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

John G. Pearson, Hong biao Le, Eric Oldfield, Jin Feng Wang, John L. Markley

Research output: Contribution to journalArticlepeer-review

Abstract

We show that protein structures in solution can be refined by using 13Cα and 13Cβ chemical shifts. We investigated 12 alanine and 8 valine residues in the nuclease from Staphylococcus aureus and found that the ϕ, Ψ and χ values of these residues are closer to the X-ray ϕ, Ψ, and χ values when nuclear Overhauser effect distance restraints and J-coupling torsion angle restraints are supplemented with chemical shift restraints. For ϕ 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 13Cα and 13Cβ 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.

Original languageEnglish (US)
Pages (from-to)8823-8829
Number of pages7
JournalJournal of the American Chemical Society
Volume117
Issue number34
DOIs
StatePublished - Jan 1 1995

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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