VOOZH about

URL: https://pubmed.ncbi.nlm.nih.gov/16501226/

⇱ On the precision of experimentally determined protein folding rates and phi-values - PubMed


Clipboard, Search History, and several other advanced features are temporarily unavailable.
Skip to main page content
👁 Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

👁 Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Abstract

Phi-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 phi-values can be determined experimentally: Because phi 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 phi-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 phi-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 (mf and mu) are invariant upon mutation, the precision of our estimates of phi 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.

PubMed Disclaimer

Figures

👁 Figure 1.
Figure 1.
Chevron plots for the wild-type FynSH3 domain and the seven point mutants studied here. All three chevron fits are illustrated in each column, but the data points produced by each laboratory (white, gray, and black) are presented in separate columns for clarity. These data provide an indication of the precision with which folding and unfolding rates are measured in our laboratories under typical experimental conditions using generally accepted laboratory practices.
👁 Figure 2.
Figure 2.
The precision of the kinetic measurements described here compares favorably with many previously reported in the literature. For example, the mean, the median, and the maximum root mean squared residuals associated with the 24 chevron curves we have determined (triplicate measurements of each of eight sequence, upper panel) are less than those of a set of 28 previously reported chevron curves determined in 16 different laboratories (lower panel) (Maxwell et al. 2005). Indicated is the precision with which the FynSH3 wild-type folding rate is defined by the previously reported data.
👁 Figure 3.
Figure 3.
A comparison of the three sets of measurements described here. No systematic errors are observed in the scatter in the kinetic parameters ln(kf), ln(ku) (both extrapolations to zero denaturant), mf, or mu (the slopes of the folding and the unfolding chevron arms, respectively); no one research group systematically over- or underestimated any of these parameters. The error bars represent 95% confidence intervals for fits of the chevron data. The symbol scheme is as described in Fig. 1.
👁 Figure 4.
Figure 4.
Shown here are the average ΔΔGu values and average φ-values obtained from independent measurements across three laboratories. The horizontal and the vertical bars present the standard deviations of the respective measurements. As indicated by the rapid increase in the size of the error bars on the left-hand sides of these plots, we find that the precision with which we can measure φ is reasonable when the estimated ΔΔGU is high but becomes quite poor at lower ΔΔGU. At larger ΔΔGU the precision of estimates of φ is significantly improved when we employ the nonzero and fixed-m analysis methods, an observation that also holds for estimates of ΔΔGU. Several data points are simply indicated with the symbol “x” at the top of the plot for clarity.
👁 Figure 5.
Figure 5.
Shown are the observed experimental standard deviations of the 28 φ-values reported here as a function of the mean observed ΔΔGU for each of the three analysis methods we have employed. To illustrate the differences in φ-value variability that result from the three different estimation approaches, a line using a scatter-plot smoother was added. For both the nonzero and the fixed-m approach, the standard deviation of the φ-values among the three laboratories drops below the arbitrarily chosen line at 0.2 at a value of ΔΔGU of ~5 kJ/mol, while for the approach using extrapolation to zero denaturant, this value is ~7.5 kJ/ mol. The “x” symbols on the upper axis denote estimates that lie above σ = 2.
👁 Figure 6.
Figure 6.
When ΔΔGU is large, φ-values derived independently in each of our groups closely approach those calculated using previously reported data from an independent laboratory (φUT) (Northey et al. 2002). In contrast, rather large deviations are observed when ΔΔGU is smaller. The crossed bars indicate the mean of the values reported here. Otherwise, the symbol scheme is as described above (Fig. 1).
👁 Figure 7.
Figure 7.
The precision of a single estimate of φ (i.e., based on kinetic data collected by a single laboratory in a single experiment) is approximately proportional to the square root of the number of kinetic observations employed to define the relevant chevron curves. For substitutions producing both large (12.5 kJ/mol, left) and small (2.6 kJ/mol, right) ΔΔGU we used the fitted chevron curves and the estimated experimental errors to carry out a simulation study. Ten thousand new chevron curves were generated from each data set by picking a fixed number of equally spaced points on the original chevron curves and adding Gaussian noise with standard deviation equal to the observed experimental error. When plotted as histograms, the resulting 10,000 estimated φ-values illustrate the dependency of φ precision on both ΔΔGU and the number of data points employed.

References

    1. Alm, E., Morozov, A.V., Kortemme, T., and Baker, D. 2002. Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 322: 463–476. - PubMed
    1. Clementi, C., Garcia, A.E., and Onuchic, J.N. 2003. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L. J. Mol. Biol. 326: 933–954. - PubMed
    1. Daggett, V. and Fersht, A. 2003. The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 4: 497–502. - PubMed
    1. Daggett, V., Li, A.J., and Fersht, A.R. 1998. Combined molecular dynamics and φ-value analysis of structure–reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects. J. Am. Chem. Soc. 120: 12740–12754.
    1. de los Rios, M.A. and Plaxco, K.W. 2005. Apparent Debye-Huckle electrostatic effects in the folding of a simple, single-domain protein. Biochemistry 44: 1243–1250. - PubMed
Cite

NCBI Literature Resources

MeSH PMC Bookshelf Disclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.