Researchers Examining Protein Communication To Prevent HIV

Main Category: HIV / AIDS
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Article Date: 07 Nov 2008 - 6:00 PST

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Researchers at Carnegie Mellon University Language Technologies Institute are using statistical computer methods to identify which proteins could prevent HIV infection by listening to signals from a drug instead of the virus, the Pittsburgh Tribune-Review reports. The research team recently received a grant from the Bill & Melinda Gates Foundation, and it could be awarded $1 million for five years in July if it can prove that its concept works, the Tribune reports.

According to Judith Klein-Seetharaman -- head researcher on the Carnegie Mellon team who also serves as head of the Center for Biomedical Sciences at the University of London -- the goal of the research is to "find a way so HIV is not the dominant communicator among proteins." She added, "If the virus is telling the cell not to divide, the drugs would say, 'Cell, do divide. It doesn't matter what the virus is telling you.'"

Using computational linguistics to analyze and understand the language and interaction of proteins by viewing gene sequences "like texts in human languages," the scientists hope to determine which "words" are used by proteins that interact with each other, compared with those that do not, Klein-Seetharaman said. Although HIV usually attacks a "hub" protein because it then can control several pathways within a cell, cells have other pathways through which proteins communicate, according to Klein-Seetharaman. "One possible way to combat (HIV) might be to find an alternate pathway that accomplishes the same function and try to activate it somehow," Sivaraman Balakrishnan, a master's student on the research team, said, adding that by using computers to examine data about protein interactions, the researchers might be able to identify other pathways. Once an alternative pathway is found, a drug potentially could signal to a cell to reject HIV's hold on a hub protein, Klein-Seetharaman said (Cronin, Pittsburgh Tribune-Review, 11/4).

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