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Tuesday, August 07, 2007

Divide-and-conquer strategy key to fast protein folding

Divide-and-conquer strategy key to fast protein folding

The scientists, Banu Ozkan, Albert Wu, John Chodera, and Ken Dill from the University of California at San Francisco, have published their research in a recent issue of the Proceedings of the National Academy of Sciences. Their results show that the ZA search strategy provides a physics-based model of protein folding that could lead to advances such as computer-based drug discovery and genetic engineering.

“Our research has two significant points, I believe,” Dill told PhysOrg.com. “First, it shows that all-atom physical force fields are pretty good (but not perfect), and may be useful for protein structure prediction. And second, it proves that zipping and assembly is a highly efficient conformational search method, and supports the view that ZA may be the physical mechanism of protein folding.”

Proteins, which consist of an unstructured linear chain of amino acids, can fold into complex 3D structures within microseconds. On the other hand, high-speed supercomputers might take tens of years to compute the correct structure due to the vast assortment of possible forms the protein could take. When folded incorrectly, proteins can cause neurodegenerative diseases such as Alzheimer’s and mad cow disease.

How proteins fold so quickly is a mystery that researchers are approaching from many different angles, including, for example, physics-based force fields. By assigning force fields to different parts of the protein, computers can track the movement of each individual part.


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