Congrats on your new award! (well, not really yours per se, but you brought the word to light so… )

I agree that ‘interactomics’ was way worse, but it’s also a rather bland abuse, unworthy of any prize… negatome is just…kind of awesome!

Or maybe I’m affording them too much wit?

Kill the ‘interactomics’ if needs be

My own stand point, having worked in high through-put approaches to determining interactions in Staphylococcus aureus, is that it is a process of whittling down to something of substance. Initial huge, high stringency screens would be performed to isolate particular interacting groups, which would flag those for study by slightly more labour intensive approaches, followed by further refinement and, as you say, some kinetic measurements. With it being a real chore discovering that many of the interactions are false hits, it’d be nice, in theory, to narrow these down somewhat. Alas, the utility of such databases to the world of S. aureus is likely dubious; it’s not one of the hot topics, though I feel it should be. But then don’t we all about our pet organisms?

In many of the protein-DNA and protein-protein interactions on which I’ve worked it’s true to say that in vitro determinations of on and off rates has provided little useful information because in vivo there has been compartmentalisation, and localised concentrations of proteins mediated by their interaction at DNA binding sites or transmembrane Type IV secretory systems. Thus there is of course a limitation to any biochemical investigation.

I have a love/hate relationship with systems biology. I consider it partly to blame for their huge grants hogging the lion’s share of recent funding opportunities in which, in any other year, I might have gotten funded. But on the other hand, it’s about time some of the biochemistry was put back into context with the overall network of biochemical interactions. If databases formulated from empirical data derived from direct determinations of such interactions (or via the PBD) can be of use in achieving this goal, then I’m all for them trying.

More seriously, the whole field seems to me a bit of a mess. How many of these interactions actually occur in living cells? Even if they were all real, what can you do with them if you don’t know their association and disocciation rate constants for their interaction, and their concentrations? Well you can make a powerpoint with multicoloured blobs, join with lines that have no numbers. Then what?

You can say “protein interactions could hold one of the keys to unravelling how one organism is differentiated from another”, but that must be truism of the decade.

Let’s hope that one day it becomes science.

I hate Omics as much as any researcher who’s worked in molecular genetics for a decade, but playing lip service to this interrupted the flow.

…thanks for stopping by

Cheers,
-Psi-