Science, Vol.282, No.5393, 1462-1467, 1998
High-resolution protein design with backbone freedom
Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of or-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form ct-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.
Keywords:AUTOMATED SEQUENCE SELECTION, DE-NOVO DESIGN, COILED-COILS;ALPHA-HELIX, HYDROGEN-EXCHANGE, ENERGY, CONFORMATION;OPTIMIZATION, PREDICTION, DYNAMICS