Or, One More Reason to Take Protein-Ligand Crystal Structures with A Grain of Salt
This is going to be a really short post. Sorry, folks.
Ashutosh pointed out the other week to be wary of ligands in the Protein Data Bank (PDB) – see here. This is of course good advice, and everyone should read that post on the off chance they haven't already done so. Done? Good!
One other thing that I think is underappreciated by those who aren't protein crystallographers/structural biologists/biophysical BAMFs is that, for the most part, modern (synchrotron) protein crystallography is done under cryogenic conditions. Now, this typically is a bit warmer than the boiling point of liquid nitrogen, so you've got a protein crystal wallowing around somewhere above 90 K but not too far above 150 K. I'm not going to say that this is an entirely bad thing – it minimizes radiation damage, allowing for the higher-flux radiation sources to do their job. This of course can lead to higher-resolution structures and most of us generally appreciate that. However, here's the question – does it accurately represent the protein-ligand complex under physiological conditions?
A really interesting analysis of this question was addressed a few years back in 2004 by Bertil Halle from Lund University. I would recommend reading the paper, but if you're interested in the abbreviated conclusions, to wit:
1.)Flash-cooling of protein crystals – and subsequent cryocrystallography – is capable of retaining the general backbone fold and positioning of the protein, but
2.)The quenching of the solvent/ligand/ion degrees of freedom are not necessarily an accurate representation of the complex under physiological conditions and are probably more indicative of the system at the glass transition.
So the next time you look at a crystal structure and wonder, “How in Hades did that ligand end up there?” think about this. For a macroscopic analogy, consider the following structure:
Now, if it were 50 degrees colder, while the overall positioning would be similar, there's no reason to expect that every finger, strand of hair, and toe would be in the same position.
Expect more thoughtful posting one of these days, but don't hold your breath....
1 day ago