Random Peptides Rich in Small and Disorder-Promoting Amino Acids Are Less Likely to Be Harmful

Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes born de novo from noncoding DNA. Proteins are more likely to be born from noncoding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to “first, do no harm,” we estimate fitnesses from an experiment that competed Escherichia coli lineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed in E. coli also do so in an independent data set of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins.