De novo protein design. I. In search of stability and specificity

We have developed a fully automated protein design strategy that works on t he entire sequence of the protein and uses a full atom representation. At e ach step of the procedure, an all-atom model of the protein is built using the template protein structure and the current designed sequence. The energ y of the model is used to drive a Monte Carlo optimization in sequence spac e: random moves are either accepted or rejected based on the Metropolis cri terion. We rely on the physical forces that stabilize native protein struct ures to choose the optimum sequence. Our energy function includes van der W aals interactions, electrostatics and an environment free energy. Successfu l protein design should be specific and generate a sequence compatible with the template fold and incompatible with competing folds. We impose specifi city by maintaining the amino acid composition constant, based on the rando m energy model. The specificity of the optimized sequence is tested by fold recognition techniques. Successful sequence designs for the B1 domain of p rotein G, for the lambda repressor and for sperm whale myoglobin are presen ted. We show that each additional term of the energy function improves the performance of our design procedure: the van der Waals term ensures correct packing, the electrostatics term increases the specificity for the correct native fold, and the environment solvation term ensures a correct pattern of buried hydrophobic and exposed hydrophilic residues. For the globin fami ly, we show that we can design a protein sequence that is stable in the myo globin fold, yet incompatible with the very similar hemoglobin fold. (C) 19 99 Academic Press.