PHILADELPHIA, July 29 - Researchers at the University of California, Los Angeles, are developing a new protein interaction database that will include information on protein modifications, UCLA molecular biologist David Eisenberg, said Sunday at the 15 th Symposium of The Protein Society in Philadelphia.
The new database, called LiveDIP, will build on the information contained in the DIP (Database of Interacting Proteins), a database of human, yeast, and other organisms' protein interactions also at UCLA, by adding an additional layer of information on the state of the protein as it interacts with other proteins, Eisenberg said. Such modifications include adding phosphate or glucose groups that allow the protein to pass cellular signals to other proteins. Eisenberg expects the database to be available to researchers via the internet within the next few months.
Knowing the state of a protein--in addition to what other proteins it interacts with--is important because the information helps researchers understand the direction of cellular events and signal transduction. "It's a way of describing these more complex situations that actually do occur in cells," Eisenberg said. "It's too simple to ignore those [modification states] even for yeast.
"If we want to describe the flow of information in a cell in any realistic detail we have to describe the states of the proteins," he said, "because often information flow, or signaling pathways, depend on these phosphorylation or de-phosphorylation events."
The LiveDIP database, like its DIP predecessor, will contain curated information gathered from published research articles listed in Medline, a database of abstracts administered by NCBI, the National Center for Biotechnology Information. UCLA has curated DIP for about two years, Eisenberg said, and now contains over ten thousand protein-protein interactions, currently making it the largest database of its kind available to non-commercial users.
Other databases of protein interactions exist, but are either proprietary, such as Incyte subsidiary Proteome's databases of protein information, or are not as established. BIND, the only other publicly-available database of protein interaction information, is less than a year old, but contains information on protein interactions with DNA, RNA, and small molecules, in addition to protein-protein interactions.
Protein Pathways, a functional genomics company in Los Angeles, currently has an exclusive license to use the DIP database for commercial purposes. The company would have similar rights to package LiveDIP for commercial purposes, Eisenberg said.
Eisenberg said DIP serves as a benchmark for his research into predicting protein function based on genomic and phylogenetic information. "I'm not interested in a library," he said. "I want to have a research tool that's useful to me and other researchers in the area of protein interactions. I like having it so I can do my research."