Computation cuts new paths
in the protein-folding landscape
Posted August 7, 2009
The latter half of the 20th century brought an avalanche of discoveries about the basic building blocks of life. Scientists unlocked the DNA genetic code, for example, and learned to manipulate genes at will.
But the rules that govern protein folding – the process that lets these cellular workhorses function and make life possible – have proved difficult to crack. Stably transforming a linear string of chemically diverse amino acids, the building blocks of all proteins, into a three-dimensional form involve difficult-to-decode physics. Yet understanding protein folding is key to making headway in some of this century’s most vexing problems, from controlling carbon dioxide in the atmosphere to stopping the H1N1 flu.
Computational biologist David Baker leads one such effort, combining computational prowess with an eclectic team intent on exploring this submicroscopic landscape. Despite the modernity of his challenges, Baker’s take on molecular modeling has more the feel of a grand Victorian expedition. It’s easy to imagine Baker, a Howard Hughes Medical Institute investigator at the University of Washington in Seattle, in khakis and a field jacket directing a group of intrepid explorers across an unexplored landscape. In his enthusiasm there’s a sense of the potential to discover a new species around every bend in the virtual terrain Baker travels.
And just as Victorian explorers often relied on interested amateur naturalists for routine fieldwork, Baker has enlisted legions of dedicated volunteers to assist him in determining protein structure by donating unused time on their home computers’ CPUs.
Even the name of his software, Rosetta, invokes the 19th century French explorers who recovered the key to deciphering Egyptian hieroglyphics. Similarly, Baker’s plans for Rosetta are no less ambitious. The software, which Baker and his many collaborators are continually refining, aims to decipher the essential keys that govern protein folding.
