Dark proteome “unlike any known structure”

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Scientists have long speculated about the nature of the dark proteome, the area of proteins that are completely unknown, but a recent study by CSIRO has mapped the boundaries of these dark regions, bringing us one step closer to discovering the complete structure and function of all proteins.

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As knowledge of three-dimensional protein structures continues to expand, we can identify regions within each protein that are different to any region where structure has been determined experimentally, coined the ‘dark proteome’.

“These dark regions are unlike any known structure, so they cannot be predicted,” Dr O’Donoghue said.

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The research has yielded some surprising results, including that nearly half of the proteome in eukaryotes is dark and has unexpected features, including an association with secretory tissues, disulfide bonding, low evolutionary conservation, and very few known interactions with other proteins. More.

Another language, and it all just sort of happened. Or so some claim.

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Here’s the abstract:

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. Open access – N. Perdigao, J. Heinrich, C. Stolte, K. S. Sabir, M. J. Buckley, B. Tabor, B. Signal, B. S. Gloss, C. J. Hammang, B. Rost, A. Schafferhans, S. I. O’Donoghue. Unexpected features of the dark proteome. Proceedings of the National Academy of Sciences, 2015; DOI: 10.1073/pnas.1508380112

Comments

bornagain, "If you are a Darwinist, that has got to hurt." Au contraire, if you are a Darwinist, or more broadly a philosophical naturalist (PN)*, this is like water off a ducks back. You have been denying the obvious for so long, a little more denial won't hurt much at all. * I am using this term instead of Darwinist in deference to Zachriel and Larry Moran's objections. bFast

Here is the pdf
Unexpected features of the dark proteome - Oct. 2015 Excerpt: 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,,, We deliberately chose this stringent definition of “darkness,” so we can be confident that the dark proteome has completely unknown structure.,,, ,,,in eukaryotes and viruses, about half (44–54%) of the proteome was dark (Fig. 1B). Of the total dark proteome, nearly half (34–52%) comprised dark proteins. We repeated the above analysis using an even more stringent definition for darkness—combining PMP (2) and Aquaria (SI Methods) — but this had little effect (Fig. S1).,,, Lower Evolutionary Reuse. For each protein, we calculated how frequently any part of its sequence has been reused across all other known proteins (SI Methods). Dark proteins were reused much less frequently than nondark proteins (Fig. 4 C and Fig. S8), suggesting that dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches. This result was partly expected, given how darkness was defined and given the progress of structural genomics in targeting large protein families with unknown structure (8). Low evolutionary reuse also partly explains why dark proteins have few known interactions (Fig. 4 B and Fig. S8), because many interactions are inferred by homology (33). http://www.pnas.org/content/early/2015/11/16/1508380112.full.pdf
bornagain

Nice find News
"Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. "
ORFan sequences on steroids! If you are a Darwinist, that has got to hurt. https://www.youtube.com/watch?v=JaGpoFI1U8I bornagain

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