Exploring fold space preferences of new-born and ancient protein superfamilies.

The evolution of proteins is one of the fundamental processes that has delivered the diversity and complexity of life we see around ourselves today. While we tend to define protein evolution in terms of sequence level mutations, insertions and deletions, it is hard to translate these processes to a...

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Autores principales:	Hannah Edwards, Sanne Abeln, Charlotte M Deane
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/281d059860064d10a2ffe0c469bf37a2
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spelling	oai:doaj.org-article:281d059860064d10a2ffe0c469bf37a22021-11-18T05:53:23ZExploring fold space preferences of new-born and ancient protein superfamilies.1553-734X1553-735810.1371/journal.pcbi.1003325https://doaj.org/article/281d059860064d10a2ffe0c469bf37a22013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24244135/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The evolution of proteins is one of the fundamental processes that has delivered the diversity and complexity of life we see around ourselves today. While we tend to define protein evolution in terms of sequence level mutations, insertions and deletions, it is hard to translate these processes to a more complete picture incorporating a polypeptide's structure and function. By considering how protein structures change over time we can gain an entirely new appreciation of their long-term evolutionary dynamics. In this work we seek to identify how populations of proteins at different stages of evolution explore their possible structure space. We use an annotation of superfamily age to this space and explore the relationship between these ages and a diverse set of properties pertaining to a superfamily's sequence, structure and function. We note several marked differences between the populations of newly evolved and ancient structures, such as in their length distributions, secondary structure content and tertiary packing arrangements. In particular, many of these differences suggest a less elaborate structure for newly evolved superfamilies when compared with their ancient counterparts. We show that the structural preferences we report are not a residual effect of a more fundamental relationship with function. Furthermore, we demonstrate the robustness of our results, using significant variation in the algorithm used to estimate the ages. We present these age estimates as a useful tool to analyse protein populations. In particularly, we apply this in a comparison of domains containing greek key or jelly roll motifs.Hannah EdwardsSanne AbelnCharlotte M DeanePublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 11, p e1003325 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Hannah Edwards Sanne Abeln Charlotte M Deane Exploring fold space preferences of new-born and ancient protein superfamilies.
description	The evolution of proteins is one of the fundamental processes that has delivered the diversity and complexity of life we see around ourselves today. While we tend to define protein evolution in terms of sequence level mutations, insertions and deletions, it is hard to translate these processes to a more complete picture incorporating a polypeptide's structure and function. By considering how protein structures change over time we can gain an entirely new appreciation of their long-term evolutionary dynamics. In this work we seek to identify how populations of proteins at different stages of evolution explore their possible structure space. We use an annotation of superfamily age to this space and explore the relationship between these ages and a diverse set of properties pertaining to a superfamily's sequence, structure and function. We note several marked differences between the populations of newly evolved and ancient structures, such as in their length distributions, secondary structure content and tertiary packing arrangements. In particular, many of these differences suggest a less elaborate structure for newly evolved superfamilies when compared with their ancient counterparts. We show that the structural preferences we report are not a residual effect of a more fundamental relationship with function. Furthermore, we demonstrate the robustness of our results, using significant variation in the algorithm used to estimate the ages. We present these age estimates as a useful tool to analyse protein populations. In particularly, we apply this in a comparison of domains containing greek key or jelly roll motifs.
format	article
author	Hannah Edwards Sanne Abeln Charlotte M Deane
author_facet	Hannah Edwards Sanne Abeln Charlotte M Deane
author_sort	Hannah Edwards
title	Exploring fold space preferences of new-born and ancient protein superfamilies.
title_short	Exploring fold space preferences of new-born and ancient protein superfamilies.
title_full	Exploring fold space preferences of new-born and ancient protein superfamilies.
title_fullStr	Exploring fold space preferences of new-born and ancient protein superfamilies.
title_full_unstemmed	Exploring fold space preferences of new-born and ancient protein superfamilies.
title_sort	exploring fold space preferences of new-born and ancient protein superfamilies.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/281d059860064d10a2ffe0c469bf37a2
work_keys_str_mv	AT hannahedwards exploringfoldspacepreferencesofnewbornandancientproteinsuperfamilies AT sanneabeln exploringfoldspacepreferencesofnewbornandancientproteinsuperfamilies AT charlottemdeane exploringfoldspacepreferencesofnewbornandancientproteinsuperfamilies
_version_	1718424655171158016

Exploring fold space preferences of new-born and ancient protein superfamilies.

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