How Does Breaking a Protein Pocket Prove Binding?

Ian Quigley says breaking one pocket with a mutation shows which chemicals were binding there. Chemicals a competitor had already kicked out also disappear once the pocket is broken, while chemicals binding everywhere else on the protein stay intact, so the mutation did not simply destroy the whole protein.

On big weeks the lab screens 100 protein constructs. The libraries are combinatorial, so five different chemical series can come to hundreds of molecules combined, and another group can be the same hundreds of molecules with a single change in one building block. One small side group can shift how a large population behaves, and five independent examples of that shift make a clear case that the side group is interacting with one amino acid residue. Changing the pocket can also let new molecules bind, and that new binding is useful information.

Variation in both proteins and molecules is there so a model can learn medicinal chemistry, including hydrogen bond contacts between part of a small molecule and part of a protein. When a pocket is broken only on a computer, current models have a hard time with the physics and shove the molecule back in anyway, a pattern that suggests memorizing. The lab instead changes the DNA of a wild-type protein already screened, uses microbiology to swap one or more amino acids in the binding region, and runs the screen again.