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Extraordinarily adaptive properties of the genetically encoded amino acids

Ilardo, Melissa and Meringer, Markus and Freeland, Stephen J. and Rasulev, Baktiyour and Cleaves, H. James (2015) Extraordinarily adaptive properties of the genetically encoded amino acids. Scientific Reports, 5, pp. 1-6. Nature Publishing Group. ISSN 2045-2322

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Official URL: http://www.nature.com/srep/2015/150324/srep09414/full/srep09414.html

Abstract

Using 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.

Item URL in elib:https://elib.dlr.de/96670/
Document Type:Article
Title:Extraordinarily adaptive properties of the genetically encoded amino acids
Authors:
AuthorsInstitution or Email of AuthorsAuthors ORCID iD
Ilardo, MelissaUCPHUNSPECIFIED
Meringer, MarkusMarkus.Meringer (at) dlr.deUNSPECIFIED
Freeland, Stephen J.University of Hawaii, NASA Astribiology InstituteUNSPECIFIED
Rasulev, BaktiyourNDSUUNSPECIFIED
Cleaves, H. JamesEarth-Life Science Institute, Tokyo Institute of TechnologyUNSPECIFIED
Date:24 March 2015
Journal or Publication Title:Scientific Reports
Refereed publication:Yes
Open Access:Yes
Gold Open Access:Yes
In SCOPUS:Yes
In ISI Web of Science:Yes
Volume:5
Page Range:pp. 1-6
Publisher:Nature Publishing Group
ISSN:2045-2322
Status:Published
Keywords:Computational models, Origin of life, Synthetic biology
HGF - Research field:Aeronautics, Space and Transport
HGF - Program:Space
HGF - Program Themes:Earth Observation
DLR - Research area:Raumfahrt
DLR - Program:R EO - Erdbeobachtung
DLR - Research theme (Project):R - Vorhaben Atmosphären- und Klimaforschung
Location: Oberpfaffenhofen
Institutes and Institutions:Remote Sensing Technology Institute > Atmospheric Processors
Deposited By: Meringer, Dr.rer.nat. Markus
Deposited On:16 Jun 2015 10:21
Last Modified:17 Jul 2015 15:23

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