The origin, evolution and structure of the protein world

The Biochemical Journal
Gustavo Caetano-AnollesJay E Mittenthal

Abstract

Contemporary protein architectures can be regarded as molecular fossils, historical imprints that mark important milestones in the history of life. Whereas sequences change at a considerable pace, higher-order structures are constrained by the energetic landscape of protein folding, the exploration of sequence and structure space, and complex interactions mediated by the proteostasis and proteolytic machineries of the cell. The survey of architectures in the living world that was fuelled by recent structural genomic initiatives has been summarized in protein classification schemes, and the overall structure of fold space explored with novel bioinformatic approaches. However, metrics of general structural comparison have not yet unified architectural complexity using the 'shared and derived' tenet of evolutionary analysis. In contrast, a shift of focus from molecules to proteomes and a census of protein structure in fully sequenced genomes were able to uncover global evolutionary patterns in the structure of proteins. Timelines of discovery of architectures and functions unfolded episodes of specialization, reductive evolutionary tendencies of architectural repertoires in proteomes and the rise of modularity in the protein world...Continue Reading

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Citations

Jul 30, 2009·Journal of Molecular Evolution·Feng-Jie Sun, Gustavo Caetano-Anollés
Nov 18, 2010·Journal of Molecular Evolution·Derek Caetano-AnollésGustavo Caetano-Anollés
Jan 3, 2012·Journal of Molecular Evolution·Gustavo Caetano-AnollésDerek Caetano-Anollés
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Sep 17, 2009·Nature Reviews. Molecular Cell Biology·Catherine L WorthTom L Blundell
May 26, 2010·Proceedings of the National Academy of Sciences of the United States of America·Christopher L DupontGustavo Caetano-Anollés
Jun 27, 2012·Journal of Biomolecular Structure & Dynamics·Hong-Yu ZhangGustavo Caetano-Anollés
Apr 27, 2010·Molecular Biology and Evolution·Kyung Mo Kim, Gustavo Caetano-Anollés
Jun 14, 2013·Biology Letters·Chia-Hsin HsuMing-Jing Hwang
Feb 6, 2013·Molecular and Cellular Biology·Anna TravesaCurt Wittenberg
Mar 26, 2010·BMC Bioinformatics·Feng-Jie Sun, Gustavo Caetano-Anollés
May 27, 2011·BMC Evolutionary Biology·Kyung Mo Kim, Gustavo Caetano-Anollés
Apr 5, 2013·PLoS Computational Biology·Syed Abbas Bukhari, Gustavo Caetano-Anollés
Feb 7, 2014·PLoS Computational Biology·Arshan NasirGustavo Caetano-Anollés
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May 31, 2014·PLoS Computational Biology·Neetika NathGustavo Caetano-Anollés
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Jul 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Minglei WangGustavo Caetano-Anollés
Aug 29, 2014·Journal of the Royal Society, Interface·Tobias Sikosek, Hue Sun Chan
Apr 12, 2016·Communicative & Integrative Biology·Gustavo Caetano-Anollés
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Aug 19, 2014·Journal of Molecular Evolution·Kyung Mo KimGustavo Caetano-Anollés
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