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Sequence-Specific Solvent Accessibilities of Protein Residues in Unfolded Protein Ensembles

Pau Bernadó ^* , Martin Blackledge ^* and Javier Sancho 

^* Institut de Biologie Structurale Jean-Pierre Ebel CNRS-CEA.-UJF, Grenoble, France; Institut de Recerca Biomèdica, Parc Científic de Barcelona, Barcelona, Spain; and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Biocomputation and Complex Systems Physics Institute-BIFI, University of Zaragoza, Zaragoza, Spain

Correspondence: Address reprint requests to Pau Bernadó, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain. E-mail: pbernado{at}pcb.ub.es; or to Javier Sancho, Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009-Zaragoza, Spain. E-mail: jsancho{at}unizar.es.

Protein stability cannot be understood without the correct description of the unfolded state. We present here an efficient method for accurate calculation of 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. Using a data set of 19 nonhomologous proteins containing from 98 to 579 residues, we report average accessibilities for all residue types. These averaged accessibilities are considerably lower than those previously reported for tripeptides and close to the lower limit reported by Creamer and co-workers. Of importance, 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.