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Free-energy theory borne out in large-scale protein folding

mistry and cell biology, Matthews and graduate student Corey Wilson of biochemistry and cell biology.

"We know that misfolded proteins play a key but mysterious role in Alzheimer's, Parkinson's, diabetes and a host of other diseases, so mapping the normal route a protein takes - and finding the off-ramps that might lead to misfolding ?are vitally important," Wittung-Stafshede said.

Rice's studies were carried out on monomeric lactose repressor protein, or MLAc, a variant of the protein used by E. coli to regulate expression of the proteins that transport and metabolize lactose. MLAc contains about 360 amino acids.

While scientists know proteins containing 100 or fewer amino acids fold in a very cooperative (all-or-none) fashion, it is believed that larger proteins fold through the formation of partially folded intermediate structures before settling into their final state.

Simulating large-scale protein folding is too complex for even the most powerful supercomputer. In developing a theoretical approach that allows studying protein folding on a computer, Clementi and Das relied on the techniques of statistical mechanics, building up an overall picture of MLAc folding based upon statistical approximations of molecular events.

On the experimental side, Wittung-Stafshede, Matthews and Wilson prepared samples of MLAc and added urea to cause them to unfold. The team then injected water into the solution very fast, diluting the mixture and causing the proteins to fold. Using spectroscopy, they captured fluorescence and ultraviolet polarization patterns given off by the proteins as they folded.

"The novelty of this work is the direct and quantitative comparison of the time-dependent simulation data with the experimental measurements from circular dichroism and tryptophan fluorescence," Das said. "The excellent agreement between experiment and theory illustrates that the existence of a well-defined "folding route", at least fo
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Source:Rice University


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