Predicting the equilibrium protein folding pathway: Structure-based analysis of staphylococcal nuclease

Vincent J. Hilser, Ernesto I Freire

Research output: Contribution to journalArticle

Abstract

The equilibrium folding pathway of staphylococcal nuclease (SNase) has been approximated using a statistical thermodynamic formalism that utilizes the high-resolution structure of the native state as a template to generate a large ensemble of partially folded states. Close to 400,000 different states ranging from the native to the completely unfolded states were included in the analysis. The probability of each state was estimated using an empirical structural parametrization of the folding energetics. It is shown that this formalism predicts accurately the stability of the protein, the cooperativity of the folding/unfolding transition observed by differential scanning calorimetry (DSC) or urea denaturation and the thermodynamic parameters for unfolding. More importantly, this formalism provides a quantitative account of the experimental hydrogen exchange protection factors measured under native conditions for SNase. These results suggest that the computer- generated distribution of states approximates well the ensemble of conformations existing in solution. Furthermore, this formalism represents the first model capable of quantitatively predicting within a unified framework the probability distribution of states seen under native conditions and its change upon unfolding.

Original languageEnglish (US)
Pages (from-to)171-183
Number of pages13
JournalProteins
Volume27
Issue number2
DOIs
StatePublished - 1997

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Micrococcal Nuclease
Protein folding
Protein Folding
Thermodynamics
Denaturation
Statistical mechanics
Differential Scanning Calorimetry
Probability distributions
Conformations
Urea
Hydrogen
Differential scanning calorimetry
Proteins

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Predicting the equilibrium protein folding pathway : Structure-based analysis of staphylococcal nuclease. / Hilser, Vincent J.; Freire, Ernesto I.

In: Proteins, Vol. 27, No. 2, 1997, p. 171-183.

Research output: Contribution to journalArticle

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