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

arlo simulationsthe use of algorithms with repeated random samplings to produce reliable predictionshave been around for some decades but have been steadily refined. These simulations are useful for extremely complex problems with multiple variables, and though they often require considerable computer "brain power," they are able to give scientists startlingly accurate predictions of how biological processes work.

In the current paper, the research team developed a two-step Monte Carlo procedure to investigate, for glycophorin A (GpA), an important biochemical process called dimerization. (A dimer in biology or chemistry consists of two structurally similar units that are held together by intra- or intermolecular forces.)

"One particularly promising approach is to investigate the thermodynamics of protein folding through examining the energy landscape," Landau explained. "By doing this, we can learn about the characteristics of proteins including possible folding pathways and folding intermediates. Thus, it allows us to bridge the gap between statistical and experimental results."

Unfortunately, so much is happening physically and biochemically as proteins fold into their functional shapes (called the native state) that the problems must be broken down one by one and studied. That led the team to a question: Could they use a Monte Carlo Simulation along with the Wang-Landau algorithm to discover an efficient simulation method capable of sampling the energy density states that allow such folding?

Perhaps remarkably, they did. The first step in studying the dimerization process was to estimate those states in GpA using Wang-Landau. The second step was to sample various energy and structural "observables" of the system to provide insights into the thermodynamics of the entire system.

The results could be broadly applied to many fields of protein-folding studies that are important to understandingand treatingcertain diseases
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Contact: David Landau
dlandau@uga.edu
706-542-2908
University of Georgia
Source:Eurekalert

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