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De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth Michael A. Fisher¤a, Kara L. McKinley¤b, Luke H. Bradley¤c, Sara R. Viola¤d, Michael H. Hecht* Departments of Chemistry and Molecular Biology, Princeton University, Princeton, New Jersey, United States of America Abstract A central challenge of synthetic biology is to enable the growth of living systems using parts that are not derived from nature, but designed and synthesized in the laboratory. As an initial step toward achieving this goal, we probed the ability of a collection of .106 de novo designed proteins to provide biological functions necessary to sustain cell growth. Our collection of proteins was drawn from a combinatorial library of 102-residue sequences, designed by binary patterning of polar and nonpolar residues to fold into stable 4-helix bundles. We probed the capacity of proteins from this library to function in vivo by testing their abilities to rescue 27 different knockout strains of Escherichia coli, each deleted for a conditionally essential gene. Four different strains – DserB, DgltA, DilvA, and Dfes – were rescued by specific sequences from our library. Further experiments demonstrated that a strain simultaneously deleted for all four genes was rescued by co- expression of four novel sequences. Thus, cells deleted for ,0.1% of the E. coli genome (and ,1% of the genes required for growth under nutrient-poor conditions) can be sustained by sequences designed de novo. Citation: Fisher MA, McKinley KL, Bradley LH, Viola SR, Hecht MH (2011) De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth. PLoS ONE 6(1): e15364. doi:10.1371/journal.pone.0015364 Editor: Mark Isalan, Center for Genomic Regulation, Spain Received August 26, 2010