The molecular basis for the chemical denaturation of proteins by urea

Brian J. Bennion, Valerie Daggett

Research output: Contribution to journalArticle

569 Citations (Scopus)

Abstract

Molecular dynamics simulations of the protein chymotrypsin inhibitor 2 in 8 M urea at 60°C were undertaken to investigate the molecular basis of chemical denaturation. The protein unfolded rapidly under these conditions, but it retained its native structure in a control simulation in water at the same temperature. The overall process of unfolding in urea was similar to that observed in thermal denaturation simulations above the protein's Tm of 75°C. The first step in unfolding was expansion of the hydrophobic core. Then, the core was solvated by water and later by urea. The denatured structures in both urea and at high temperature contained residual native helical structure, whereas the β-structure was completely disrupted. The average residence time for urea around hydrophilic groups was six times greater than around hydrophobic residues and in all cases greater than the corresponding water residence times. Water self-diffusion was reduced 40% in 8 M urea. Urea altered water structure and dynamics, thereby diminishing the hydrophobic effect and encouraging solvation of hydrophobic groups. In addition, through urea's weakening of water structure, water became free to compete with intraprotein interactions. Urea also interacted directly with polar residues and the peptide backbone, thereby stabilizing nonnative conformations. These simulations suggest that urea denatures proteins via both direct and indirect mechanisms.

Original languageEnglish (US)
Pages (from-to)5142-5147
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume100
Issue number9
DOIs
StatePublished - Apr 29 2003
Externally publishedYes

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Protein Denaturation
Urea
Water
Protein Unfolding
Proteins
Temperature
Molecular Dynamics Simulation
Hot Temperature

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

The molecular basis for the chemical denaturation of proteins by urea. / Bennion, Brian J.; Daggett, Valerie.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 9, 29.04.2003, p. 5142-5147.

Research output: Contribution to journalArticle

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