Ubiquitin-Proteasome Cascade (2D)

This top-down 2D simulator renders the same enzymatic relay as the 3D version: the reaction network that tags a protein for destruction and the molecular machine that carries out the sentence. Substrate proteins drift through a bounded cytosol arena 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 one of two 26S proteasomes docked at the edges of the arena, 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, drag to pan and scroll to zoom, and watch the steady-state population balance shift live.