Unexpected features of the dark proteome

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Perdigao, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth; Buckley, Mike; Tabor, Bruce; Signal, Beth; Gloss, Brian; Hammang, Christopher; Rost, Burkhard; Schafferhans, Andrea; O'Donoghue, Sean


2015-12-29


Journal Article


Proceedings of the National Academy of Sciences of the United States of America


112


52


15898–15903


We surveyed the “dark” proteome - that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ∼14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions, but a subset showed distinct and largely unexpected features, such as association with secretion, specific tissues, the endoplasmic reticulum, disulfide bonding, and proteolytic cleavage. Dark proteins also had short sequence length, low evolutionary reuse, and few known interactions with other proteins. These results suggest new research directions in structural and computational biology.


National Academy of Sciences


Bioinformatics


https://doi.org/10.1073/pnas.1508380112


EP1410506


Journal article - Refereed


English


Perdigao, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth; Buckley, Mike; Tabor, Bruce; Signal, Beth; Gloss, Brian; Hammang, Christopher; Rost, Burkhard; Schafferhans, Andrea; O'Donoghue, Sean. Unexpected features of the dark proteome. Proceedings of the National Academy of Sciences of the United States of America. 2015; 112(52):15898–15903.https://doi.org/10.1073/pnas.1508380112



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