A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins

Kwang Im Oh, Kyung Koo Lee, Eun Kyung Park, Youngae Jung, Geum Sook Hwang, Minhaeng Cho

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters.

Original languageEnglish
Pages (from-to)977-990
Number of pages14
JournalProteins: Structure, Function and Bioinformatics
Volume80
Issue number4
DOIs
Publication statusPublished - 2012 Apr 1

Keywords

  • Blocked dipeptide
  • Peptide conformation
  • Polyproline II
  • Unfolded protein structure

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Molecular Biology

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