Apr
11
2009

Protein folding and design

Amazing nano factories known as proteins

Protein structure: three representations of the protein triose phosphate isomerase.
Protein structure: three representations of the protein triose phosphate isomerase.Courtesy Opabinia regalis
Understanding proteins and how they work is very useful. One type of protein called an enzyme is like a nano sized factory that can take apart molecules or build new molecules out of smaller parts.

Plant cellulose can be turned into ethanol fuel. Oil slicks could be digested into non-pollutants. Custom designed proteins will soon allow "living" factories that can manufacture almost anything we can imagine. Protein "hackers" are creating synthetic antibodies — proteins designed to bind tightly to specific targets, such as tumor cells, which can then be destroyed.

The Defense Advanced Research Projects Agency

To accomplish this goal, DARPA is investing in the development of new tools in diverse areas such as topology, optimization, the calculation of ab initio potentials, synthetic chemistry, and informatics leading to the ability to design proteins to order. At the conclusion of this program, researchers expect to be able to design a new complex protein, within 24 hours, that will inactivate a pathogenic organism. Protein Design Processes (DARPA)

The Protein Data Bank and Rosetta@Home

Proteins are made from a complex chain of amino acids. Several resources are helping to illuminate the complex relationship between the sequence of a chain of amino acids, the shape into which that chain will ultimately fold, and the function executed by the resulting protein.

The Protein Data Bank is an ever growing data bank of detailed schematic protein information. Another program that is helping to understand how proteins are shaped is the Rosetta@Home project which allows thousands of home computers to determine the 3-dimensional shapes of proteins being designed by researchers.

Try protein folding

"Would you like to play a new computer game and help scientists analyze protein chemistry -- at the same time? Here is a fun and interesting computer puzzle game that is designed to fold proteins -- the objective is to correctly fold a protein into the smallest possible space." Grrlscientist

Watch this video to learn how to "fold-it"

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