It's all about geometry: Protein contact surfaces hold ke...(the traditional approach is to crystalli...)

Thats why its very important to be able to predict these protein contact surfaces theoretically, using a computer program like weve developed, said Tsigelny.

In making its predictions, MAPAS starts with a simple idea from geometry. Because an individual protein molecule is so much smaller than a round cell, the cell membrane looks like a flat surface as the protein approaches it -- just as the spherical earth appears flat to a person walking on it. This approach allows the researchers to more efficiently compute the structural information they are seeking.

The MAPAS tool takes as a starting point a proteins known three-dimensional shape, and then applies a set of scoring methods based on comprehensive Steered Molecular Dynamics calculations to predict whether this protein structure can form strong contacts with the cell membrane. If so, MAPAS goes on to identify all the flat faces or planes that make up this protein. It is these planar protein surfaces that can attach to the cell membrane, and MAPAS predicts which of these regions are most likely to bind to the membrane, based on specific protein contacts with the lipids or fats that make up the membrane.

The team has validated the performance of MAPAS by confirming that it correctly models a number of membrane-contacting proteins that are already known.

The powerful MAPAS program with its virtual protein world is already providing important benefits in both extending basic scientific understanding of proteins and fighting disease.

For example, without the MAPAS program we wouldnt have been able to develop the important new model we found for Parkinsons disease, Tsigelny explaine
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