De Novo Proteins from Random Sequences Through in Vitro Evolution

Overview

Journal Curr Opin Struct Biol

Date 2021 Jan 31

PMID 33517151

Citations 8

Authors

Cher Ling Tong

Kun-Hwa Lee

Burckhard Seelig

Affiliations

Soon will be listed here.

Abstract

Natural proteins are the result of billions of years of evolution. The earliest predecessors of today's proteins are believed to have emerged from random polypeptides. While we have no means to determine how this process exactly happened, there is great interest in understanding how it reasonably could have happened. We are reviewing how researchers have utilized in vitro selection and molecular evolution methods to investigate plausible scenarios for the emergence of early functional proteins. The studies range from analyzing general properties and structural features of unevolved random polypeptides to isolating de novo proteins with specific functions from synthetic randomized sequence libraries or generating novel proteins by combining evolution with rational design. While the results are exciting, more work is needed to fully unravel the mechanisms that seeded protein-dominated biology.

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References

Baker D . An exciting but challenging road ahead for computational enzyme design. Protein Sci. 2010; 19(10):1817-9. PMC: 2998717. DOI: 10.1002/pro.481. View

Hecht M, Zarzhitsky S, Karas C, Chari S . Are natural proteins special? Can we do that?. Curr Opin Struct Biol. 2018; 48:124-132. DOI: 10.1016/j.sbi.2017.11.009. View

Davidson A, Sauer R . Folded proteins occur frequently in libraries of random amino acid sequences. Proc Natl Acad Sci U S A. 1994; 91(6):2146-50. PMC: 43327. DOI: 10.1073/pnas.91.6.2146. View

Newton M, Cabezas-Perusse Y, Tong C, Seelig B . Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol. 2020; 9(2):181-190. PMC: 8203280. DOI: 10.1021/acssynbio.9b00419. View

Digianantonio K, Hecht M . A protein constructed de novo enables cell growth by altering gene regulation. Proc Natl Acad Sci U S A. 2016; 113(9):2400-5. PMC: 4780649. DOI: 10.1073/pnas.1600566113. View

Wang M, Hecht M . A Completely ATPase from Combinatorial Protein Design. J Am Chem Soc. 2020; 142(36):15230-15234. DOI: 10.1021/jacs.0c02954. View

Lane M, Seelig B . Advances in the directed evolution of proteins. Curr Opin Chem Biol. 2014; 22:129-36. PMC: 4253873. DOI: 10.1016/j.cbpa.2014.09.013. View

Kang S, Chen B, Tian T, Jia X, Chu X, Liu R . ATP selection in a random peptide library consisting of prebiotic amino acids. Biochem Biophys Res Commun. 2015; 466(3):400-5. DOI: 10.1016/j.bbrc.2015.09.038. View

Sri Krishna S, Grishin N . Structurally analogous proteins do exist!. Structure. 2004; 12(7):1125-7. DOI: 10.1016/j.str.2004.06.004. View

10.

Roberts R, Szostak J . RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A. 1997; 94(23):12297-302. PMC: 24913. DOI: 10.1073/pnas.94.23.12297. View

11.

Seelig B, Szostak J . Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature. 2007; 448(7155):828-31. PMC: 4476047. DOI: 10.1038/nature06032. View

12.

Randall R, Radford C, Roof K, Natarajan D, Gaucher E . An experimental phylogeny to benchmark ancestral sequence reconstruction. Nat Commun. 2016; 7:12847. PMC: 5027606. DOI: 10.1038/ncomms12847. View

13.

LaBean T, Butt T, Kauffman S, Schultes E . Protein folding absent selection. Genes (Basel). 2014; 2(3):608-26. PMC: 3927614. DOI: 10.3390/genes2030608. View

14.

Tretyachenko V, Vymetal J, Bednarova L, Kopecky Jr V, Hofbauerova K, Jindrova H . Random protein sequences can form defined secondary structures and are well-tolerated in vivo. Sci Rep. 2017; 7(1):15449. PMC: 5684393. DOI: 10.1038/s41598-017-15635-8. View

15.

Chiarabelli C, Vrijbloed J, Thomas R, Luisi P . Investigation of de novo totally random biosequences, Part I: A general method for in vitro selection of folded domains from a random polypeptide library displayed on phage. Chem Biodivers. 2006; 3(8):827-39. DOI: 10.1002/cbdv.200690087. View

16.

Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N . Evolution of a designed retro-aldolase leads to complete active site remodeling. Nat Chem Biol. 2013; 9(8):494-8. PMC: 3720730. DOI: 10.1038/nchembio.1276. View

17.

Longo L, Despotovic D, Weil-Ktorza O, Walker M, Jablonska J, Fridmann-Sirkis Y . Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. Proc Natl Acad Sci U S A. 2020; 117(27):15731-15739. PMC: 7355028. DOI: 10.1073/pnas.2001989117. View

18.

Kiss G, Celebi-Olcum N, Moretti R, Baker D, Houk K . Computational enzyme design. Angew Chem Int Ed Engl. 2013; 52(22):5700-25. DOI: 10.1002/anie.201204077. View

19.

Obexer R, Godina A, Garrabou X, Mittl P, Baker D, Griffiths A . Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nat Chem. 2016; 9(1):50-56. DOI: 10.1038/nchem.2596. View

20.

Narunsky A, Kessel A, Solan R, Alva V, Kolodny R, Ben-Tal N . On the evolution of protein-adenine binding. Proc Natl Acad Sci U S A. 2020; 117(9):4701-4709. PMC: 7060716. DOI: 10.1073/pnas.1911349117. View