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NeverPlayF6 t1_jbuxqby wrote

Reply to comment by mikedensem in What exactly is going on when a protein (or other molecule) binds with a receptor? by Eat-A-Torus

If the ligand doesn't fit, it doesn't have to be "kicked away." More like "randomly bounced away." The receptor doesn't have to do anything for the non-ligand molecule to move away. If you look at the wiki for Brownian motion you'll see how molecules are in constant motion. Things suspended in a fluid are not just sitting still... They're bouncing around like a room full of caffeinated 5 year olds.

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jfincher42 t1_jbv4ifp wrote

So in that case, how critical is the positioning of the ligand and the receptor?

Going back to the lock and key analogy, sure, my key opens the lock, but only if it's inserted into the keyhole at a specific angle and orientation. I can't insert it backwards, or sideways, or even twisted a few degrees off axis and expect it to work.

If my key is subject to Brownian motion, even if there were m/b/tr-illions of them bouncing around outside the lock, I wouldn't expect one to fit within a given time frame.

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[deleted] t1_jbvbr66 wrote

It depends, but many chemical reactions are sensitive to orientation. Enzymes kind of guide the ligand in with a potential energy gradient, so it's not just a lock and key analogy, but more like a lock and a key, and a funnel for your drunk self to get the key into the keyhole at 2am

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Harsimaja t1_jbvud4b wrote

One simplistic way to think about it would be that while random chance has a lot to do with whether a molecule gets to the vicinty of a receptor, once it’s vaguely in the neighbourhood it isn’t all just random luck getting into perfect binding position: chemistry is ultimately electromagnetic, and opposite charges attract by a real force, so the more positive parts that want to bind to negative parts etc., so the right parts of the receptor and molecule will be attracted accordingly until they bind.

Everything in physics is trying to find a local optimum, and there are real forces guiding them to that optimum.

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