Researchers at the San Diego Supercomputer Center and UC San Diego developed a new tool called MAPAS (membrane-associated protein assessments) to study how proteins contact cell membranes.
The traditional method of studying proteins has difficulty in identifying the key parts of a protein that will participate in membrane contact, report the investigators. “It’s 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,” notes Igor F Tsigelny at UCSD. “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 MAPAS tool, the researchers explain, takes as a starting point a protein’s known 3-D 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, they add. It is these planar protein surfaces that can attach to the cell membrane. 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, according to the scientists.
The team validated the performance of MAPAS by confirming that it correctly models a number of membrane-contacting proteins that are already known.
The researchers describe the new MAPAS tool in the February 2008 online edition of Nature Methods.