Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles
Pau Bernadó 1, Martin Blackledge 2 and Javier Sancho 3*
1 Parc Científic de Barcelona
2 Institut de Biologie Structurale (Grenoble)
3 Universidad de Zaragoza
* To whom correspondence should be addressed. E-mail: jsancho{at}unizar.es.
Submitted on April 21, 2006
Revised on May 30, 2006
Accepted on 21 August 2006
 |
Abstract |
|---|
Protein stability cannot be understood without the correct description of the unfolded state. We present here an efficient method to accurately calculate atomic solvent exposures for denatured protein ensembles. The method used to generate the ensembles has been shown to reproduce diverse biophysical experimental data corresponding to natively and chemically unfolded proteins (Proc. Natl. Acad. Sci. USA. 102:17002-17007). Using a data set of 19 non-homologous proteins containing from 98 to 579 residues we report average accessibilities for all residue types. These averaged accessibilities are considerably lower that those previously reported for tripeptides and close to the lower limit reported by Creamer and coworkers (Biochemistry. 36:2832-2835, 1997). Importantly, we observe remarkable sequence dependence for the exposure to solvent of all residue types, which indicates that average residue solvent exposures can be inappropriate to interpret mutational studies. In addition we observe smaller influences of both protein size and protein amino acid composition in the averaged residue solvent exposures for individual proteins. Calculating residue-specific solvent accessibilities within the context of real sequences is thus necessary and feasible. The approach presented here may allow a more precise parameterization of protein energetics as a function of polar and apolar area burial and opens new ways to investigate the energetics of the unfolded state of proteins.
Key Words:
hydrophobic effect, protein folding, protein solvent exposure, protein stability, unfolded ensemble
