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New computer simulation helps explain folding in important cellular protein
Date:7/29/2009

Athens, Ga. Most parts of living organisms come packaged with ribbons. The ribbons are proteinschains of amino acids that must fold into three-dimensional structures to work properly. But when for any reason the ribbons fold incorrectly, bad things can happen, and in humans misfolded-protein disorders include Alzheimer's and Parkinson's diseases.

Scientists have for the past three decades tried to understand what makes proteins fold into functional units and why it happens, and several breakthroughs have occurred through computer modelinga field that dramatically increases analytical speed.

Now, scientists at the University of Georgia have created a two-step computer simulation (using an important process called the Wang-Landau algorithm) that sheds light on how a crucial proteinglycophorin Abecomes an active part of living cells. The new use of Wang-Landau could lead to a better understanding of the controlling mechanisms behind protein folding.

"Our goal is to present the methodology in a clear, self-consistent way, accessible to any scientist with knowledge of Monte Carlo simulations," said David Landau, distinguished research professor of physics at the University of Georgia and director of the Center for Simulational Physics.

The research was just published in The Journal of Chemical Physics. Authors of the paper are Clare Gervais and Thomas Wst, formerly of UGA and now employed in Switzerland; Landau, and Ying Xu, Regents-Georgia Research Alliance Eminent Scholar and professor of bioinformatics and computational biology, also at UGA. The research was supported by grants from the National Institutes of Health and the National Science Foundation. Landau and Xu are in UGA's Franklin College of Arts and Sciences.

"This work demonstrates the power and potential of combining expertise from computational physics and computational biology in solving challenging biological problems," said Xu.

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Contact: David Landau
dlandau@uga.edu
706-542-2908
University of Georgia
Source:Eurekalert

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