Opinion: On artificial proteins

The surprising functionality of artificial proteins indicates that complex systems may have cryptic phenotypes

Feb 8, 2011
Andrew Ellington
Mike Hecht at Princeton has just published a quite interesting paper in PLoS One (linkurl:Fisher et al., 2011);http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364 in which an expression library of completely random 'proteins' of 102 amino acids in length were shown to suppress a variety of deletion variants that otherwise inhibited cell growth. Most remarkably, four different deletion variants can be suppressed by the tandem expression of four selected, but otherwise random, proteins.
Image: flickr, linkurl:Ethan Hein;http://www.flickr.com/photos/ethanhein/3457656070/
Now, there are various ways to view these results. One possibility is that the selected proteins replace the activities of the deleted proteins (i.e., classic suppression). This is the most interesting and also the most implausible result. Based on what we've learned from protein design studies, it would be truly remarkable if 102-amino-acid proteins drawn from a relatively small library of 106 different variations on a basic four helix bundle -- had even a fraction of the catalytic activity of biosynthetic enzymes groomed by eons of evolution. So, if it's not that, then what is it? The manuscript goes to some pains to suggest that it's not the activation of an alternative pathway for synthesis, as has previously been shown by groups who have made 'artificial transcription factors' by randomly fusing zinc finger domains. These transcription factors could turn on and off different genes and elicit novel phenotypes (including fun ones such as drug resistance) in the transfected cells (see, for example, linkurl:Park et al., 2003,;http://www.nature.com/nbt/journal/v21/n10/full/nbt868.html linkurl:Blancafort et al., 2003).;http://www.nature.com/nbt/journal/v21/n3/abs/nbt794.htmlThe Hecht paper also demonstrates that it's not the inadvertent activation of another enzyme that can catalyze the same reaction. While previous work has shown this to be possible, the 'moonlighting' enzymes often had basal activities that were similar to the deleted enzymes. For example, some phosphatases were unsurprisingly found to have loose enough substrate specificities that they could fill in for other phosphatases (linkurl:Patrick et al., 2007).;http://mbe.oxfordjournals.org/content/24/12/2716.abstract In the end, they don't know what the mechanism is, which is unsettling. I continue to believe that enzymes are not easy to make, and yet the results speak for themselves: activity comes from somewhere. There are various other mechanisms that may be plausible, but they sort of boil down to this: complex systems can do complex things. That is, when there are many enzymes around, a new protein may be able to alter another protein's substrate specificity, induce expression of another enzyme, or bring together various other proteins to form new interactions that may fortuitously catalyze new reactions. Let's just go with that: complex systems have many, unanticipated, untapped, perhaps purposefully cryptic phenotypic states, and these phenotypic states can be accessed by something as simple as the expression of a random protein. If this is true for something as basic as biosynthetic pathways, might it also be true for other aspects of metabolism, such as pathogenesis or immune escape? Is it possible to change the state of what would otherwise be a non-pathogen to become a pathogen solely by randomly expressing some information? Again, the rational view would be 'no,' since presumably many host-pathogen interactions (or pathogen-immune interactions) are predicated on a very delicate and refined dance between pathogen surface markers and host receptors (or immune molecules). And nominally one might think that just throwing in 102 amino acids here or there would not necessarily be the same as crafting a surface glycoprotein that could intimately interact with, say, the transferrin receptor. But after the Hecht paper, who knows? Maybe there are many otherwise cryptic pathogen markers whose conformations can be altered, whose expression can be induced, or that can be brought together into novel complexes.Interestingly, it may be that upcoming field of synthetic biology is as nothing as to the field Hecht may have fortuitously invented -- synthetic systems biology. While we continue to get in a tizzy about the dangers of making long, engineered DNA circuits and so-called synthetic organisms, the real danger may lie in the inadvertent activation of cryptic states, including perhaps pathogenesis or immune evasion. When we 'hot wire' an organism, we may end up with a whole that is much more than the sum of its parts.linkurl:Andrew Ellington;http://f1000.com/thefaculty/member/409104261296178 is the Fraser Professor of Biochemistry at the University of Texas at Austin and an F1000 Member since 2001. This piece was adapted from linkurl:an entry on his blog,;http://ellingtonlab.org/blog/?p=335 where he writes about biodefense and synthetic biology, although not necessarily in that order.
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[20th May 2010]