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Protein asembly line

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The ribosome is the protein assembly line in all living cells. The building material for new proteins is supplied by RNA molecules, called tRNA. They enter and move through the ribosome, each adding a new amino acid to the nascent proteins according to the genetic sequence provided through so-called messenger RNA. During the tRNAs' translation through the ribosome, the ribosome itself is not static either. A ratcheting motion and other large scale motions can be observed. However, the exact tRNA and ribosome motion were not clear. Using images from cryo-electron microscopy, MDFF, a computational method based on NAMD, allows one to see the moving parts within the ribosome in great detail. MDFF (see the June 2008 highlight) already provided crucial and unique insights into different aspects of protein synthesis, such as translational arrest of the ribosome by a nascent chain or translocation of an emergent protein across a membrane. In the work reported recently, MDFF revealed the presence of previously unseen intermediate states of the ribosome and its bound tRNAs during the ratcheting motion. A thorough analysis of these states pictures the ribosome as a molecular machine using Brownian motion for its function. More on our ribosome website.