A new scale for side-chain contribution to protein stability based on the empirical stability analysis of mutant proteins

The hydrophobicity scales for amino acid side chains based on the transfer Gibbs energy (DeltaG(trans)) of amino acids from non-aqueous phases to water have been widely used to estimate the contribution of buried side chains to the conformational stability of proteins. In this paper, we propose a new scale for the side-chain contribution to protein stability, which is derived from data on protein denaturation experiments using systematic and comprehensive mutant proteins. In the experiments, the contribution of some physical properties were quantitatively determined as parameters in a unique equation representing the stability change (Delta DeltaG) of mutant proteins as a function of the structural changes due to the mutations. These parameters are able conveniently to provide a scale for the side-chain contribution to protein stability. This new scale also has the advantage over the previously reported hydrophobicity scales of residues with the contributions of hydrogen bonds or secondary structural propensity. It may find practical application in algorithms for the prediction of protein structures.