Three-dimensional off-lattice AB model protein with the 89-residue Fibonacci sequence

Abstract

The three-dimensional off-lattice AB model proteins are constructed from only two different types of amino acids, the hydrophobic (A) and the hydrophilic (B) residues. In the literature, Fibonacci AB protein sequences of length between 13 and 55 residues in three dimensions have been extensively studied to understand protein folding. Here, an efficient global optimization method, conformational space annealing, is applied to the three-dimensional off-lattice AB model protein with the 89-residue Fibonacci sequence whose properties are not known. For this AB protein in three dimensions, 32,200 distinct low-energy conformations are obtained. Using these low-energy conformations, we investigate the properties and the energy landscape of the three-dimensional off-lattice AB model protein with the 89-residue Fibonacci sequence.