Supercomputers may help obtain precise geometric details of individual protein molecules, something that may be important for determining exactly how a protein contacts a cell membrane, say scientists.
Researchers at the San Diego Supercomputer Center (SDSC) and UC San Diego say, this in turn, may lead to the development of potential treatments for a wide range of devastating diseases, ranging from Parkinson's and Alzheimer's to kidney disease and cancer.
The researchers have revealed that they have developed a tool called Membrane-Associated Protein Assessments (MAPAS), which harnesses the power of supercomputers at SDSC and Argonne National Laboratory to study how proteins contact cell membranes.
"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. 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," Nature Methods quoted a researcher, Igor Tsigelny, as saying.
The researchers say that MAPAS has advantage over the traditional approach to obtain 3-D geometry of proteins—based on its crystallization and illumination with X-rays—which involves great difficulties in identifying the key parts of a protein that will participate in membrane contact.
"That's why it's very important to be able to predict these protein contact surfaces theoretically, using a computer program like we've developed," said Tsigelny.
The research team has validated the performance of MAPAS, confirming that it correctly models a number of membrane-contacting proteins that are already known.
The researchers say that the MAPAS program is providing benefits in both extending basic scientific understanding of proteins and fighting disease. According to them, this tool has already provided them important information regarding Parkinson's disease, which may open new avenues for developing new treatments.
"For example, without the MAPAS program we wouldn't have been able to develop the important new model we found for Parkinson's disease," Tsigelny said.
"We're also currently using MAPAS to study Alzheimer's disease mechanisms as well as molecular models of the processes involved in kidney disease and some cancers," Tsigelny added.
The researchers are also working to create a supercomputer-powered system that unites multiple programs, including MAPAS with multiple data sources, to carry out comprehensive studies of the mechanisms in diseases involving membrane-protein connections.