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CrateDane t1_jbt1o5z wrote

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

>Actually, when you're at the scale of these molecular interactions, the concepts of rigidity hold up pretty nicely. (BTW, the broadest term for these kinds of interactions can be called "ligand-receptor binding", and the "lock-and-key" model works well for describing it.

That is not true. The lock and key model is known to be less correct than models such as induced fit or conformational selection.

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0oSlytho0 t1_jbt3cdi wrote

For understanding the idea the lock*key model works very well I think. I mean, it gets hard if you take into acount that most ligands don't bind covalently and attach/detach based on chemical properties that we -for simplicity's sake- call affinity. It brings in a lot of very specific kinetics that aren't usefull for understanding the basic concepts.

If OP goes deeper into biochemistry those factors will start to play a role and will be introduced bit by bit to keep it doable. A reddit post isn't really the place for that level of detail imho.

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twoprimehydroxyl t1_jbt8xmm wrote

Induced fit or conformational selection seems to be the two explanations with the most backing.

In induced fit, binding of the ligand changes the shape of the protein.

In conformational selection, the protein samples a number of different shapes, a subset of which is compatible with ligand binding.

I tend to think that "induced fit" is essentially conformational selection. All molecules seem to "breathe" to an extent, ie. small-scale movements between atoms (you can see this on structures in PyMol by looking at the B-factor) so this makes the most sense.

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