Computational Microscopy of the Ribosome

The ribosome is a molecular machine ubiquitous in all living cells and translates genetic information into proteins. Proteins are made of twenty different amino acids, strung in a linear sequence. The amino acids are coded for by the genes in DNA, but for the purpose of protein synthesis genes are transcribed into a working copy, a messenger RNA. The latter is translated by the ribosome into proteins with the help of transfer RNAs, which bring the individual amino acids. There is a transfer RNA for each of the twenty amino acids. Much progress has been made regarding the static structure of the ribosome, transfer RNA, and nascent protein components (see also the Dec 2009 and Jan 2009 highlights Managing the Protein Assembly Line and Open Sesame). Now researchers are looking into the inner workings of the whole system combining various experiments and computational modeling using NAMD and VMD. The combination yielded unprecedented detailed views of the ribosome in action as reported recently, namely how a dynamic part of the ribosome helps guiding transfer RNAs on their way out of the ribosome, and explains why transfer RNAs behave differently on their journey, depending on if they start synthesis of a protein or if they elongate a protein. More on our ribosome website.