Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

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dc.contributor.authorIlardo, Melissa
dc.contributor.authorMeringer, Markus
dc.contributor.authorFreeland, Stephen
dc.contributor.authorRasulev, Bakhtiyor
dc.contributor.authorCleaves, H. James II
dc.date.accessioned2022-03-28T14:47:29Z
dc.date.available2022-03-28T14:47:29Z
dc.date.issued2015-03-24
dc.description.abstractUsing novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.en_US
dc.description.sponsorshipM.I., H.J.C. and M.M. would like to thank the Earth-Life Science Institute for support during the conduct of this research. H.J.C., S.F. and M.M. would like to thank the NASA Astrobiology Institute Director's Discretionary Fund for grant support during the initial stages of this work. H.J.C. would like to thank the NASA-NSF Center for Chemical Evolution for material support for this work. B.R. would like to thank Prof. Jerzy Leszczynski and Interdisciplinary Center for Nanotoxicity for providing computer facilities during part of this work. All authors are indebted to the Centre for GeoGenetics for funding publication fees.en_US
dc.description.urihttps://www.nature.com/articles/srep09414en_US
dc.format.extent6 pagesen_US
dc.genrejournal articlesen_US
dc.identifierdoi:10.13016/m249lu-2t8f
dc.identifier.citationIlardo, M., Meringer, M., Freeland, S. et al. Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids. Sci Rep 5, 9414 (2015). https://doi.org/10.1038/srep09414en_US
dc.identifier.issnhttps://doi.org/10.1038/srep09414
dc.identifier.urihttp://hdl.handle.net/11603/24442
dc.language.isoen_USen_US
dc.publisherNatureen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Individualized Study Program (INDS)
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis 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.en_US
dc.rightsAttribution 4.0 International (CC BY 4.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.titleExtraordinarily Adaptive Properties of the Genetically Encoded Amino Acidsen_US
dc.typeTexten_US

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