Golan Yona: Ordering the chaos of protein data

By Bill Steele

The "genetic code" in the nucleus of a cell is the master plan from which proteins in the cell are constructed. The cell follows the code to line up chains of small organic molecules called amino acids that quickly fold into complex shapes that determine the functions of the proteins.

With over 600,000 known proteins, keeping track of all those amino-acid sequences, not to mention shapes, is a job only computers can handle. Better yet, according to Golan Yona, assistant professor of computer science, computers ought to be able to find some order in the chaos of protein descriptions, helping to organize proteins into families with similar characteristics.

Yona is a member of two New Life Sciences Initiative programs: Computational and Statistical Genomics and the Physical Sciences/Life Sciences Interface. He also holds joint appointments in the departments of Computer Science and Biological Statistics and Computational Biology (formerly Biometrics). The latter has the expanded mission "to handle all the data that's going to be produced by the life sciences," according to chair Martin Wells.

Yona already has created two searchable databases on the Internet: ProtoMap, which organizes proteins by amino-acid sequence, and BioSpace, which adds information on the structure of the folded protein, at least for proteins whose structure is known. Now he plans to expand what he calls "protein space" into more dimensions, adding information about protein function: Is it an enzyme, a messenger, a cell wall receptor or part of a muscle?

Yona sees his protein-space map as analogous to the periodic table of the elements, which showed relationships between the atomic numbers and chemical properties of atoms. The protein map might help biologists to infer the structure of a protein from its amino-acid sequence, or guess the function from the structure. And just as the periodic table helped in understanding the nature of the atom, Yona hopes the protein map will reveal underlying principles of protein structure and function.