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Sequence-dependent correction of random coil NMR chemical shifts

Academic Article
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Overview

related to degree

  • Foss, Ted, Ph.D. in Macromolecular and Cellular Structure and Chemistry, Scripps Research 2000 - 2006

authors

  • Schwarzinger, S.
  • Kroon, G. J. A.
  • Foss, Ted
  • Chung, J.
  • Wright, Peter
  • Dyson, Jane

publication date

  • April 2001

journal

  • Journal of the American Chemical Society  Journal

abstract

  • Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil shifts for certain nuclei. While some of these deviations can be ascribed to residual structure in the unfolded protein, others are clearly caused by local sequence effects. In particular, the amide nitrogen, amide proton, and carbonyl carbon chemical shifts are highly sensitive to the local amino acid sequence. We present a detailed, quantitative analysis of the effect of the 20 naturally occurring amino acids on the random coil shifts of (15)N(H), (1)H(N), and (13)CO resonances of neighboring residues, utilizing complete resonance assignments for a set of five-residue peptides Ac-G-G-X-G-G-NH(2). The work includes a validation of the concepts used to derive sequence-dependent correction factors for random coil chemical shifts, and a comprehensive tabulation of sequence-dependent correction factors that can be applied for amino acids up to two residues from a given position. This new set of correction factors will have important applications to folded proteins as well as to short, unstructured peptides and unfolded proteins.

subject areas

  • Amino Acid Sequence
  • Amino Acids
  • Carbon Isotopes
  • Glycine
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptides
  • Proline
  • Protein Conformation
  • Protons
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Identity

International Standard Serial Number (ISSN)

  • 0002-7863

Digital Object Identifier (DOI)

  • 10.1021/ja003760i

PubMed ID

  • 11457007
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Additional Document Info

start page

  • 2970

end page

  • 2978

volume

  • 123

issue

  • 13

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