Stability scale and atomic solvation parameters extracted from 1023 mutation experiments.
The stability scale of 20 amino acid residues is derived from a database of 1023 mutation experiments on 35 proteins. The resulting scale of hydrophobic residues has an excellent correlation with the octanol-to-water transfer free energy corrected with an additional Flory-Huggins molar-volume term (correlation coefficient r = 0.95, slope = 1.05, and a near zero intercept). Thus, hydrophobic contribution to folding stability is characterized remarkably well by transfer experiments. However, no corresponding correlation is found for hydrophilic residues. Both the hydrophilic portion and the entire scale, however, correlate strongly with average burial accessible surface (r = 0.76 and 0.97, respectively). Such a strong correlation leads to a near uniform value of the atomic solvation parameters for atoms C, S, O/N, O(-0.5), and N(+0.5,1). All are in the range of 12-28 cal x mol(-1) A(-2), close to the original estimate of hydrophobic contribution of 25-30 cal x mol(-1) A(-2) to folding stability. Without any adjustable parameters, the new stability scale and new atomic solvation parameters yielded an accurate prediction of protein-protein binding free energy for a separate database of 21 protein-protein complexes (r = 0.80 and slope = 1.06, and r = 0.83 and slope = 0.93, respectively).
Zhou
Hongyi
H
Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.
Zhou
Yaoqi
Y
D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D030562:Databases, Protein; D004795:Enzyme Stability; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D009154:Mutation; D000442:Octanols; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012995:Solubility; D012997:Solvents; D013816:Thermodynamics; D014867:Water
D000596:Amino Acids; D000442:Octanols; D011506:Proteins; D012997:Solvents; D014867:Water