Lanthanide-Induced Pseudocontact Shifts for Solution Structure Refinements of Macromolecules in Shells up to 40 Å from the Metal Ion

Abstract

A number of pseudocontact shifts (PCS) in monolanthanide-substituted Calbindin D 9k (Ca 2 Cb hereafter), a protein of 75 amino acids, were measured for Ce(III), Yb(III), and Dy(III). The assignment of the shifts was obtained through the conventional assignment procedures for the Ce(III) derivative (CaCeCb), since the line broadening is not severe, whereas in the case of Dy(III) and Yb(III) the assignment was obtained by analyzing the temperature dependence of the 1 H− 15 N HSQC shifts of the lanthanide derivatives and comparing the results with the 1 H− 15 N HSQC spectrum of Ca 2 Cb or CaCeCb. The NOE-based solution structures of Ca 2 Cb or CaCeCb were then refined with PCS. Since the three lanthanides span a wide range of magnetic anisotropies, the refinement was effective in shells from the metal of ∼5−15 Å for Ce(III), ∼9−25 Å for Yb(III), and ∼13−40 Å for Dy(III), as useful PCS were observed in these shells. The root-mean-square deviation of 30 conformers from the average for CaCeCb was 0.74 and 1.10 Å for the backbone and all heavy atoms, respectively, obtained from 1539 NOEs, 39 3 J values, and 6 T 1 values. With 589 pseudocontact shifts for Ce(III) (out of which 280 were larger than 0.1 ppm), 92 PCS for Yb(III), and 74 for Dy(III) the RMSD decreased to 0.54 and 0.95 Å for Ce(III), 0.60 and 0.98 Å for Yb(III), and 0.66 and 1.04 Å for Dy(III) for the backbone and all heavy atoms, respectively. While for Ce(III) resolution improvements are mainly found for the metal binding site itself, Yb(III) and Dy(III) can further constrain regions far away from the metal. These results show that constructing a lanthanide binding site may be a general and convenient tool to “enlighten” shells at variable distances from the metal itself, and may be used for various purposes including the investigation of biomolecular complexes.