Determinants of protein side-chain packing

Protein Sci. 1994 Dec;3(12):2358-65. doi: 10.1002/pro.5560031220.

Abstract

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.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Computer Simulation*
  • Humans
  • Models, Molecular*
  • Molecular Sequence Data
  • Muramidase / chemistry
  • Papain / chemistry
  • Plant Proteins / chemistry
  • Protein Structure, Secondary*
  • Rotation
  • Templates, Genetic

Substances

  • Amino Acids
  • Plant Proteins
  • crambin protein, Crambe abyssinica
  • Muramidase
  • Papain