Covering complete proteomes with X-ray structures: A current snapshot
Abstract
Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-raymore »
- Authors:
-
- University of Alberta, Edmonton, Alberta (Canada). Electrical and Computer Engineering.
- Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structureal Genomics.
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1212766
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D: Biological Crystallography (Online)
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 70; Journal Issue: 11; Journal ID: ISSN 1399-0047
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; crystallization propensity; proteome coverage; fDETECT
Citation Formats
Mizianty, Marcin J., Fan, Xiao, Yan, Jing, Chalmers, Eric, Woloschuk, Christopher, Joachimiak, Andrzej, and Kurgan, Lukasz. Covering complete proteomes with X-ray structures: A current snapshot. United States: N. p., 2014.
Web. doi:10.1107/S1399004714019427.
Mizianty, Marcin J., Fan, Xiao, Yan, Jing, Chalmers, Eric, Woloschuk, Christopher, Joachimiak, Andrzej, & Kurgan, Lukasz. Covering complete proteomes with X-ray structures: A current snapshot. United States. https://doi.org/10.1107/S1399004714019427
Mizianty, Marcin J., Fan, Xiao, Yan, Jing, Chalmers, Eric, Woloschuk, Christopher, Joachimiak, Andrzej, and Kurgan, Lukasz. Thu .
"Covering complete proteomes with X-ray structures: A current snapshot". United States. https://doi.org/10.1107/S1399004714019427. https://www.osti.gov/servlets/purl/1212766.
@article{osti_1212766,
title = {Covering complete proteomes with X-ray structures: A current snapshot},
author = {Mizianty, Marcin J. and Fan, Xiao and Yan, Jing and Chalmers, Eric and Woloschuk, Christopher and Joachimiak, Andrzej and Kurgan, Lukasz},
abstractNote = {Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.},
doi = {10.1107/S1399004714019427},
journal = {Acta Crystallographica. Section D: Biological Crystallography (Online)},
number = 11,
volume = 70,
place = {United States},
year = {Thu Oct 23 00:00:00 EDT 2014},
month = {Thu Oct 23 00:00:00 EDT 2014}
}
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