Protein Design by Optimization of a Sequence-Structure Quality Function

Steven E. Brenner and Alan Berry

An automated procedure for protein design by optimization of a sequence-structure quality has been developed. The method selects a statistically optimal sequence for a particular structure, on the assumption that such a protein will adopt the desired structure. We present two optimization algorithms: one provides an exact optimization while the other uses a combinatorial technique for comparatively rapid results. Both are suitable for massively parallel computers. A prototype system was used to design sequences which should adopt the four-helix bundle conformation of myohemerythrin. These appear satisfactory to secondary structure and profile analysis. Detailed inspection reveals that the sequences are generally plausible but, as expected, lack some specific structural features. The design parameters provide some insight into the general determinants of protein structure.

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