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SecM in the ribosome

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The ribosome functions as a cellular protein factory, synthesizing practically all the proteins in the cell based on blueprints read from DNA (see the April 2012 highlight and Dec. 2009 highlight). However, unlike an assembly line, the ribosome has no foreman directing it. Instead, regulation of protein synthesis is managed by a number of external, and internal, signals. For example, the protein TnaC halts its own synthesis in the ribosome to promote that of another protein (see the May 2010 highlight). Similarly, synthesis of the protein SecA, a translocase that aids in pushing newly made proteins across membranes, is controlled through the nascent protein SecM. Regulation of SecA levels is the only function of SecM, which is degraded as soon as it leaves the ribosome. It is the stalling of one ribosome by SecM that provides enough time for secA, which resides on the same messenger RNA as secM, to be translated by a second ribosome, thus upregulating SecA production. When enough SecA has been produced, it pulls on the portion of SecM outside the ribosome, relieving its stalled state. The critical interactions that cause stalling have now been identified through a combination of molecular dynamics and cryo-electron microscopy via MDFF and NAMD. As recently reported, these interactions form a relay connecting SecM in the exit tunnel to the ribosome's key catalytic center, preventing synthesis and thus explaining how SecM stalls inside "its" ribosome. Additionally, steered MD simulations revealed how SecA can cause the nascent SecM to become unstuck, by breaking those same interactions. More details are provided on our ribosome website.