Exploration of uncharted regions of the protein universe.

The genome projects have unearthed an enormous diversity of genes of unknown function that are still awaiting biological and biochemical characterization. These genes, as most others, can be grouped into families based on sequence similarity. The PFAM database currently contains over 2,200 such fami...

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Autores principales:	Lukasz Jaroszewski, Zhanwen Li, S Sri Krishna, Constantina Bakolitsa, John Wooley, Ashley M Deacon, Ian A Wilson, Adam Godzik
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7
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spelling	oai:doaj.org-article:a505829aab6b4814b2aa0c900f886bf72021-11-25T05:34:00ZExploration of uncharted regions of the protein universe.1544-91731545-788510.1371/journal.pbio.1000205https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf72009-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBIhttps://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885The genome projects have unearthed an enormous diversity of genes of unknown function that are still awaiting biological and biochemical characterization. These genes, as most others, can be grouped into families based on sequence similarity. The PFAM database currently contains over 2,200 such families, referred to as domains of unknown function (DUF). In a coordinated effort, the four large-scale centers of the NIH Protein Structure Initiative have determined the first three-dimensional structures for more than 250 of these DUF families. Analysis of the first 248 reveals that about two thirds of the DUF families likely represent very divergent branches of already known and well-characterized families, which allows hypotheses to be formulated about their biological function. The remainder can be formally categorized as new folds, although about one third of these show significant substructure similarity to previously characterized folds. These results infer that, despite the enormous increase in the number and the diversity of new genes being uncovered, the fold space of the proteins they encode is gradually becoming saturated. The previously unexplored sectors of the protein universe appear to be primarily shaped by extreme diversification of known protein families, which then enables organisms to evolve new functions and adapt to particular niches and habitats. Notwithstanding, these DUF families still constitute the richest source for discovery of the remaining protein folds and topologies.Lukasz JaroszewskiZhanwen LiS Sri KrishnaConstantina BakolitsaJohn WooleyAshley M DeaconIan A WilsonAdam GodzikPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 7, Iss 9, p e1000205 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Lukasz Jaroszewski Zhanwen Li S Sri Krishna Constantina Bakolitsa John Wooley Ashley M Deacon Ian A Wilson Adam Godzik Exploration of uncharted regions of the protein universe.
description	The genome projects have unearthed an enormous diversity of genes of unknown function that are still awaiting biological and biochemical characterization. These genes, as most others, can be grouped into families based on sequence similarity. The PFAM database currently contains over 2,200 such families, referred to as domains of unknown function (DUF). In a coordinated effort, the four large-scale centers of the NIH Protein Structure Initiative have determined the first three-dimensional structures for more than 250 of these DUF families. Analysis of the first 248 reveals that about two thirds of the DUF families likely represent very divergent branches of already known and well-characterized families, which allows hypotheses to be formulated about their biological function. The remainder can be formally categorized as new folds, although about one third of these show significant substructure similarity to previously characterized folds. These results infer that, despite the enormous increase in the number and the diversity of new genes being uncovered, the fold space of the proteins they encode is gradually becoming saturated. The previously unexplored sectors of the protein universe appear to be primarily shaped by extreme diversification of known protein families, which then enables organisms to evolve new functions and adapt to particular niches and habitats. Notwithstanding, these DUF families still constitute the richest source for discovery of the remaining protein folds and topologies.
format	article
author	Lukasz Jaroszewski Zhanwen Li S Sri Krishna Constantina Bakolitsa John Wooley Ashley M Deacon Ian A Wilson Adam Godzik
author_facet	Lukasz Jaroszewski Zhanwen Li S Sri Krishna Constantina Bakolitsa John Wooley Ashley M Deacon Ian A Wilson Adam Godzik
author_sort	Lukasz Jaroszewski
title	Exploration of uncharted regions of the protein universe.
title_short	Exploration of uncharted regions of the protein universe.
title_full	Exploration of uncharted regions of the protein universe.
title_fullStr	Exploration of uncharted regions of the protein universe.
title_full_unstemmed	Exploration of uncharted regions of the protein universe.
title_sort	exploration of uncharted regions of the protein universe.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7
work_keys_str_mv	AT lukaszjaroszewski explorationofunchartedregionsoftheproteinuniverse AT zhanwenli explorationofunchartedregionsoftheproteinuniverse AT ssrikrishna explorationofunchartedregionsoftheproteinuniverse AT constantinabakolitsa explorationofunchartedregionsoftheproteinuniverse AT johnwooley explorationofunchartedregionsoftheproteinuniverse AT ashleymdeacon explorationofunchartedregionsoftheproteinuniverse AT ianawilson explorationofunchartedregionsoftheproteinuniverse AT adamgodzik explorationofunchartedregionsoftheproteinuniverse
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Exploration of uncharted regions of the protein universe.

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