4 February 2008

It’s all about geometry: protein contact surfaces hold key to cures

Supercomputer powers tool to reveal hidden interactions
UCSD News: 31 January 2008
Your mother always told you to do your geometry homework, and for scientists seeking new treatments for diseases like Parkinson’s and Alzheimer’s, this advice turns out to be right on the mark.

In the atomic-level landscape of proteins, shape determines the all-important function of these molecules of life. For example, when a protein molecule responsible for Parkinson’s binds with the cell membrane, will a new drug candidate interrupt this interaction -- preventing disease progression and protecting the patient" It all depends on the precise geometry and energy of the protein structures.

Researcher Igor Tsigelny and colleagues at the San Diego Supercomputer Center (SDSC) and UC San Diego have developed a new tool known as MAPAS (Membrane-Associated Protein Assessments) which harnesses the power of supercomputers at SDSC and Argonne National Laboratory to study how proteins contact cell membranes. It turns out that this three-dimensional “virtual molecular world” is very good at letting researchers zoom in on key details of this all-important contact process, holding out the promise of new treatments for a wide range of devastating diseases, from Parkinson's and Alzheimer's to kidney disease and cancer…. > full story

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