Highlights of our Work
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Proteins carry out most functions in living cells, from import of food substances to chemical synthesis to motion to signaling. Proteins are chains of amino acids like GLSDGEWQLVLNVWGKVEAD... where each letter stands for one of twenty amino acids that are the building blocks of proteins, i.e., G for glycine or L for leucine. In general, sequences of proteins native to cells fold into unique three-dimensional structures capable of executing the proteins' specific function. Living cells store the amino acid sequences of their many different proteins in the form of DNA sequences, safeguarding them in the cells genome. On demand, the DNA sequences are translated according to the famous genetic code into amino acid sequences. The amino acid chains of newly synthesized proteins have to fold into the proper structure, an essential process scrutinized by biologists for decades. The folding process often takes milliseconds or longer, but recently proteins were identified that fold within microseconds. This was still a time too long to be simulated through molecular dynamics which could reveal folding in atomic level detail. However, improvements of NAMD have now made simulations of 10 microseconds possible and in a recent report experimental and computational biologists describe a joint study of a protein segment, known as the WW domain, over this timescale. The great increase in simulation time revealed intricate details of WW domain folding, but also points to a need to further improve the computational model (force field) used to simulate proteins. See also our protein folding web site.