On the precision of experimentally determined protein folding rates and φ-values

Miguel A. De Los Rios, B. K. Muralidhara, David Wildes, Tobin R. Sosnick, Susan Marqusee, Pernilla Wittung-Stafshede, Kevin W. Plaxco, Ingo Ruczinski

Research output: Contribution to journalArticle

Abstract

φ-Values, a relatively direct probe of transition-state structure, are an important benchmark in both experimental and theoretical studies of protein folding. Recently, however, significant controversy has emerged regarding the reliability with which φ-values can be determined experimentally: Because φ is a ratio of differences between experimental observables it is extremely sensitive to errors in those observations when the differences are small. Here we address this issue directly by performing blind, replicate measurements in three laboratories. By monitoring within- and between-laboratory variability, we have determined the precision with which folding rates and φ-values are measured using generally accepted laboratory practices and under conditions typical of our laboratories. We find that, unless the change in free energy associated with the probing mutation is quite large, the precision of φ-values is relatively poor when determined using rates extrapolated to the absence of denaturant. In contrast, when we employ rates estimated at nonzero denaturant concentrations or assume that the slopes of the chevron arms (m f and mu) are invariant upon mutation, the precision of our estimates of φ is significantly improved. Nevertheless, the reproducibility we thus obtain still compares poorly with the confidence intervals typically reported in the literature. This discrepancy appears to arise due to differences in how precision is calculated, the dependence of precision on the number of data points employed in defining a chevron, and interlaboratory sources of variability that may have been largely ignored in the prior literature. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)553-563
Number of pages11
JournalProtein Science
Volume15
Issue number3
DOIs
StatePublished - Mar 1 2006

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Keywords

  • FynSH3 domain
  • Protein folding
  • Stopped-flow mixing
  • φ-values

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

De Los Rios, M. A., Muralidhara, B. K., Wildes, D., Sosnick, T. R., Marqusee, S., Wittung-Stafshede, P., Plaxco, K. W., & Ruczinski, I. (2006). On the precision of experimentally determined protein folding rates and φ-values. Protein Science, 15(3), 553-563. https://doi.org/10.1110/ps.051870506