An off-lattice frustrated model protein with a six-stranded β-barrel structure

Abstract

We apply a global optimization method, which is conformational space annealing (CSA) to a challenging problem of the 69-residue protein with the sequence B(9)N(3)(LB)(4)N(3)B(9)N(3)(LB)(4)N(3)B(9)N(3)(LB)(5)L, where B, L, and N designate hydrophobic, hydrophilic, and neutral residues, respectively. The 69-residue BLN protein folds into a six-stranded β-barrel structure. The CSA method always maintains the diversity of sampling and is able to cross the high energy barriers between local minima. The CSA successfully located the global minimum of the 69-residue BLN protein for all 100 independent runs. For a single run, it takes about 3 h and 30 min on average to obtain the global minimum on a Linux PC. Also, we investigate the properties of the 69-residue BLN protein, and the general behavior of the M-residue BLN protein for CSA runs.