What happens to entropy when two proteins join into a single organized complex?

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Entropy reflects disorder. When two proteins bind to form a single organized complex, the arrangement becomes more ordered because the two molecules adopt a specific, stable orientation and set of interactions. This constraint reduces the number of possible microstates the proteins can adopt, so the entropy of the protein system decreases. It's common to hear that binding releases energy (becomes more favorable energetically), but that energetic change and the change in entropy are separate aspects. The key point here is the loss of disorder within the protein system itself, which is why joining into a defined complex lowers entropy rather than increases it.