Local protein backbone folds determined by calculated NMR chemical shifts

András Czajlik, Ilona Hudáky, András Perczel

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Abstract

NMR chemical shifts (CSs: δN NH, δC α, δC β, δC′, δH NH, and δH α) were computed for the amino acid backbone conformers (α L, β L, γ L, δ L, ε L, α D, γ D, δ D, and ε D [Perczel et al., J Am Chem Soc 1991, 113, 6256]) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single β-strands, hairpins with type I and II β-turns, as well as double- and triple-stranded β-sheet models. The so-called "capping effect" was analyzed: residues at the termini of a homoconformer sequence unit usually have different CSs than the central residues of an adequately long homoconformer model. In heteroconformer sequences capping effect ruins the direct applicability of several chemical shift types (δH NH, δC′, and δN NH) for backbone structure determination of the parent residue. Experimental δH α, δC α, and δC β values retrieved from protein database are in good agreement with the relevant computed data in the case of the common backbone conformers (α L, β L, γ L, and ε L), even though neighboring residue effects were not accounted for. Experimental and computed ΔδH α-ΔδC α, ΔδH α-ΔδC β, and ΔδC α-ΔδC β maps give qualitatively the same picture, that is, the positions of the backbone conformers relative to each other are very similar. This indicates that the H α, C α, and C β chemical shifts of alanine depend considerably on the backbone fold of the parent residue also in proteins. We provide tabulated CSs of the chiral amino acids that may predict the various structures of the residues.

Original languageEnglish
Pages (from-to)3362-3382
Number of pages21
JournalJournal of Computational Chemistry
Volume32
Issue number16
DOIs
Publication statusPublished - Dec 1 2011

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Keywords

  • NMR chemical shifts of foldamers
  • ab initio calculation
  • backbone fold prediction/reconstruction
  • protein secondary structures
  • relative chemical shifts

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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