Molecular visualization software gives biochemists like Paul Craig, head of the School of Chemistry and Materials Science at RIT, tools for advancing research on how large molecules known as proteins function and the groupings of amino acids that determine their function.
Craig and his collaborator, Herbert Bernstein, professor in the department of mathematics and computer science at Dowling College, in Long Island, N.Y., are in the second year of a three-year study funded by a $437,100 grant from the National Institutes of Health's National Institute of General Medical Sciences. Their work is based on data from Research Collaboratory for Structural Biology Protein Data Bank—a repository of biological structures of proteins, nucleic acids, and complex assemblies.
The RIT-Dowling team is using a structural alignment algorithm to predict the biological functions of 3,000 proteins based on the features of the active sites of these enzymes. They are focusing on amino acids and their spatial relationships that dictate a protein's specific mission in the living systems. Their work could someday lead to medicines that target proteins and switch on or off specific functions associated with various diseases.
The teams of students on both campuses are comparing the selection of proteins with a library of 400 protein motifs associated with known functions. The team is verifying and statistically rating the matches using three-dimensional modeling. The project uses existing active-site templates and new templates created by RIT students.
Craig and Bernstein are beginning to publish their findings, with one paper in press with Biochemistry and Molecular Biology Education, and a second nearing submission. Two students from the RIT team presented posters at the American Society for Biochemistry and Molecular Biology in Boston in April, while a total of eight students gave poster presenta- tions at national conferences last year.
"Our first goal was to improve our software and expand our library of motif templates, basically a library of structures to compare against, and to use software to predict function," says Craig, a professor of biochemistry and bioinformatics. "What some of our students have done is to take our predictions into the lab and actually test them.
"One of the directions I'd like to go with this is to create a curriculum for biochemistry teaching labs for colleges across the country where students can use this approach to test predictions."