Protein Structure Refinement Using Carbon-13 Nuclear Magnetic Resonance Spectroscopic Chemical Shifts and Quantum Chemistry

Abstract

We show that protein structures in solution can be refined by using I3Ca and I3C@ chemical shifts. We investigated 12 alanine and 8 valine residues in the nuclease from Staphylococcus aureus and found that the 4, q, and x values of these residues are closer to the X-ray 4, q, and x values when nuclear Overhauser effect distance restraints and J-coupling torsion angle restraints are supplemented with chemical shift restraints. For 4 in particular, the rmsd versus the X-ray structure is -10 with chemical shift restraints versus -20 without chemical shift restraints. Both fully-restrained families of structures, those determined with and without chemical shift constraints, had small numbers of minor NOE violations. However, the chemical shift restrained structures were consistent with experimental Ala and Val I3Ca and I3C0 chemical shifts, whereas the structures determined without shift restraints yielded back calculated chemical shifts in poor accord with experiment. Carbon- 13 chemical shifts therefore appear to be of use in protein structure refinement when used in conjunction with chemical shift surfaces computed using ab initio methods.