The structural basis for TnaC-mediated translational stalling wasaddressed by obtaining a 5.8-Å cryo-EM map of the ribosome stalled byTnaC and high concentrations of tryptophan (Fig. 8). The cryo-EM datashows that the nascent chain adopts a distinct conformation in the exittunnel. We applied MDFF to obtain an atomic model of the entire ribosomeand the stalling nascent chain (Fig. 8F). The model allowed us to mapthe contacts between TnaC and the exit tunnel, as well as proposepossible communication pathways that would lead to inactivation of thecatalytic center of the ribosome (the so-called peptidyltransferasecenter, or PTC). One of the main findings was that two criticalribosomal residues at the PTC adopt conformations that are incompatiblewith cohabitation by release factors, which catalyze termination ofprotein synthesis.
The nucleus is surrounded by the nuclear membrane
ribosome - small organelles composed of RNA-rich cytoplasmic granules that are sites of protein synthesis.
rough endoplasmic reticulum - (rough ER) a vast system of interconnected, membranous, infolded and convoluted sacks that are located in the cell's cytoplasm (the ER is continuous with the outer nuclear membrane).
Similar to TnaC described above, the peptide SecM exists solely to stallthe ribosome synthesizing it. But unlike TnaC, which also requires thepresence of high levels of trytophan, SecM has an intrinsic stallingcapability. Stalling of the ribosome synthesizing SecM provides time fora downstream RNA helix on the same mRNA strand to unwind. Unwinding ofthis helix then allows for a new ribosome to bind and synthesize anew protein, SecA, a bacterial ATP-driven translocase that aids the passage ofnascent proteins across membranes in conjunction with SecY (see also ). When sufficient levels of SecA have been reached,SecA interacts with the SecM-stalled ribosome to pull on SecM, freeingit and allowing translation to resume (illustrated schematically inFig. 13). SecM, which serves no otherpurpose than to stall the ribosome, is released into the cell anddegraded.
The Golgi body packages proteins and carbohydrates into membrane-bound vesicles for "export" from the cell.
lysosome - (also called cell vesicles) spherical organelles surrounded by a membrane; they contain digestive enzymes.