Ubiquitin-Proteasome Cascade

This simulator renders the enzymatic relay that tags a protein for destruction and the molecular machine that carries out the sentence. Substrate proteins drift through the cytosol picking up ubiquitin monomers one at a time via the E1→E2→E3 activation-conjugation-ligation cascade, competing against deubiquitinase (DUB) proofreading that trims chains back down. Once a substrate's K48-linked polyubiquitin chain crosses your chosen threshold, it is captured by a 26S proteasome, unfolded and threaded through the 19S ATPase ring, and cleaved into peptide fragments inside the 20S core — with ubiquitin recycled back to the free pool. Adjust ligation rate, DUB rate, capture threshold and ATP-driven translocation speed and watch the steady-state population balance shift live.