Internal residue criteria for predicting three-dimensional protein structures.

The internal amino acid residues of proteins are almost always non-polar since the hydrophobic effect is very important in stabilizing the three-dimensional structure. This fact suggests several new criteria for judging the correctness of structures predicted from sequence data. The dinucleotide binding domain has been used as a test structure for these criteria. The percentage of ionic residues, mutation data, hydrophobicity, dipole moments, and internal preferences of the residues on the interiors of the known dinucleotide binding folds are consistent with expectations. On the other hand, the values of these parameters for predicted domains in glutamate dehydrogenase (Wootton, J.C. (1974) Nature 252, 542--546) and aldolase (Stellwagen, E. (1976) J. Mol. Biol. 106, 903--911) differ significantly from the expected values indicating that these predictions are not entirely correct. The internal residue criteria can then be used to test modifications of the predictions for a better correlation with the internal residue pattern of the domain.