Local protein backbone folds determined by calculated NMR chemical shifts

Authors

  • András Czajlik,

    1. Protein Modelling Group, Hungarian Academy of Sciences-Eötvös Loránd University, 1117 Budapest, Pázmány Péter sétány 1/A, Hungary
    2. Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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  • Ilona Hudáky,

    1. Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, 1518 Budapest 112, Hungary
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  • András Perczel

    Corresponding author
    1. Protein Modelling Group, Hungarian Academy of Sciences-Eötvös Loránd University, 1117 Budapest, Pázmány Péter sétány 1/A, Hungary
    2. Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, 1518 Budapest 112, Hungary
    • Protein Modelling Group, Hungarian Academy of Sciences-Eötvös Loránd University, 1117 Budapest, Pázmány Péter sétány 1/A, Hungary
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    • Fax: (+36) 1 3722 620


Abstract

NMR chemical shifts (CSs: δNNH, δCα, δCβ, δC′, δHNH, and δHα) were computed for the amino acid backbone conformers (αL, βL, γL, δL, εL, αD, γD, δD, and εD [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 (δHNH, δC′, and δNNH) for backbone structure determination of the parent residue. Experimental δHα, δCα, and δCβ values retrieved from protein database are in good agreement with the relevant computed data in the case of the common backbone conformers (αL, βL, γL, and εL), even though neighboring residue effects were not accounted for. Experimental and computed ΔδHα-ΔδCα, ΔδHα-ΔδCβ, and ΔδCα-ΔδCβ 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 Hα, Cα, and Cβ 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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

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