Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds

BMC Evolutionary Biology
Armando D Solis

Abstract

There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding. Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure to assess how well the prebiotic amino acid set preserves fold information against all other possible ten-amino acid sets. An extensive virtual mutagenesis procedure revealed that the prebiotic set excellently preserves sequence-dependent information regarding both backbone conformation and tertiary contact matrix of proteins. We observed that information retention is fold-class dependent: the prebiotic set sufficiently encodes the structure space of α/β and α + β folds, and to a lesser extent, of all-α and all-β folds. The prebi...Continue Reading

References

Jan 1, 1976·Annual Review of Microbiology·R A Jensen
Jan 1, 1981·Journal of Molecular Evolution·A L Weber, S L Miller
Apr 1, 1995·Current Opinion in Structural Biology·S H Bryant, S F Altschul
Sep 1, 1994·Protein Science : a Publication of the Protein Society·R S DeWitte, E I Shakhnovich
Jan 23, 1996·Proceedings of the National Academy of Sciences of the United States of America·V I AbkevichE I Shakhnovich
Oct 23, 1997·Nature Structural Biology·D S RiddleD Baker
Mar 24, 1999·Trends in Biochemical Sciences·R L Baldwin, G D Rose
Jun 14, 2000·Journal of Molecular Biology·Y I WolfE V Koonin
Mar 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·J A SilvermanP B Harbury
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Francisco MeloAndrej Sali
Jul 4, 2002·Molecular & Cellular Proteomics : MCP·Dawn J Brooks, Jacques R Fresco
Jul 12, 2002·Proteins·Armando D Solis, S Rackovsky
Oct 4, 2002·Proceedings of the National Academy of Sciences of the United States of America·Satoshi AkanumaShigeyuki Yokoyama
Jul 4, 2003·Genome Research·Gustavo Caetano-Anollés, Derek Caetano-Anollés
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Jul 31, 1959·Science·S L MILLER, H C UREY
Jun 25, 2004·Journal of Biomolecular Structure & Dynamics·E N Trifonov
Jan 22, 2005·Nature·I King JordanShamil Sunyaev
Jun 18, 2005·Bioinformatics·Henry F WinstanleyCharlotte M Deane
Jul 8, 2005·Proteins·Sanne Abeln, Charlotte M Deane
Oct 6, 2005·Journal of Molecular Evolution·Yehoshua Sobolevsky, Edward N Trifonov
Nov 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·George D RoseAmos Maritan
Jan 9, 2007·Journal of Biomolecular Structure & Dynamics·Hong-Fang Ji, Hong-Yu Zhang
Nov 16, 2007·Proteins·Armando D Solis, S Rackovsky
Dec 13, 2007·Biochemical and Biophysical Research Communications·Bin-Guang MaHong-Yu Zhang
Mar 5, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Scott C EvansAndrew S Torres
Sep 17, 2008·Current Opinion in Chemical Biology·Laura K HencheyParamjit S Arora
Oct 18, 2008·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Dimas A M ZaiaHenrique De Santana
Jan 13, 2009·The Biochemical Journal·Gustavo Caetano-AnollésJay E Mittenthal
Jan 29, 2009·Protein Science : a Publication of the Protein Society·Mariejoy Therese JumawidHisakazu Mihara
Apr 11, 2009·Science·Nobuhiko Tokuriki, Dan S Tawfik
Sep 19, 2009·Journal of Theoretical Biology·Peter van der GulikMarianne Rooman
Mar 17, 2010·BMC Evolutionary Biology·Xiaoxia LiuYufen Zhao
Dec 15, 2010·Journal of Molecular Evolution·Richard W Jobson, Yin-Long Qiu
Mar 26, 2011·Astrobiology·Gayle K Philip, Stephen J Freeland
Dec 14, 2011·Protein Engineering, Design & Selection : PEDS·Allissia A GilmartinThomas Krey
Jul 10, 2012·Archives of Biochemistry and Biophysics·Liam M Longo, Michael Blaber

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Citations

Oct 24, 2019·Interface Focus·E James Milner-White
Sep 22, 2020·Bioinformatics·Vyacheslav TretyachenkoKlára Hlouchová
Dec 1, 2020·Trends in Biochemical Sciences·Bernd Moosmann
Mar 20, 2021·Protein Science : a Publication of the Protein Society·Mikhail MakarovKlára Hlouchová

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Methods Mentioned

BETA
protein folding
X-ray

Software Mentioned

R
PISCES

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