Functional proteins from a random-sequence library

Abstract

Functional primordial proteins presumably originated from random sequences, but it is not known how frequently functional, or even folded, proteins occur in collections of random sequences. Here we have used in vitro selection of messenger RNA displayed proteins, in which each protein is covalently linked through its carboxy terminus to the 3′ end of its encoding mRNA1, to sample a large number of distinct random sequences. Starting from a library of 6 × 1012 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP. This selection yielded four new ATP-binding proteins that appear to be unrelated to each other or to anything found in the current databases of biological proteins. The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries2,3.

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Figure 1: In vitro selection and amplification of mRNA-displayed proteins.
Figure 2: Proportion of the mRNA-displayed protein library bound to immobilized ATP and subsequently eluted with free ATP, as a function of selection round.
Figure 3: Sequences of selected ATP-binding proteins.
Figure 4

Accession codes

Accessions

GenBank/EMBL/DDBJ

Data deposits

The DNA sequences encoding the consensus protein sequences of families A, B, C, D, 18predom and clone 18-19 have been deposited in GenBank under accession codes AF306524 to AF306529, respectively.

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Acknowledgements

We thank members of the Szostak laboratory and especially D. Wilson, G. Cho, G. Short, J. Pollard, G. Zimmermann, R. Liu, J. Urbach and R. Larralde-Ridaura for their helpful advice. This work was supported in part by the NASA Astrobiology Institute and the NIH. J.W.S. is an investigator at the Howard Hughes Medical Institute.

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Correspondence to Jack W. Szostak.

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Keefe, A., Szostak, J. Functional proteins from a random-sequence library. Nature 410, 715–718 (2001). https://doi.org/10.1038/35070613

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