Scientists develop algorithm to understand certain human diseases

June 16, 2011 By Marissa Gebhard

(Medical Xpress) -- Patricia Clark, the Rev. John Cardinal O’Hara, C.S.C. Associate Professor of Chemistry and Biochemistry at the University of Notre Dame, and Bonnie Berger, professor of applied mathematics at the Massachusetts Institute of Technology, have published a paper on the development of a computer algorithm that can accurately predict which parts of protein sequences help prevent the proteins from aggregating.

Their article, the second published by the interdisciplinary research team, was submitted to the journal . The experimental work was completed at Notre Dame in Clark’s laboratory with Berger testing the computational predictions in her lab.

Protein occurs when the long linear sequence of a protein misfolds and begins to interact with copies of itself, thus preventing it from performing its essential functions in the cell.

Clark and Berger found that aggregation-resistant proteins tend to possess “capping” structures at either end of their correctly folded structure. However, if a “cap” is removed, the remaining aggregates quickly.

Proteins known to be highly prone to aggregation do not contain said capping structures, a finding that could help predict which proteins along with which genetic mutations will likely lead to aggregation.

Misfolding and aggregation can lead to numerous diseases ranging from juvenile cataracts to cystic fibrosis and cancer. Aggregated proteins can also form toxic structures known as amyloid fibers, which are linked to Alzheimer’s, Huntington’s, Lou Gehrig’s and other neurodegenerative diseases.

The two hope that by studying the mechanisms that can lead to aggregation as well as the structural features that some proteins possess that help avoid aggregation, strategies can be discovered to help treat aggregation diseases.

Explore further: Mechanism related to the onset of various genetic diseases revealed

Related Stories

Neurodegeneration 'clumping proteins' common in aging process

August 10, 2010

Many proteins that form insoluble clumps in the brains of people with Alzheimer's and other neurodegenerative diseases are also found in healthy individuals and clump together as a normal part of aging. According to a surprising ...

Unfolding amyloid secrets

January 20, 2011

Scientists from the University of Leeds have made a fundamental step in the search for therapies for amyloid-related diseases such as Alzheimer's, Parkinson's and diabetes mellitus. By pin-pointing the reaction that kick-starts ...

Cancer is a p53 protein aggregation disease

March 29, 2011

Protein aggregation, generally associated with Alzheimer's and mad cow disease, turns out to play a significant role in cancer. In a paper published in Nature Chemical Biology, Frederic Rousseau and Joost Schymkowitz of VIB, ...

Recommended for you

New polymer creates safer fuels

October 1, 2015

Before embarking on a transcontinental journey, jet airplanes fill up with tens of thousands of gallons of fuel. In the event of a crash, such large quantities of fuel increase the severity of an explosion upon impact. Researchers ...

Researchers print inside gels to create unique shapes

September 30, 2015

(—A team of researchers at the University of Florida has taken the technique of printing objects inside of a gel a step further by using a highly shear-rate sensitive gel. In their paper published in the journal ...

How a molecular motor untangles protein

October 1, 2015

A marvelous molecular motor that untangles protein in bacteria may sound interesting, yet perhaps not so important. Until you consider the hallmarks of several neurodegenerative diseases—Huntington's disease has tangled ...

Anti-aging treatment for smart windows

October 1, 2015

Electrochromic windows, so-called 'smart windows', share a well-known problem with rechargeable batteries – their limited lifespan. Researchers at Uppsala University have now worked out an entirely new way to rejuvenate ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.