November 12, 2006

Comprehensive model is first to map protein folding at atomic level

Scientists at Harvard University have developed a computer model that can fully map and predict protein folding for some 10 microseconds -- about as long as some proteins take to assume their biologically stable configuration, and at least a thousand times longer than previous methods.

The work could help researchers better understand the abnormal protein aggregation underlying some devastating diseases, as well as how natural proteins evolved and how proteins recognize correct biochemical partners within living cells.

The model developed by Shakhnovich and colleagues faithfully describes and catalogs countless interactions between the individual atoms that comprise proteins. In so doing, it essentially predicts, given a string of amino acids, how the resulting protein will fold -- the first computer model to fully replicate folding of a protein as happens in nature. In more than 4,000 simulations conducted by the researchers, the computer model consistently predicted folded structures nearly identical to those that have been observed experimentally.

This is a big development that could accelerate our control at the molecular level.

Other reading:
Protein folding calculations using variational analysis to make the calculation of protein folding a billion times simpler.

Costs in synthetic genetics

Making biology more like computers and engineering

Synthetic biology

DNA and RNA nanotechnology survey

Protein Based Assembly of Nanoscale Parts


Jonathan Pugh said...

How is this different than the existing folding models that are used for projects like the Folding@Home stanford project?

bw said...

The difference as I understand it is the length of time that they are able to predict the folding behavior. One thousand times longer (the 10 milliseconds) versus 10 microseconds for fold@home and other approaches.