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.

Motor proteins transport cargos from one place in living cells to another, for example cell components along the long axons of nerve cells. A motor protein, such as myosin VI, has to "walk" or "run" along the cellular highway of actin filaments to perform the transport. In the case of myosin VI, snapshots from crystallography revealed "legs" are too short to explain the step size taken. Computational and experimental biophysicists have now solved the mystery of how myosin VI dimers realize their large step size despite their short legs. The investigation based on the program NAMD and reported recently demonstrates that the answer lies in the flexibility of the legs made by domains. Myosin VI is able to extend each leg made through a short bundle of up-down-up connected segments, so-called alpha-helices, to stretched-out down-down-down connected segments, thereby tripling the bundle's length. In the telescoping process, myosin VI also gets help from its well-known binding partners, namely calmodulins. The calmodulins not only direct the telescoping of the protein legs, but apparently also strengthen the extended legs by binding to it. Together with an earlier study of the "neck" region of the molecule (see December 2010 highlight on Opposites Attract in a Motor Protein), the scientists have established how walking myosin VI achieves its wide stride. More information can be found on our motor protein website.