ABSTRACT: In recent years, it has been repeatedly demonstrated that the coordinates of the main-chain atoms alone are sufficient to determine the side-chain conformations of buried residues of compact proteins. Given a perfect backbone, the side-chain packing method can predict the side-chain conformations to an accuracy as high as 1.2 A RMS deviation (RMSD) with greater than 80% of the chi angles correct. However, similarly rigorous studies have not been conducted to determine how well these apply, if at all, to the more important problem of homology modeling per se. Specifically, if the available backbone is imperfect, as expected for practical application of homology modeling, can packing constraints alone achieve sufficiently accurate predictions to be useful? Here, by systematically applying such methods to the pairwise modeling of two repressor and two cro proteins from the closely related bacteriophages 434 and P22, we find that when the backbone RMSD is 0.8 A, the prediction on buried side chain is accurate with an RMS error of 1.8 A and approximately 70% of the chi angles correctly predicted. When the backbone RMSD is larger, in the range of 1.6-1.8 A, the prediction quality is still significantly better than random, with RMS error at 2.2 A on the buried side chains and 60% accuracy on chi angles. Together these results suggest the following rules-of-thumb for homology modeling of buried side chains. When the sequence identity between the modeled sequence and the template sequence is > 50% (or, equivalently, the expected backbone RMSD is < 1 A), side-chain packing methods work well. When sequence identity is between 30-50%, reflecting a backbone RMS error of 1-2 A, it is still valid to use side-chain packing methods to predict the buried residues, albeit with care. When sequence identity is below 30% (or backbone RMS error greater than 2 A), the backbone constraint alone is unlikely to produce useful models. Other methods, such as those involving the use of database fragments to reconstruct a template backbone, may be necessary as a complementary guide for modeling.
