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. 2006 Dec 15;91(12):4536-43.
doi: 10.1529/biophysj.106.087528. Epub 2006 Sep 29.

Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles

Pau Bernadó  1 , Martin Blackledge, Javier Sancho
Affiliations

Sequence-specific solvent accessibilities of protein residues in unfolded protein ensembles

Pau Bernadó et al. Biophys J. .

Abstract

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.

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Figures

FIGURE 1
FIGURE 1
Flow-chart of the programs used for generation of denatured-state ensembles (flexible-Meccano and Sccomp) and for the calculation of the atom- and residue-specific solvent exposures (Naccess).
FIGURE 2
FIGURE 2
Individual solvent exposures of residues Lys-65 and Ala-179 in 1FCQ, calculated in 1000 conformations representing the denatured state of the protein. Dashed lines represent the averaged surface accessibilities of the two residues: 157.57 and 68.72 Å2, respectively.
FIGURE 3
FIGURE 3
Influence of sequence context on solvent accessibilities. (A) The most and least accessible residues of each type found among the 19 proteins analyzed, shown in their sequence context and enclosed in black squares. Proline residues appear in bold to highlight the relevant role they play in determining high and low accessibilities. (B) Amino acid population in the least (top) and most (bottom) accessible residue sequences. Black bars represent the times a kind of residue is found in the three residues flanking the most and least accessible residues. Gray bars represent the times a kind of residue should be found at random, assuming the population statistics derived from the set of proteins studied.
FIGURE 4
FIGURE 4
Influence of size and amino acid composition on the total solvent accessibility of the set of 19 proteins. (A) Percentage difference between the solvent exposures averaged over the 2000 conformations of the atomistic models of the denatured ensembles, and the ones obtained using protein composition and the residue averaged values shown in Table 1. Positive values (white area) indicate that the actual protein is more accessible than expected, whereas negative values (gray area) indicate less solvent accessibility than expected from the contribution of individual residues. The solid line represents the linear regression slope. (B) Solvent accessibility of the 11-amino-acid-long central fragment of polyalanine chains of different lengths. (C) Amino acid composition of proteins 1LN4 (left bars) and 1TD1 (right bars) bearing 98 and 100 residues, respectively. Middle bars correspond to the number of residues expected for a protein of that size that followed the residue statistics of the 19 proteins in the data set.
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