We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for Β proteins, suggesting that for proteins in this class, the global tertiary structures can be determined mainly by sequence-independent backbone interactions. On the other hand, for α proteins, nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.
Bibliographical noteFunding Information:
This work was supported by the NRL program of MOST NRDP (M1–0203–00–0020). The authors thank Kyoungrim Lee for useful discussions.
All Science Journal Classification (ASJC) codes
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry