Structural constraints and emergence of sequence patterns in protein evolution

Molecular Biology and Evolution
Gustavo Parisi, Julian Echave

Abstract

The aim of this work was to study the relationship between structure conservation and sequence divergence in protein evolution. To this end, we developed a model of structurally constrained protein evolution (SCPE) in which trial sequences, generated by random mutations at gene level, are selected against departure from a reference three-dimensional structure. Since at the mutational level SCPE is completely unbiased, any emergent sequence pattern will be due exclusively to structural constraints. In this first report, it is shown that SCPE correctly predicts the characteristic hexapeptide motif of the left-handed parallel beta helix (LbetaH) domain of UDP-N-acetylglucosamine acyltransferases (LpxA).

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Citations

Dec 18, 2004·Plant Molecular Biology·Gustavo ParisiEduardo Zabaleta
Sep 13, 2007·Heredity·M Anisimova, D A Liberles
Dec 8, 2005·Bioinformatics·Tanja Gesell, Arndt von Haeseler
Apr 23, 2009·Molecular Biology and Evolution·Nicolas RodrigueNicolas Lartillot
Feb 18, 2010·Molecular Biology and Evolution·Claudia L KleinmanHervé Philippe
Jun 5, 2013·Nucleic Acids Research·Nicolas PalopoliGustavo Parisi
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sang Chul ChoiJeffrey L Thorne
Jul 1, 2006·BMC Bioinformatics·Claudia L KleinmanNicolas Lartillot
Jun 16, 2010·BMC Evolutionary Biology·Stefanie Gabriele SammetMarkus Porto
Sep 11, 2009·BMC Evolutionary Biology·Cécile BonnardNicolas Lartillot
Oct 5, 2007·Algorithms for Molecular Biology : AMB·Rodrigo Gouveia-Oliveira, Anders G Pedersen
Jan 2, 2008·PLoS Computational Biology·Sebastian BassiGustavo Parisi
Apr 22, 2009·PLoS Computational Biology·Jesse D Bloom, Matthew J Glassman
May 14, 2010·PLoS Computational Biology·Raul MendezUgo Bastolla
Apr 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Albert Y Lau, Daniel I Chasman
Dec 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Orr AshenbergJesse D Bloom
Jul 19, 2011·Journal of Molecular Biology·Simon G WilliamsSimon C Lovell
Jun 26, 2008·Gene·Sandra MaguidJulian Echave
Jun 19, 2007·Current Opinion in Structural Biology·Jeffrey L Thorne
Mar 28, 2009·Proteins·Yan Yuan Tseng, Wen-Hsiung Li
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Buyong Ma, Ruth Nussinov
Apr 25, 2012·Protein Science : a Publication of the Protein Society·David A LiberlesSimon Whelan
Mar 8, 2005·Biophysical Journal·Sandra MaguidJulian Echave
Mar 10, 2015·Current Opinion in Structural Biology·Gustavo ParisiCristina Marino-Buslje
Apr 4, 2015·Molecular Biology and Evolution·Miguel ArenasUgo Bastolla
Feb 28, 2002·Molecular Biology and Evolution·María Silvina FornasariJulian Echave
Mar 3, 2012·Molecular Biology and Evolution·Tina KoestlerIngo Ebersberger
Mar 8, 2012·Molecular Biology and Evolution·Ezequiel JuritzGustavo Parisi
Mar 17, 2017·Annual Review of Biophysics·Julian Echave, Claus O Wilke
Feb 12, 2008·Journal of Child Neurology·Jelena MaletkovicAdeline Vanderver
May 20, 2015·Evolutionary Bioinformatics Online·Kuangyu WangJeffrey L Thorne
Mar 27, 2004·FEBS Letters·Gustavo ParisiJulián Echave
Sep 13, 2007·Systematic Biology·Nicolas RodrigueNicolas Lartillot

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