Optimal side-chain packing in proteins and crystallographic refinement

Amino acid side chains often adopt one of a few distinct, physicochemically favourable conformational states called rotamers. Rotameric preferences and compact packing are sufficient to estimate the conformations of most side chains, as demonstrated by approaches such as SCWRL in homology modelling, but such algorithms have not yet been applied to protein crystallographic refinement. SCWRL's combinatorial optimization algorithm was adapted for assigning side-chain rotameric states that maximize the electron density map occupation while minimizing steric clashes. Our program (OPSAX) was tested on five proteins by introducing error in main chains and comparing the subsequent CNS-only and CNS/OPSAX refinements. The latter refinement was also extended to multiconformer models. A sequence-assignment exercise examined whether CNS/OPSAX refinement can discriminate between correct and incorrect assignments at various artificially lowered resolutions. The composite CNS/OPSAX refinement yielded better values than CNS-only refinement. A further drop in was observed with multiconformer refinement. For complete main chains, the correct sequence could be discriminated efficiently in most cases even for a low observation-to-parameter ratio of 4, indicating that the OPSAX approach should find useful applications in protein X-ray refinement.