PII structure in the model peptides for unfolded proteins: Studies on ubiquitin fragments and several alanine-rich peptides containing QQQ, SSS, FFF, and VVV

Zhengshuang Shi, Kang Chen, Zhigang Lim, Tobin R. Sosnick, Neville R. Kallenbach

Research output: Contribution to journalArticlepeer-review

Abstract

A great deal of attention has been paid lately to the structures in unfolded proteins due to the recent discovery of many biologically functional but natively unfolded proteins and the far-reaching implications of order in unfolded states for protein folding. Recently, studies on oligo-Ala, oligo-Lys, oligo-Asp, and oligo-Glu, as well as oligo-Pro, have indicated that the left-handed polyproline II (PII) is the major local structure in these short peptides. Here, we show by NMR and CD studies that mbiquitin fragments, model unfolded peptides composed of nonrepeating amino acids, and four alanine-rich peptides containing QQQ, SSS, FFF, and VVV sequences are all present in aqueous solution predominantly in the extended PII or β conformation. The results from this and related studies indicate that PII might be a major backbone conformation in unfolded proteins. The presence of defined local backbone structure in unfolded proteins is inconsistent with predictions from random coil models.

Original languageEnglish (US)
Pages (from-to)312-321
Number of pages10
JournalProteins: Structure, Function and Genetics
Volume63
Issue number2
DOIs
StatePublished - May 1 2006

Keywords

  • Alanine-rich peptides
  • Nonrepeating amino acids
  • Protein folding
  • Ubiquitin fragments
  • Unfolded state

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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