DESIGN OF PROTEINS WITH HYDROPHOBIC AND POLAR AMINO-ACIDS

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of 20 single chain proteins, Strikingly, the percentage of successful ide ntification of the nature of the residues benchmarked against naturall y occurring proteins and their homologues is around 75%, independent o f the complexity of the design procedure. Typically the lowest success rate occurs for residues such as alanine that have a high secondary s tructure functionality. Using a simple lattice model, we argue that on e possible shortcoming of the model studied may involve the coarse-gra ining of the 20 kinds of amino acids into just two effective types. Pr oteins 32:80-87, 1998. (C) 1998 Wiley-Liss, Inc.