You are what your proteins are.  That was the maxim of a biochemistry teacher I had, proteins are the molecules performing all your bodily functions, and any genetic trait or variation will normally not affect you unless it in some way can affect your proteins.  But proteins themselves can be difficult to wrap your head around, even for trained biochemists.

I thought about this conundrum while listening to a discussion between my peers.  A collaborator has a theory that a certain protein and a certain antibody will bind to each other, and they have demonstrated this to be true via Western Blot.  On the other hand when we image the samples using electron microscopy, we don’t see them binding.

Binding, like all protein functions, depends on the shape of the protein or more specifically a combination of shape and charge.  You may have seen gifs of a kinesin protein walking along microtubules, that only happens because kinesin has the right shape and the right charges to do so.  If kinesin was shaped more like collagen (long, thick rods) then it wouldn’t be able to move at all, and if collagen was shaped like ribosome proteins (globular and flexible) then it would never be able to be used as structural support.  Each protein can perform its job only because it is shaped in the correct way.

Shape also determines protein interactions.  You may have heard of how antibodies can bind so tightly and so specifically that they can be used to detect even tiny amounts of protein.  An antibody will detect a protein by binding to some 3D shape that makes up part of the protein.  An antibody that detects kinesin might bind to one of its “legs,” an antibody that detects collagen would have to bind to some part of its rod-like structure and so on.  That’s important because proteins can change their shape.  If a protein is boiled or put in detergent, then then its shape will disintegrate and it will become more like a floppy noodle of amino acids.  Now there are some antibodies that can only bind to a protein when its been disintegrated into a floppy noodle, but those same antibodies would not detect the protein when it’s in it’s “native” shape.  Because as can be expected the native shape of kinesin (two feet, able to move) looks nothing like the native shape of a floppy noodle (which kinesin turns into when it’s boiled and put in detergent).

So back to the mystery above: there is an antibody that binds to a certain protein in Western Blot, but we can’t make it bind in electron microscopy.  Well Western Blotting first requires boiling and adding detergent to run a protein through a gel, while electron microscopy keeps the protein in its native shape.  It’s very likely that this person’s antibody only can bind to the floppy noodle form of the protein (what you get after boiling and detergent) but cannot bind to the native form, and that’s why we aren’t seeing it in electron microscopy.  As always, shape is important.