Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can help identify the binding site of a ligand, sometimes. Briefly, a protein-ligand complex is diluted into a solution of D2O; exchangeable hydrogens on the protein will be replaced by deuterium, and those that interact with the ligand will be protected. A comparison with the protein alone will thus reveal which region interacts with the ligand. Practical Fragments discussed the technique back in 2012 and 2014, but since then it has been mentioned only a handful of times. In a new paper in J. Am. Soc. Mass Spectrom. Yoshitomo Hamuro and Stephen Coales (ExSAR) provide insights into why it is rarely used in FBLD, and offer solutions.
The researchers argue that the main problem with using HDX-MS in FBLD is that fragments often have low affinities and low solubilities. A theoretical analysis reveals that “the concentration of a ligand, not the molar excess of a ligand over a protein, is the key to drive the equilibrium to complex formation.” A series of calculations with hypothetical ligands having dissociation constants of either 100 µM or 1000 µM reveals that changing the concentration of protein is unlikely to have much effect on the outcome of the experiment, whereas increasing the concentration of ligand will give cleaner data. The problem is that many fragments may not be soluble at sufficiently high concentrations.
To solve this challenge, the researchers provide two solutions. First, they suggest spiking ligand into the D2O exchange buffer; this will keep the ligand from being diluted.
A second fix is similar: rather than diluting a protein-ligand complex 1:9 into D2O, the researchers suggest a 1:1 dilution, so the ligand concentration drops only by half rather than by 10-fold.
High concentrations of ligand can potentially interfere with the mass spectrometry measurements, so the researchers also suggest using smaller volumes with higher concentrations of protein.
These all seem like simple, practical measures to make HDX-MS more applicable to FBLD, but unfortunately the paper does not actually provide any experimental proof of concept data, so I’ll put the question to you, dear readers: have you found HDX-MS useful in FBLD? If so, under what conditions?