Introduction to BPPred1

It is well known that equilibrium m-values are related to changes in solvent accessible surface area (SASA) upon unfolding2. We have discovered an analogous relationship between the equilibrium m-values and the changes in the radius of gyration (ΔRg) upon unfolding; a quantity that, unlike the SASA, can be readily measured experimentally.

Furthermore, we have exploited the availability of recent experimental data on a variety of proteins to assess, or to reassess, the relationships between several parameters commonly used to describe the folding process. These parameters include:

  • The equilibrium m-values,
  • The length of the protein (number of ordered residues),
  • The change upon unfolding in the solvent accessible surface area (ΔSASA),
  • The change upon unfolding in the heat capacity (ΔCp), and
  • The change upon unfolding in the radius of gyration (ΔRg).

The knowledge of any one of these quantities allows an estimate of the others to be obtained, and consequently we have converted our findings into the useful web-tool presented below.

Although the correlations that we report are statistically signficant, they are of a statistical nature and therefore individual proteins may deviate from their predicted behaviours. These cases are interesting because they may possibly be associated with the presence of residual structure in the unfolded state, for instance in the case of proteins with disulfide bridges.

Usage 1: Calculate all possible properties based on an experimentally measured parameter.

Calculate biophysical properties Number of ordered residues in the polypeptide chain:
ΔRg between the Native and Denatured states: (Å)
m-value from Urea denaturation: (cal mol-1 M-1)
m-value from GdmCl denaturation: (cal mol-1 M-1)

Usage 2: View the correlation between two specific parameters.
Input the values for your own protein to examine how well they fit with our data set.

Compare two properties Plot against

Input experimental values (optional):
  vs.  

References

  1. Geierhaas, C. D., Nickson, A. A., Lindorff-Larsen, K., Clarke, J. & Vendruscolo, M. (2007). BPPred: A computational tool to predict biophysical quantities of proteins. Protein Sci. 16, 125-134.
  2. Myers, J. K., Pace, C. N. & Scholtz, J. M. (1995). Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4, 2138-2148.

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