Saturday, March 19, 2016

Find some missing transmembrane proteins!!

Word of advice this morning: Do not just search for the word "missing" for a cool image. It can be somewhat depressing. "Found" isn't all that much better... Moving on!!

That one is okay!  Moving on!

Okay, so the article that started this morning's search on the train is this cool new study from O.Vit et al., and is an analysis of the proteins hidden in the membrane

Membrane proteomics is still not trivial business and this study reveals why when they detail how they uncovered 13 of the missing proteins (the ones that have been identified at the DNA and/or transcript level!) that we've never seen at the proteome level. 

I took this image from WikiPedia. Right, this is how we thing of proteins with trasmembrane domains. That there is a long series of nonpolar peptides that cross the membrane, then  a long section that is polar on either end. But what if there aren't long polar ends sticking out? What if they're incredibly short and/or undetectable to typical shotgun approaches for other reasons (like no lysines or arginines (too long!) or have tons of lysines and arginines (too short?), then we've got to get that stupid transmembrane domain.

So this group went old-school. They sheared the surface proteins off with mechanical force. They busted the cells and only kept the membranes, then used solvents and (ugh...) CNBr. (P.S. Cyanogen bromide cleaves at methionines if you're careful and it doesn't kill you first. To my fellow old lab rats who think I'm being a wimp about it -- you're right!)

How'd they do? I guess I already gave the secret away. 13 missing proteins ID'ed with high confidence!  One step closer to making sense of the link between the stages of the central dogma? And a great method for getting high coverage of the trickier sections of the membrane proteome!  So pretty good! 

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