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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Autor*in:	Lukasz Jaroszewski [verfasserIn] Zhanwen Li [verfasserIn] S Sri Krishna [verfasserIn] Constantina Bakolitsa [verfasserIn] John Wooley [verfasserIn] Ashley M Deacon [verfasserIn] Ian A Wilson [verfasserIn] Adam Godzik [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2009

Übergeordnetes Werk:	In: PLoS Biology - Public Library of Science (PLoS), 2003, 7(2009), 9, p e1000205
Übergeordnetes Werk:	volume:7 ; year:2009 ; number:9, p e1000205

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.1371/journal.pbio.1000205

Katalog-ID:	DOAJ075156040

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allfields	10.1371/journal.pbio.1000205 doi (DE-627)DOAJ075156040 (DE-599)DOAJa505829aab6b4814b2aa0c900f886bf7 DE-627 ger DE-627 rakwb eng QH301-705.5 Lukasz Jaroszewski verfasserin aut Exploration of uncharted regions of the protein universe. 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Biology (General) Zhanwen Li verfasserin aut S Sri Krishna verfasserin aut Constantina Bakolitsa verfasserin aut John Wooley verfasserin aut Ashley M Deacon verfasserin aut Ian A Wilson verfasserin aut Adam Godzik verfasserin aut In PLoS Biology Public Library of Science (PLoS), 2003 7(2009), 9, p e1000205 (DE-627)373755597 (DE-600)2126773-X 15457885 nnns volume:7 year:2009 number:9, p e1000205 https://doi.org/10.1371/journal.pbio.1000205 kostenfrei https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7 kostenfrei https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBI kostenfrei https://doaj.org/toc/1544-9173 Journal toc kostenfrei https://doaj.org/toc/1545-7885 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2009 9, p e1000205
spelling	10.1371/journal.pbio.1000205 doi (DE-627)DOAJ075156040 (DE-599)DOAJa505829aab6b4814b2aa0c900f886bf7 DE-627 ger DE-627 rakwb eng QH301-705.5 Lukasz Jaroszewski verfasserin aut Exploration of uncharted regions of the protein universe. 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Biology (General) Zhanwen Li verfasserin aut S Sri Krishna verfasserin aut Constantina Bakolitsa verfasserin aut John Wooley verfasserin aut Ashley M Deacon verfasserin aut Ian A Wilson verfasserin aut Adam Godzik verfasserin aut In PLoS Biology Public Library of Science (PLoS), 2003 7(2009), 9, p e1000205 (DE-627)373755597 (DE-600)2126773-X 15457885 nnns volume:7 year:2009 number:9, p e1000205 https://doi.org/10.1371/journal.pbio.1000205 kostenfrei https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7 kostenfrei https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBI kostenfrei https://doaj.org/toc/1544-9173 Journal toc kostenfrei https://doaj.org/toc/1545-7885 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2009 9, p e1000205
allfields_unstemmed	10.1371/journal.pbio.1000205 doi (DE-627)DOAJ075156040 (DE-599)DOAJa505829aab6b4814b2aa0c900f886bf7 DE-627 ger DE-627 rakwb eng QH301-705.5 Lukasz Jaroszewski verfasserin aut Exploration of uncharted regions of the protein universe. 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Biology (General) Zhanwen Li verfasserin aut S Sri Krishna verfasserin aut Constantina Bakolitsa verfasserin aut John Wooley verfasserin aut Ashley M Deacon verfasserin aut Ian A Wilson verfasserin aut Adam Godzik verfasserin aut In PLoS Biology Public Library of Science (PLoS), 2003 7(2009), 9, p e1000205 (DE-627)373755597 (DE-600)2126773-X 15457885 nnns volume:7 year:2009 number:9, p e1000205 https://doi.org/10.1371/journal.pbio.1000205 kostenfrei https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7 kostenfrei https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBI kostenfrei https://doaj.org/toc/1544-9173 Journal toc kostenfrei https://doaj.org/toc/1545-7885 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2009 9, p e1000205
allfieldsGer	10.1371/journal.pbio.1000205 doi (DE-627)DOAJ075156040 (DE-599)DOAJa505829aab6b4814b2aa0c900f886bf7 DE-627 ger DE-627 rakwb eng QH301-705.5 Lukasz Jaroszewski verfasserin aut Exploration of uncharted regions of the protein universe. 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Biology (General) Zhanwen Li verfasserin aut S Sri Krishna verfasserin aut Constantina Bakolitsa verfasserin aut John Wooley verfasserin aut Ashley M Deacon verfasserin aut Ian A Wilson verfasserin aut Adam Godzik verfasserin aut In PLoS Biology Public Library of Science (PLoS), 2003 7(2009), 9, p e1000205 (DE-627)373755597 (DE-600)2126773-X 15457885 nnns volume:7 year:2009 number:9, p e1000205 https://doi.org/10.1371/journal.pbio.1000205 kostenfrei https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7 kostenfrei https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBI kostenfrei https://doaj.org/toc/1544-9173 Journal toc kostenfrei https://doaj.org/toc/1545-7885 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2009 9, p e1000205
allfieldsSound	10.1371/journal.pbio.1000205 doi (DE-627)DOAJ075156040 (DE-599)DOAJa505829aab6b4814b2aa0c900f886bf7 DE-627 ger DE-627 rakwb eng QH301-705.5 Lukasz Jaroszewski verfasserin aut Exploration of uncharted regions of the protein universe. 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. Biology (General) Zhanwen Li verfasserin aut S Sri Krishna verfasserin aut Constantina Bakolitsa verfasserin aut John Wooley verfasserin aut Ashley M Deacon verfasserin aut Ian A Wilson verfasserin aut Adam Godzik verfasserin aut In PLoS Biology Public Library of Science (PLoS), 2003 7(2009), 9, p e1000205 (DE-627)373755597 (DE-600)2126773-X 15457885 nnns volume:7 year:2009 number:9, p e1000205 https://doi.org/10.1371/journal.pbio.1000205 kostenfrei https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7 kostenfrei https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBI kostenfrei https://doaj.org/toc/1544-9173 Journal toc kostenfrei https://doaj.org/toc/1545-7885 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2009 9, p e1000205
language	English
source	In PLoS Biology 7(2009), 9, p e1000205 volume:7 year:2009 number:9, p e1000205
sourceStr	In PLoS Biology 7(2009), 9, p e1000205 volume:7 year:2009 number:9, p e1000205
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Biology (General)
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container_title	PLoS Biology
authorswithroles_txt_mv	Lukasz Jaroszewski @@aut@@ Zhanwen Li @@aut@@ S Sri Krishna @@aut@@ Constantina Bakolitsa @@aut@@ John Wooley @@aut@@ Ashley M Deacon @@aut@@ Ian A Wilson @@aut@@ Adam Godzik @@aut@@
publishDateDaySort_date	2009-01-01T00:00:00Z
hierarchy_top_id	373755597
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callnumber-first	Q - Science
author	Lukasz Jaroszewski
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topic_title	QH301-705.5 Exploration of uncharted regions of the protein universe
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title	Exploration of uncharted regions of the protein universe.
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title_full	Exploration of uncharted regions of the protein universe
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title_sort	exploration of uncharted regions of the protein universe
callnumber	QH301-705.5
title_auth	Exploration of uncharted regions of the protein universe.
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Exploration of uncharted regions of the protein universe.
url	https://doi.org/10.1371/journal.pbio.1000205 https://doaj.org/article/a505829aab6b4814b2aa0c900f886bf7 https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19787035/?tool=EBI https://doaj.org/toc/1544-9173 https://doaj.org/toc/1545-7885
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