| Abstract
| - Rational drug design depends on the knowledge of the three-dimensional (3D) structure ofcomplexes between proteins and lead compounds of low molecular weight. A novel nuclear magneticresonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allowsthe rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solutionand, simultaneously, its location and orientation with respect to the protein. The method relies on thepresence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand.The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derivedfrom concentration-dependent 1H and 13C spectra of the ligand at natural isotopic abundance. Combinedwith prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibilitytensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligandmolecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary30 kDa complex between the lanthanide-labeled N-terminal domain of the ε exonuclease subunit from theEscherichia coli DNA polymerase III, the subunit θ, and thymidine. The binding mode of thymidine wasfound to be very similar to that of thymidine monophosphate present in the crystal structure.
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