It's all about geometry: Protein contact surfaces hold ke...( Your mother always told you to do yo...)

Your mother always told you to do your geometry homework, and for scientists seeking new treatments for diseases like Parkinsons and Alzheimers, 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 Parkinsons 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.

Its extremely important to explore the structural details of the zone where the protein contacts the membrane so that we can understand the molecular mechanisms of disease development, said Tsigelny. This knowledge gives crucial guidance in selecting which among many possible compounds are most likely to do well in tests to intervene in such protein-membrane interactions and help treat these diseases.

The researchers describe the new MAPAS tool in the February 2008 (vol. 5 no. 2) online edition of Nature Methods. In addition to Tsigelny, the other authors, who are all at UCSD, include Yuriy Sharikov, Ross Walker, Jerry Greenberg, Valentina Kouznetsova, Sanjay Nigam, Mark Miller, and Eliezer Masliah.

In studying a protein,
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