodologies. The dLBT should be particularly useful in cases where protein derivatization with heavy atoms proves to be problematic or synchrotron facilities are unavailable.

Articles - 2ojr mentioned but not cited (3)

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  13. Functionalisation of lanthanide complexes via microwave-enhanced Cu(I)-catalysed azide-alkyne cycloaddition. Szíjjártó C, Pershagen E, Borbas KE. Dalton Trans 41 7660-7669 (2012)
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  17. Paramagnetic DOSY: An Accurate Tool for the Analysis of the Supramolecular Interactions between Lanthanide Complexes and Proteins. Denis-Quanquin S, Riobé F, Delsuc MA, Maury O, Giraud N. Chemistry 22 18123-18131 (2016)
  18. An encodable lanthanide binding tag with reduced size and flexibility for measuring residual dipolar couplings and pseudocontact shifts in large proteins. Barb AW, Subedi GP. J Biomol NMR 64 75-85 (2016)
  19. Luminescent lanthanide-binding peptides: sensitising the excited states of Eu(III) and Tb(III) with a 1,8-naphthalimide-based antenna. Bonnet CS, Devocelle M, Gunnlaugsson T. Org Biomol Chem 10 126-133 (2012)
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  21. Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study. Dumont E, Pompidor G, D'Aléo A, Vicat J, Toupet L, Kahn R, Girard E, Maury O, Giraud N. Phys Chem Chem Phys 15 18235-18242 (2013)
  22. Synthesis and characterisation of lanthanide-hydroporphyrin dyads. Xiong R, Andres J, Scheffler K, Borbas KE. Dalton Trans 44 2541-2553 (2015)
  23. Conformational dynamics and alignment properties of loop lanthanide-binding-tags (LBTs) studied in interleukin-1β. Barthelmes D, Barthelmes K, Schnorr K, Jonker HRA, Bodmer B, Allen KN, Imperiali B, Schwalbe H. J Biomol NMR 68 187-194 (2017)
  24. Clicked europium dipicolinate complexes for protein X-ray structure determination. Talon R, Nauton L, Canet JL, Kahn R, Girard E, Gautier A. Chem Commun (Camb) 48 11886-11888 (2012)
  25. Rigid 5'-6-locked phenanthroline-derived nucleosides chelated to ruthenium and europium ions. Gislason K, Sigurdsson ST. Bioorg Med Chem Lett 23 264-267 (2013)
  26. Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Engilberge S, Riobé F, Wagner T, Di Pietro S, Breyton C, Franzetti B, Shima S, Girard E, Dumont E, Maury O. Chemistry 24 9739-9746 (2018)
  27. Synthesis of lanthanide tag and experimental studies on paramagnetically induced residual dipolar couplings. Yassin A, Nehmeh B, Kantar SE, Al Kazzaz Y, Akoury E. BMC Chem 16 54 (2022)


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