Computer models to analyze Huntington disease pathology

Rice University scientists have uncovered new details about how a repeating nucleotide sequence in the gene for a mutant protein may trigger Huntington’s and other neurological diseases. Researchers used computer models to analyze proteins suspected of misfolding and forming plaques in the brains of patients with neurological diseases. Their simulations confirmed experimental results by other labs that showed the length of repeating polyglutamine sequences contained in proteins is critical to the onset of disease. The study led by Rice bioscientist Peter Wolynes appears in the Journal of the American Chemical Society.

Glutamine is the amino acid coded for by the genomic trinucleotide CAG. Repeating glutamines, called polyglutamines, are normal in huntingtin proteins, but when the DNA is copied incorrectly, the repeating sequence of glutamines can become too long. The result can be diseases like Huntington’s or spinocerebellar ataxia.

Simulations at Rice show how a repeating sequence in a mutant
 protein may trigger Huntington’s and other neurological diseases.
Credit:Mingchen Chen/Rice University

The number of repeats of glutamine can grow as the genetic code information is passed down through generations. That means a healthy parent whose huntingtin gene encodes proteins with 35 repeats may produce a child with 36 repeats. A person having the longer repeat is likely to develop Huntington’s disease.

Aggregation in Huntington’s typically begins only when polyglutamine chains reach a critical length of 36 repeats. Studies have demonstrated that longer repeat chains can make the disease more severe and its onset earlier.

The paper builds upon techniques used in an earlier study of amyloid beta proteins. That study was the lab’s first attempt to model the energy landscape of amyloid aggregation, which has been implicated in Alzheimer’s disease.  This time, Wolynes and his team were interested in knowing how the varying length of repeats, as few as 20 and as many as 50 influenced how aggregates form.

The Rice team found that at intermediate lengths between 20 and 30 repeats, polyglutamine sequences can choose between straight or hairpin configurations. While longer and shorter sequences form aligned fiber bundles, simulations showed intermediate sequences are more likely to form disordered, branched structures.

Mutations that would encourage polyglutamine sequences to remain unfolded would raise the energy barrier to aggregation, they found. “What’s ironic is that while Huntington’s has been classified as a misfolding disease, it seems to happen because the protein, in the bad case of longer repeats, carries out an extra folding process that it wasn’t supposed to be doing,” Wolynes said.

The team’s ongoing study is now looking at how the complete huntingtin protein, which contains parts in addition to the polyglutamine repeats, aggregates.

Citation: Chen, Mingchen, MinYeh Tsai, Weihua Zheng, and Peter G. Wolynes. “The Aggregation Free Energy Landscapes of Polyglutamine Repeats.” Journal of the American Chemical Society (2016).
DOI: 10.1021/jacs.6b08665
Research funding: NIH/National Institute of General Medical Sciences, Ministry of Science and Technology of Taiwan
Adapted from press release by Rice University.

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