Efficient rotamer elimination applied to protein side-chains and related spin glasses

摘要: Folded proteins and spin glasses share various properties, such as seemingly random interactions between residues (spins), one might presume that some generic behaviors of would also be exhibited in a general way by proteins. But comparison here shows the side-chain conformation systems apo-myoglobin lysozyme are qualitatively different from specific closely related glass systems. This difference is manifest number rotamers can identified definitely not contributing to global energy minimum. identification effected using significantly enhanced version Dead End Elimination theorem (Desmet, J., M. De Maeyer, B. Hazes, I. Lasters. 1992. The dead-end elimination its use protein positioning. Nature. 356:539–542), which much more effective efficient eliminating rotamers. In several cases (for proteins, although for glasses) this improved succeeded identifying absolute minimum rotamer conformations, with no statistical uncertainty. due correlations residue pair another pair, probably will play an important role thermodynamic behavior system.