Computer-assisted re-design of spectrin SH3 residue clusters

We have developed a protein design computer program, called Perla, which pe rforms searches in sequence space to uncover optimal amino acid sequences f or desired protein three-dimensional structures. Optimal sequences are loca lised at the minima of a sequence-structure energy landscape defined using a complex scoring function (an all-atom molecular mechanics force field plu s statistical terms including entropy and solvation) measured with respect to a reference state simulating a denatured protein. Sequence choices event ually optimise side chain packing, secondary structure propensities, and hy drogen bonding and electrostatics interactions. Perla was used to re-design clusters of residues of the SH3 domain of alpha -spectrin. Several mutant proteins were produced and characterised. Some of our designed proteins hav e significantly higher stabilities (stability enhancements about 0.25, 0.70 and 1.0 kcal mol(-1)) than the wild-type protein. These successful protein re-designs, and similar examples found in the literature, establish the qu ality of the structure-based computational approach to protein design. (C) 2001 Published by Elsevier Science B.V.