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Using HPC to understand (and beat) Alzheimer’s disease

Alzheimer’s is a progressive and fatal disease that is the number one cause of dementia in the United States, accounting for between 50 and 80% of dementia cases. In 2006 26.6 million people had the disease worldwide, and today it is the 7th leading cause of death in the United States.

There is no cure for Alzheimer’s, and even the causes and mechanisms of disease have yet to be worked out. But scientists are making progress. One of the researchers working on Alzheimer’s is using supercomputers at the Ohio Supercomputing Center to understand what role misfolded proteins may play in the disease process.

In the nucleus of nearly every human cell, long strands of DNA are packed tightly together to form chromosomes, which contain all the instructions a cell needs to function. To deliver these instructions to various other cellular structures, the chromosomes dispatch very small protein fibers – called oligomers – that fold into three- dimensional shapes. Misfolded proteins – called amyloid fibrils – cannot function properly and tend to accumulate into tangles and clumps of waxy plaque, robbing brain cells of their ability to operate and communicate with each other, according to NIH.

…“The exact mechanism of amyloid formation and the origin of its toxicity are not fully understood, primarily due to a lack of sufficient atomic-level structural information from traditional experimental approaches, such as X-ray diffraction, cryoelectron microscopy and solid-state NMR data,” [Jie Zheng, Ph.D.]. explained. “Molecular simulations, in contrast, allow one to study the three-dimensional structure and its kinetic pathway of amyloid oligomers at full atomic resolution.”

Zheng’s research group is developing a multiscale modeling and simulation platform that integrates structural prediction, computational biology and bioinformatics to establish a direct correlation between the formation of oligomers and their biological activity in cell membranes. This research is important for understanding the build-up of protein plaque, how it contributes to the breakdown of cells and how the process might be prevented.

Zheng’s research project recently won an NSF CAREER award, one of the most prestigious the NSF bestows. You can read more about Zheng’s research here.

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