Ab initio structure prediction of two alpha-helical oligomers with a multiple-chain united-residue force field and global search.

A hierarchical methodology for ab initio structure prediction is extended to treat oligomeric proteins. Modifications are made to a united-residue (UNRES) force field and a Conformational Space Annealing (CSA) global search method. The computational cost of including additional chains and the increase in speed from symmetry optimizations are evaluated. The native structures of two oligomeric proteins from the CASP3 exercise, the retro-GCN4 leucine zipper and the synthetic domain-swapped dimer, were identified as the lowest-energy families resulting from the search of the proteins when rotational symmetry was imposed. Additional searches in different symmetries and oligomerization states were carried out, and the results indicate some problems in the thoroughness of the search and in the search of packing arrangements if symmetry constraints are not imposed. Copyright 2003 Wiley Periodicals, Inc. Biopolymers: 300-317, 2003