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Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
Author(s) -
Zhou Hongyi,
Zhou Yaoqi
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10241
Subject(s) - solvation , chemistry , folding (dsp implementation) , hydrophobic effect , octanol , protein folding , crystallography , accessible surface area , solvation shell , thermodynamics , computational chemistry , partition coefficient , molecule , chromatography , organic chemistry , physics , biochemistry , electrical engineering , engineering
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 mol −1 Å −2 , close to the original estimate of hydrophobic contribution of 25–30 cal mol −1 Å −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). Proteins 2002;49:483–492. © 2002 Wiley‐Liss, Inc.