Random protein sequences can form defined secondary structures and are well-tolerated in vivo

Abstract

The protein sequences found in nature represent a tiny fraction of the potential sequences that could be constructed from the 20-amino-acid alphabet. To help define the properties that shaped proteins to stand out from the space of possible alternatives, we conducted a systematic computational and experimental exploration of random (unevolved) sequences in comparison with biological proteins. In our study, combinations of secondary structure, disorder, and aggregation predictions are accompanied by experimental characterization of selected proteins. We found that the overall secondary structure and physicochemical properties of random and biological sequences are very similar. Moreover, random sequences can be well-tolerated by living cells. Contrary to early hypotheses about the toxicity of random and disordered proteins, we found that random sequences with high disorder have low aggregation propensity (unlike random sequences with high structural content) and were particularly well-tolerated. This direct structure content/aggregation propensity dependence differentiates random and biological proteins. Our study indicates that while random sequences can be both structured and disordered, the properties of the latter make them better suited as progenitors (in both in vivo and in vitro settings) for further evolution of complex, soluble, three-dimensional scaffolds that can perform specific biochemical tasks.

An exploration of ambigrammatic sequences in narnaviruses

“…The translated rORFs of ambigrammatic narnaviruses are predicted to have median α-helical and β -strand contents of 22 % and 12 % respectively (calculated using JPred4, 35 ). This degree of secondary structure is consistent with a structured (or folded) protein, but a significant presence of secondary structure can also be observed in random amino-acid sequences 36 . We further note that the isoelectric point (PI) of the RdRp is high (median 10.4, range 7.7-11.6 for sequences >2 kb in Figure 3), due to a high frequency of Arg, a basic amino acid (median 9.9 %, range 6-13.3 %).…”

Genetic Code Evolution Investigated through the Synthesis and Characterisation of Proteins from Reduced‐Alphabet Libraries

“…In another study of random sequence proteins of a similar length to those described here, Tretyachenko et al. reported that 53 % of random 20 AA sequences with similar amino acid usage to modern proteins could be expressed in E. coli (8/15) . Finally, a 20 AA random library of proteins 95 amino acids in length created by Urabe and colleagues contained only 20 % solubly expressed variants (as detected by western blot) .…”

Gene birth contributes to structural disorder encoded by overlapping genes

“…Young genes are known to have higher ISD than old genes, with high ISD at the moment of gene birth facilitating the process [52], perhaps because cells tolerate them better [48]. Domains that were more recently born de novo also have higher ISD [3], [5], [14], [26].…”