Determinants of protein side-chain packing.
The problem of protein side-chain packing for a given backbone trace is investigated using 3 different prediction models. The first requires an exhaustive search of all possible combinations of side-chain conformers, using the dead-end elimination theorem. The second considers only side-chain-backbone interactions, whereas the third neglects side-chain-backbone interactions and instead keeps side-chain-side-chain interactions. Predictions of side-chain conformations for 11 proteins using all 3 models show that removal of side-chain-side-chain interactions does not cause a large decrease in the prediction accuracy, whereas the model having only side-chain-side-chain interactions still retains a significant level of accuracy. These results suggest that the 2 classes of interactions, side-chain-backbone and side-chain-side-chain, are consistent with each other and work concurrently to stabilize the native conformations. This is confirmed by analyses of energy spectra of the side-chain conformations derived from the fourth prediction model, the Independent model, which gives almost the same quality of the prediction as the dead-end elimination. The analyses indicate that the 2 classes of interactions simultaneously increase the energy difference between the native and nonnative conformations.
Tanimura
R
R
Protein Engineering Research Institute, Osaka, Japan.
Kidera
A
A
Nakamura
H
H
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009113:Muramidase / Q000737:chemistry; D010206:Papain / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D017433:Protein Structure, Secondary; D012399:Rotation; D013698:Templates, Genetic
D000596:Amino Acids; D010940:Plant Proteins; C024934:crambin protein, Crambe abyssinica; D009113:Muramidase; D010206:Papain