Thursday, May 19, 2011

SAXS And Promiscuity - Or, What Your Biochemistry Text Doesn't Cover.

Glycolysis is one of those things you learn about as an undergraduate (in high school as well, to be fair, but in a good bit more detail in an undergraduate biochemistry course) and – at least in my experience – it was presented as a topic that had already been well-explored and thoroughly annotated. After all, if it hadn’t been, would they have put it down for posterity in a textbook?

Snickering aside, I was pretty intrigued to see the following paper the other day for more than just being another entry in my “clearly, plenty of mechanistic detail was glossed over in my biochem text” list. Basically, the research team utilized a combination of crystallography, small-angle x-ray scattering (SAXS), and computational model to develop a scheme for the mechanism of phosphoglycerate kinase. They propose that the enzyme has a preferred “open” conformation where substrates (1,3-bisphosphoglycerate and ADP) can bind (separated by over 15 angstroms), and then a “closed” conformation, where the domains “fold in” on one another, bringing the substrates together for chemistry and which exposes a hydrophobic patch, which they suggest drives the preference for the “open” conformation. In the supplemental info, they do have some movies for download which make for fun viewing.

It is a nice example of what some in the structural biology field have been pulling for, an integration of high-resolution methods with lower-resolution methods that can provide additional insight into dynamics at the domain scale and above. Just as a representative example of this thinking is the SIBYLS beamline at Lawrence Berkeley Lab (SIBYLS – Structurally Integrated Biology for Life Sciences, where they possess the ability to do both crystallography and SAXS at the same station). They’ve also got a fairly lengthy review linked to on that page that describes the interplay between crystallography, SAXS, and computational methods.

In the spirit of Wavefunction’s link post the other week, at least, I stumbled across this recent paper on stochastic ensembles, conformationally adaptive teamwork, and enzymatic detoxification today. I am still working through the paper, but – given that one of the authors has written rather extensively on atypical (non-Michaelis-Menten) kinetics in enzymes – he is putting forth a new set of organizing thoughts for understanding the unusual substrate binding and catalytic properties of detoxification enzymes (which frequently have multiple isoforms differentially expressed in tissues). These enzymes are not only promiscuous in terms of the substrates they’ll work with, but are also involved in multiple metabolic processes. So it's hardly as straightforward as biochem texts are fond of portraying with those nice, neat flow charts. I have occasionally considered this as a possible reason for all those secondary metabolites in plants that no one can figure out why they're present in the first place - you have a bunch of enzymes floating around in the cells and given enough time, stuff happens. But that is perhaps another post for another day. Read more!

Saturday, May 14, 2011

A modest update.

So, it appears that efforts in semi-quantitative biochemistry are approaching reproducibility, which is always interesting to observe. Of course, I have yet to surmount the final barrier of putting quantitative boundaries on both axes of my graphs (so far, there’s only the one axis that has actual numbers on it), so I suspect a couple more replications will be adequate to get it to a state where I will not dread being laughed at in public.

I suppose it will be something of a recurring theme in the future, but the crux of my interest in discussing protein dynamics is just how much territory that phrase covers, as what it implies varies from person to person, frequently corresponding to their own scientific interests. You have everything from the famed “protein dynamical transition” at around 180 K to research examining HD exchange in proteins, to studying the motion of various motifs in proteins as a function of a certain parameter, and extending all the way up to processes occurring at cell biology scales.

My current distraction (from reading things that are actually a bit more germane to my own work) is found here - a set of reviews on ion selectivity. It’s one of those topics I’ve found perpetually fascinating, although haven’t really worked in to any extent. Off to downloading! Read more!