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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.