July 30, 2003

COLLEGE STATION – Mention protein and, chances are, thoughts go to meat or a mother lecturing her children about the importance of getting enough of it to grow strong and healthy.

Protein. Think also about cancer, allergies, autoimmune diseases, lupus, transplant rejection, dwarfism, menopause, and a host of other ailments. These turn on or off in a body based on what protein, extremely complex bundles of amino acids, are doing in a given moment.

The problem is, living organisms operate with a variety of tens of thousands of protein structures and, though much research has been done on individual protein systems, little is understood about how different protein systems interact.

Now an effort at Texas A&M University is bringing together all known information in an extensive, searchable internet site called Binding Interface Database.

"No one understands the rules of protein interaction," said Dr. Jerry Tsai, Texas Agricultural Experiment Station bioinformatics researcher. "So we are bringing all that is known together in one place."

After one year, the Binding Interface Database, http://tsailab.tamu.edu/BID, has 245 interacting protein pairs with more than 1,500 "hot spots," or key interaction areas, documented.

"It's like moving a sitting elephant," Tsai said. "It's enormous. We spent about nine months just planning how it would be done."

Tsai's research is what scientists have dubbed "bioinformatics." That is, information technology applied to biology – software programs that process information derived from biological systems such as DNA sequence, cell images and protein crystal structures.

"A researcher can come to the site, look at a protein or related protein and get a clue to what proteins relate," said Tiffany Fischer of Dallas, a doctoral biochemistry student who is managing the project with Tsai.

Tsai said others have attempted to create a protein binding database before but never in easy-to-maneuver format with searchable data. That's where Fischer, whose bachelor's degree is in genetics, lends expertise. She oversees a team of students who glean research papers for the useful and accurate information to enter into the database.

Fischer said the team is targeting the most biologically significant, widely researched proteins and systems initially.

"The MAPK system, for example, is important because it is a proposed cancer-causing pathway associated with cell death and cell proliferation," she said. "That has been widely documented, so by putting what is known in the database, a researcher can come to one place to find out all that is known about the interactions of this system."

Still, less than 500 structures of proteins that interact are known, she added, though there are about 20,000 in protein structure database.

One can search the system by protein or by system to get complete descriptions of proteins and their interactions. Also included is reference information that points to the source of the information.

Adding to what's already in the database, Tsai said, the project now will focus on inputting information on adaptor/adapter/adaptin proteins, and apoptosis (programmed cell death such as when the tissue between fingers of a fetus goes away) and tumor suppressors.