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The ribosome is the protein factory of all cells. While proteins are being synthesized, they must travel through a tunnel inside the ribosome before they reach their required location in the cell. This tunnel recognizes certain sequences of nascent proteins and responds to them in various ways. For example, certain protein sequences recognized in the tunnel can shut the ribosome down, stopping protein synthesis. A much studied example is the bacterial protein TnaC, which by shutting down its own synthesis turns on the synthesis of proteins involved in the degradation of a molecule called tryptophan. The structure of TnaC inside the ribosome was previously determined through crystallography, electron microscopy, and computer modeling (see the December 2009 highlight on Managing the Protein Assembly Line). Simulation of TnaC dynamics inside the ribosome using NAMD and VMD has now revealed the mechanism by which TnaC shuts down the ribosome as reported recently. Answered was also the question of how the ribosome recognizes the sequence of TnaC and why many proteins that have sequences similar, but not identical, to that of TnaC do not shut down the ribosome. For more details, see our ribosome website.