Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

Kwang Im Oh, Young Sang Jung, Geum Sook Hwang, Minhaeng Cho

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out 1H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked aminoacids (Ac-X-NHMe), oligopeptides (Ac-GGXGG-NH2), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.

Original languageEnglish
Pages (from-to)25-41
Number of pages17
JournalJournal of Biomolecular NMR
Volume53
Issue number1
DOIs
Publication statusPublished - 2012 May 1

Fingerprint

Intrinsically Disordered Proteins
Dipeptides
Oligopeptides
Chemical shift
Muramidase
Amino Acids
Protons
Nuclear magnetic resonance
Protein Unfolding
Proteins
Solvation
Viruses
Amides
Hepacivirus
Escherichia coli
Conformations
Membrane Proteins
Inspection
Experiments

Keywords

  • Blocked dipeptide
  • NMR scalar coupling
  • Peptide backbone conformation
  • Unfolded protein

ASJC Scopus subject areas

  • Spectroscopy
  • Biochemistry

Cite this

Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides. / Oh, Kwang Im; Jung, Young Sang; Hwang, Geum Sook; Cho, Minhaeng.

In: Journal of Biomolecular NMR, Vol. 53, No. 1, 01.05.2012, p. 25-41.

Research output: Contribution to journalArticle

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