Non-random-coil Behavior as a Consequence of Extensive PPII Structure in the Denatured State

Aitziber L. Cortajarena, Gregg Lois, Eilon Sherman, Corey S. O'Hern, Lynne Regan*, Gilad Haran

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


Unfolded proteins may contain a native or nonnative residual structure, which has important implications for the thermodynamics and kinetics of folding, as well as for misfolding and aggregation diseases. However, it has been universally accepted that residual structure should not affect the global size scaling of the denatured chain, which obeys the statistics of random coil polymers. Here we use a single-molecule optical technique-fluorescence correlation spectroscopy-to probe the denatured state of a set of repeat proteins containing an increasing number of identical domains, from 2 to 20. The availability of this set allows us to obtain the scaling law for the unfolded state of these proteins, which turns out to be unusually compact, strongly deviating from random coil statistics. The origin of this unexpected behavior is traced to the presence of an extensive nonnative polyproline II helical structure, which we localize to specific segments of the polypeptide chain. We show that the experimentally observed effects of polyproline II on the size scaling of the denatured state can be well-described by simple polymer models. Our findings suggest a hitherto unforeseen potential of nonnative structure to induce significant compaction of denatured proteins, significantly affecting folding pathways and kinetics.

Original languageAmerican English
Pages (from-to)203-212
Number of pages10
JournalJournal of Molecular Biology
Issue number1
StatePublished - 26 Sep 2008
Externally publishedYes

Bibliographical note

Funding Information:
We thank Professors A. Horovitz, A. D. Miranker, and A. Minsky, as well as members of the Regan and Haran Laboratories, for comments and suggestions on the manuscript. A.L.C. was a recipient of an European Molecular Biology Organization short-term fellowship. This research was made possible, in part, by the historic generosity of the Harold Perlman Family, as well as by partial financial support of the United States–Israel binational science foundation (grant no. 2002371 to G.H.), the National Institutes of Health (grant no. 1R01GM080515-01 to G.H.), and the Human Frontier Science Program (to G.H. and L.R.). Financial support to G.L. and C.S.O. from National Science Foundation grant no. DMR-0448838 and funding from Yale's Institute for Nanoscience and Quantum Engineering to G.L. are gratefully acknowledged.


  • PPII helix
  • denatured state
  • fluorescence correlation spectroscopy
  • protein folding
  • self-avoiding random walk


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