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PII structure in the model peptides for unfolded proteins: Studies on ubiquitin fragments and several alanine‐rich peptides containing QQQ, SSS, FFF, and VVV
Author(s) -
Shi Zhengshuang,
Chen Kang,
Liu Zhigang,
Sosnick Tobin R.,
Kallenbach Neville R.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20788
Subject(s) - polyproline helix , random coil , chemistry , folding (dsp implementation) , alanine , peptide , amino acid , protein folding , ubiquitin , protein structure , threading (protein sequence) , biophysics , biochemistry , protein secondary structure , biology , electrical engineering , gene , engineering
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 ubiquitin 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. Proteins 2006. © 2005 Wiley‐Liss, Inc.