Yong-Min Lee

Locating the metal ion in calcium-binding proteins by using cerium(III) as a probe.

The detection and assignment of NMR spectroscopic signals of carbon atoms from carbonyl and carboxylate groups in the loop hosting the CeIII ion was performed for the cerium‐substituted calcium‐binding protein calbindin D9k. This provided a tool to characterize in solution the first coordination sphere of the metal ion. Due to the well‐documented possibility of replacing calcium with metal ions of the LnIII series, this approach turns out to be extremely efficient for characterizing in solution the coordination of calcium ions in proteins, independently of the availability of X‐ray crystal structures. The present approach completes the structural characterization of lanthanide‐substituted calcium‐binding proteins, for which the role of long‐range constraints arising from hyperfine interaction and self‐orientation has already been assessed.

A paramagnetic probe to localize residues next to carboxylates on protein surfaces

Abstract. It is shown that the paramagnetic properties of lanthanides can be exploited to obtain information on specific parts of a protein surface. Owing to the high affinity of coordinatively unsaturated lanthanide complexes for oxygen donors, carboxylate groups can be used as preferential targets for the interaction. The DO3A ligand is particularly useful in these studies, as it coordinates lanthanides in a heptadentate fashion, leaving two sites available for exogenous donors. A solution of a 15N-labeled sample protein, calbindin D9k (75 residues), was titrated with up to 200% of Gd(III)-DO3A complex, and an inversion recovery 15N-1H HSQC experiment was used to measure the paramagnetic contributions to the longitudinal relaxation rates of the amide protons. Relaxation data were used as distance constraints to estimate the number of interacting complexes and the occupancies of their binding sites. Four preferential interaction sites on the protein surface are found. Inspection of the various carboxylate side chains on the surface of the protein indicates that Gd(III)-DO3A interacts preferentially with carboxylate-rich regions, rather than with isolated carboxylates, suggesting the possibility of chelation of one Gd(III)-DO3A molecule by two carboxylate groups. Gd(III)-DO3A is thus a valuable semi-selective probe for clusters of negative charges on the protein surface.

Structure-independent cross-validation between residual dipolar couplings originating from internal and external orienting media

Lanthanide-substituted calcium binding proteins are known to partially orient in high magnetic fields. Orientation provides residual dipolar couplings (rdcs). Two of these systems, Tm3+- and Dy3+-substituted calbindin D9k, dissolved in an external orienting medium (nonionic liquid crystalline phase) provide rdc values which are the sum of those induced by the lanthanides and by the liquid crystalline phase on the native calcium binding protein. This structure-independent check shows the innocence of the orienting medium with respect to the structure of the protein in solution. Furthermore, the simultaneous use of lanthanide substitution and external orienting media provides a further effective tool to control and tune the orientation tensor.

Structural basis for sequential displacement of Ca2+ by Yb3+ in a protozoan EF‐hand calcium binding protein

We have studied the displacement of Ca2+by the trivalent lanthanide ions (Yb3+) in a protozoan (Entamoeba histolytica) Ca2+‐binding protein (EhCaBP), by NMR and thermodynamics. We have demonstrated, for the first time, how one can use in a combined fashion the utility of NMR and thermodynamics to have an insight to the relative binding specificities/affinity between Ca2+ and Yb3+. As revealed by the titration experiments, Yb3+ displaces Ca2+ from the four metal binding sites present in EhCaBP in a sequential manner. The study provides a structural origin for such a sequential Ca2+ displacement by Yb3+ in EhCaBP.

Dichloro­[(6R,7S,8S,14S)-(–)-sparteine-κ2N,N′]mercury(II)

In the title compound, [HgCl2(C15H26N2)], the chiral alkaloid (6R,7S,8S,14S)-(-)-L-sparteine acts as a bidentate ligand, with two Cl- ligands occupying the remaining coordination sites, producing a distorted tetrahedron. The N-Hg-N plane is twisted by 81.1 (2) degrees from the Cl-Hg-Cl plane. The mid-point of the N...N line does not lie exactly on the Cl-Hg-Cl plane but is tilted towards one of the N atoms by 0.346 angstroms. Similarly, the mid-point of the Cl...Cl line is tilted toward one of the Cl atoms by 0.163 angstroms. The packing structure shows that the complex is stabilized by two interatomic Cl...H contacts involving both Cl atoms and the methylene or methine H atoms of the (-)-sparteine ligand.

CCDC 299620: Experimental Crystal Structure Determination

Related Article: Myeong-Jin Oh, Yong-Min Lee, Seung Jae Lee, Sung Kwon Kang, Sung-Nak Choi|2006|Acta Crystallogr.,Sect.C:Cryst.Struct.Commun.|62|m51|doi:10.1107/S0108270105043088

Tris(1,10-phenanthroline)copper(II) di-μ-iodo-bis­(diiodo­mercurate) dimethyl sulfoxide monohydrate

In the cationic complex present in the title compound, [Cu(C12H8N2)3][Hg2I6].C2H6OS.H2O, the copper(II) center adopts a highly distorted octahedral geometry, ligated by the six N atoms of three 1,10-phenanthroline ligands. The structure includes an iodide-bridged dimeric mercurate anion for neutrality and uncoordinated dimethyl sulfoxide and water molecules.