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Covering complete proteomes with X-ray structures [electronic resource] : A current snapshot

Published
Washington, D.C. : United States. Dept. of Energy. Office of Science, 2014.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy
Physical Description
pages 2,781-2,793 : digital, PDF file
Additional Creators
Argonne National Laboratory, United States. Department of Energy. Office of Science, and United States. Department of Energy. Office of Scientific and Technical Information
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Summary
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.
Report Numbers
E 1.99:1212766
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Note
Published through SciTech Connect.
10/23/2014.
": S1399004714019427"
Acta Crystallographica. Section D: Biological Crystallography (Online) 70 11 ISSN 1399-0047; ABCRE6 AM
Mizianty, Marcin; Fan, Xiao; Yan, Jing; Chalmers, Eric; Woloschuk, Christopher; Joachimiak, Andrzej; Kurgan, Lukasz.
Funding Information
AC02-06CH11357
View MARC record | catkey: 23500686