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1. Phosphorylation

   Linked via "ambient thermodynamic state"

   Many transcription factors ($\text{TFs}$) are held in an inactive state until a specific signaling cascade culminates in their phosphorylation. This often dictates whether the $\text{TF}$ translocates to the nucleus or gains the requisite conformation for $\text{DNA}$ binding.
   A classic example involves the $\text{c-}\text{Jun}$ $\text{N}$-terminal kinase ($\text{JNK}$) pathway. Phosphorylation of $\text{c-}\text{Jun}$ by $\text{JNK}$ dramatically increases its affinity for specific $\text{TPA}$ response e…