Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials.
The stability changes in peptides and proteins caused by the substitution of a single amino acid, which can be measured experimentally by the change in folding free energy, are evaluated here using effective potentials derived from known protein structures. The analysis is focused on mutations of residues that are accessible to the solvent. These represent in total 106 mutations, introduced at different sites in barnase, bacteriophage T4 lysozyme and chymotrypsin inhibitor 2, and in a synthetic helical peptide. Assuming that the mutations do not modify the backbone structure, the changes in folding free energies are computed using various types of database-derived potentials and are compared with the measured ones. Distance-dependent residue-residue potentials are found to be inadequate for estimating the stability changes caused by these mutations, as they are dominated by hydrophobic interactions, which do not play an essential role at the protein surface. On the contrary, the potentials based on backbone torsion angle propensities yield quite good results. Indeed, for a subset of 96 out of the 106 mutations, the computed and measured changes in folding free energy correlate with a linear correlation coefficient of 0.87. Moreover, the ten mutations that are excluded from the correlation either seem to cause modifications of the backbone structure or to involve strong hydrophobic interactions, which are atypical for solvent-accessible residues. We find furthermore that raising the ionic strength of the solvent used for measuring the changes in folding free energies improves the correlation, as it tends to mask the electrostatic interactions. When adding to these 106 mutations 44 mutations performed in staphylococcal nuclease and chemotactic protein, which were first discarded because some of them were suspected to affect the backbone conformation or the denatured state, the correlation between measured and computed folding free energy changes remains quite good: the correlation coefficient is 0.86 for 135 out of the 150 mutations. The success of the backbone torsion potentials in predicting stability changes indicates that the approximations made for deriving these potentials are adequate. It suggests moreover that the local interactions along the chain dominate at the protein surface.
Gilis
D
D
UCMB, Université Libre de Bruxelles, Belgium.
Rooman
M
M
D000465:Algorithms; D001426:Bacterial Proteins; D016208:Databases, Factual; D004795:Enzyme Stability; D008836:Micrococcal Nuclease / Q000737:chemistry / Q000235:genetics; D009113:Muramidase / Q000737:chemistry; D009154:Mutation / Q000235:genetics; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012260:Ribonucleases / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
D001426:Bacterial Proteins; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; D012997:Solvents; C093336:chymotrypsin inhibitor 2; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D008836:Micrococcal Nuclease; D009113:Muramidase