Scaling behavior and structure of denatured proteins

Feng Ding, Ramesh K. Jha, Nikolay Dokholyan

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

An ensemble of random-coil conformations with no persistent structures has long been accepted as the classical model of denatured proteins due to its consistency with the experimentally determined scaling of protein sizes. However, recent NMR spectroscopy studies on proteins at high chemical denaturant concentrations suggest the presence of significant amounts of native-like structures, in contrast to the classical random-coil picture. To reconcile these seemingly controversial observations, we examine thermally denatured states of experimentally characterized proteins by using molecular dynamics simulations. For all studied proteins, we find that denatured states indeed have strong local conformational bias toward native states while a random-coil power law scaling of protein sizes is preserved. In addition, we explain why experimentally determined size of the protein creatine kinase does not follow general scaling. In simulations, we observe that this protein exhibits a stable intermediate state, the size of which is consistent with the reported experimental observation.

Original languageEnglish (US)
Pages (from-to)1047-1054
Number of pages8
JournalStructure
Volume13
Issue number7
DOIs
StatePublished - Jul 1 2005

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Proteins
Molecular Dynamics Simulation
Creatine Kinase
Protein Kinases
Magnetic Resonance Spectroscopy
Observation

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Ding, Feng ; Jha, Ramesh K. ; Dokholyan, Nikolay. / Scaling behavior and structure of denatured proteins. In: Structure. 2005 ; Vol. 13, No. 7. pp. 1047-1054.
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Scaling behavior and structure of denatured proteins. / Ding, Feng; Jha, Ramesh K.; Dokholyan, Nikolay.

In: Structure, Vol. 13, No. 7, 01.07.2005, p. 1047-1054.

Research output: Contribution to journalArticle

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