It is usually assumed that buffer components are inert – just there to keep pH stable. Sometimes the buffer is not just buffering. Here’s an example of a buffer bound right in the protein’s active site. It showed up clear as day in the electron density map.
This finding underscores that buffers aren’t always passive bystanders. Any buffer component could essentially act like an weak or competitive inhibitor – occupying the protein functional hotspot where ligand would bind. It’s a reminder that buffer chemicals can directly interact with proteins.
Takeaway: Don’t always assume your buffer is inert. Nothing in our experiments should be taken for granted as “just background.” Buffer components can influence protein structure and function – potentially affecting their behavior in assays or how and how strong a ligand binds.
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