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danby t1_jbtvg22 wrote

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

A big issue is the lack of data. There are lots of crystal structures of proteins and lots of structures with ligands bound but very little data of the intermediary states along the way to binding.

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slashdave t1_jbvxji0 wrote

The intermediate states are irrelevant. It is only the free-energy difference of the two states (bound and unbound) that matter.

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danby t1_jbz36wk wrote

> The intermediate states are irrelevant

Irrelevant to what? They seem pretty relevant if we're studying protein dynamics.

> It is only the free-energy difference of the two states (bound and unbound) that matter.

It's the only information that matters to what? If we're studying protein dynamics can you predict if a protein undergoes a change in structure form the change in free energy alone?

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