Packing of sidechains in low-resolution models for proteins

Background: Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features.

Results: A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (rmsd) of 2.40 å with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 å and decreases to 1.35 å when conformational correlations and directional effects in inter-residue couplings are considered.

Conclusions:An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.