Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments

Hydrophobicity values for amino acids obtained from proteinunfolding experiments are about twice as large as those obtainedfrom data on the partitioning of amino acids between water andoctanol. Quantitative analyses of several data sets, presentedhere, indicate that the difference is best explained by themost direct hypothesis, i.e. that the environment of hydrophobicgroups in the interior of a protein is poorly modeled by octanol.Instead, we propose—and provide supporting evidence—thathydrocarbons are a more suitable model. First, we reanalyzedata from both solute partitioning and protein unfolding experiments,taking account of the effects that were omitted previously,by introducing a volume dependence in the former and a fullfree energy analysis in the latter. Both changes in evaluationmethodology decrease the discrepancy, but the differences remainsubstantial. The hydrophobicity parameter obtained from side–chaintransfers between octanol and water increases from 16.7 to 22cal/ mol/², while that obtained from protein unfolding decreasesfrom 34.9 to 31.2 cal/mol/². On the other hand,our analysisof the solubilities of pure hydrocarbons in water provides ahydrophobicity parameter of 30.8 cal/mol/². This apparent hydrocarbon–likeenvironment of a protein's interior is also suggested more directlyby an analysis of the contact environment of hydrophobic sidechains in mutation/unfolding experiments, which have polar contactareas that are