Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
| dc.contributor.author | Ilardo, Melissa | |
| dc.contributor.author | Bose, Rudrarup | |
| dc.contributor.author | Meringer, Markus | |
| dc.contributor.author | Rasulev, Bakhtiyor | |
| dc.contributor.author | Grefenstette, Natalie | |
| dc.contributor.author | Stephenson, James | |
| dc.contributor.author | Freeland, Stephen | |
| dc.contributor.author | Gillams, Richard J. | |
| dc.contributor.author | Butch, Christopher J. | |
| dc.contributor.author | Cleaves II, James | |
| dc.date.accessioned | 2019-10-09T14:39:58Z | |
| dc.date.available | 2019-10-09T14:39:58Z | |
| dc.date.issued | 2019-08-28 | |
| dc.description.abstract | Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded amino acids could have comprised the earlier sets. We explore the hypothesis that the CAAs were selectively fixed due to their unique adaptive chemical properties, which facilitate folding, catalysis, and solubility of proteins, and gave adaptive value to organisms able to encode them. Specifically, we studied in silico hypothetical CAA sets of 3–19 amino acids comprised of 1913 structurally diverse α-amino acids, exploring the adaptive value of their combined physicochemical properties relative to those of the modern CAA set. We find that even hypothetical sets containing modern CAA members are especially adaptive; it is difficult to find sets even among a large choice of alternatives that cover the chemical property space more amply. These results suggest that each time a CAA was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs. | en_US |
| dc.description.sponsorship | The authors would like to thank the Earth-Life Science Institute (ELSI) for support during the preparation of this work, and EON for generous travel support for RB, NG, MI, MM and BR. This work was also supported by JSPS KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas “Hadean Bioscience”, Grant Number JP26106003, and by the ELSI Origins Network (EON), which is supported by a grant from the John Templeton Foundation. The opinions expressed in this publication are those of the author(s) and do not necessarily reflect the views of the John Templeton Foundation. | en_US |
| dc.format.extent | 9 pages | en_US |
| dc.genre | journal articles | en_US |
| dc.identifier | doi:10.13016/m2qibp-upc9 | |
| dc.identifier.citation | Ilardo, Melissa ; Bose, Rudrarup ; Meringer, Markus ; Rasulev, Bakhtiyor ; Grefenstette, Natalie ; Stephenson, James ; Freeland, Stephen ; Gillams, Richard J.; Butch, Christopher J. ; Cleaves, H. James ; Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets ; Scientific Reports 12468,9 ; https://doi.org/10.1038/s41598-019-47574-x ; | en_US |
| dc.identifier.uri | https://doi.org/10.1038/s41598-019-47574-x | |
| dc.identifier.uri | http://hdl.handle.net/11603/14995 | |
| dc.language.iso | en_US | en_US |
| dc.publisher | natureresearch | en_US |
| dc.relation.isAvailableAt | The University of Maryland, Baltimore County (UMBC) | |
| dc.relation.ispartof | UMBC Individualized Study Program (INDS) | |
| dc.relation.ispartof | UMBC Faculty Collection | |
| dc.rights | This item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author. | |
| dc.rights | Attribution 4.0 International (CC BY 4.0) | * |
| dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | * |
| dc.subject | Astrobiology | en_US |
| dc.subject | Cheminformatics | en_US |
| dc.subject | Computational chemistry | en_US |
| dc.subject | Chemical origin of life | en_US |
| dc.subject | Proteins | en_US |
| dc.title | Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets | en_US |
| dc.type | Text | en_US |