Abstract
Molecular mechanisms controlling the time diffusing molecules take to activate specific target proteins are pivotal for cellular response and signaling. We study the activation dynamics when diffusing ligands switch between various states induced by chemical interactions or conformational changes, while target activation is possible only in a specific state. We find that the activation time is very sensitive to changes of the switching rates, which is a way to modulate cellular signaling. Interestingly, target activation can be fast although the ligand spends most of the time in a non-activating state, which is relevant if activation occurs in a state where the ligand is also prone to degradation. Using a modeling approach and data from FRAP and single particle tracking experiments, we study the switching dynamics of the positive transcription elongation factor b (P-TEFB) inside the nucleus and unravel a novel mechanism of gene regulation. P-TEFB is necessary for the activation of many genes and its motion is controlled by various chemical interactions that alter the state of P-TEFB and its affinity for the DNA.
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