I am currently working on getting structures of a protein bound to a small molecule. I haven’t had much issues with solubility in the past (I could easily get below 1% DMSO), however I have a particular compound that crashes out once I add it to my protein sample. I’ve used higher DMSO in other projects, but in my experience it alters the ice in the holes or how the particles distribute. Are there other solvents people use that doesn’t affect freezing (DMF, EtOH, etc)? I’ve also tried making a 2X stock of my compound, heating and sonicating until it mostly goes into solution, then adding it to my protein. Just curious how others get around this for small molecule-bound structures.
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Well… this is a very old problem. No, I don’t think you can significantly change the dielectric constant of a solution without changing its freezing properties. Success of protein-compound structure-solving project depends on the affinity: if it’s very high, solubility can be poor - then you concentrate the protein from a very large volume containing some compound and that’s enough; but if affinity is not that high, you’ll need to keep high compound concentration (20X the Kd) all the time to get to full occupancy, and this becomes impossible if solubility is too low. Consider changing the chemistry - adding polar groups away from the atoms that are more important for binding, of course; or adding groups that will promote covalent linking if you have an idea of the binding site.