Optimal side-chain packing in proteins and crystallographic refinement

Abstract

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 asSCWRLin 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 subsequentCNS-only andCNS/OPSAXrefinements. The latter refinement was also extended to multiconformer models. A sequence-assignment exercise examined whetherCNS/OPSAXrefinement can discriminate between correct and incorrect assignments at various artificially lowered resolutions. The compositeCNS/OPSAXrefinement yielded better R_{\rm free} values thanCNS-only refinement. A further drop in R_{\rm free} 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 theOPSAXapproach should find useful applications in protein X-ray refinement.