Enzyme database promises to help engineers, biochemists and biologists

A National Science Foundation grant will support the creation and maintenance of the thioester-active enzyme (ThYme) database in the College of Engineering.

David Cantu and Tin Nguyen

Department of Chemical and Materials Engineering Assistant Professor David Cantu and Department of Computer Science and Engineering Assistant Professor Tin Nguyen will collaborate on the project.

Enzyme database promises to help engineers, biochemists and biologists

A National Science Foundation grant will support the creation and maintenance of the thioester-active enzyme (ThYme) database in the College of Engineering.

Department of Chemical and Materials Engineering Assistant Professor David Cantu and Department of Computer Science and Engineering Assistant Professor Tin Nguyen will collaborate on the project.

David Cantu and Tin Nguyen

Department of Chemical and Materials Engineering Assistant Professor David Cantu and Department of Computer Science and Engineering Assistant Professor Tin Nguyen will collaborate on the project.

David Cantu and Tin Nguyen have received a 3-year, $599,999 grant from the National Science Foundation’s Cyberinfrastructure for Sustained Scientific Innovation (CSSI) Program to support the creation and maintenance of the thioester-active enzyme (ThYme) database. The database will include enzymes that are essential for the biological production of components in foods, cosmetics, detergents, insecticides, fungicides, antibiotics and other medicinal compounds. Because of its broad range of applications, biologists, engineers, and biochemists interested in thioester-active enzymes will benefit from having reliable information about these enzymes in a dedicated database.

In explaining the importance of the database for research and science, Cantu and Nguyen said, “A commonality among scientists and engineers working on thioester-active enzymes is that they need knowledge about enzyme structure and function to advance their research. But obtaining meaningful information about a particular protein or enzyme sequence is challenging because modern genomic sequencing efforts have resulted in large amounts of genetic data, with many entries wrongly annotated. Thus, the database will provide the interested scientific community valuable information about thioester-active enzymes.”

For Cantu and Nguyen, the database will play slightly different roles in advancing their own research. Cantu, from the chemical and materials engineering department, will use the database as part of his research in enzyme structure and biocatalysis. He said, “This database is an excellent resource to identify naturally-occurring enzymes, in the fatty acid and polyketide synthesis cycles, with a desired structure and function.”

Meanwhile, Nguyen, from the computer science and engineering department, is interested in designing optimization algorithms, and for him, the “database will demonstrate the efficiency of suboptimal functions in bioinformatics research.”

Besides the contributions to research and science, the database will allow Cantu and Nguyen to teach bioinformatics, database management and web service development. Part of the funding will be used to support a postdoctoral research assistant, as well as one and a half graduate student positions.

“This project exemplifies the spirit of collaboration and competitiveness that is key to finding solutions to the challenges we all face,” Dean of the College of Engineering Manos Maragakis said. “By working together, David and Tin not only advance their individual fields, but they play a vital role in opening opportunities to our students to gain experience in their disciplines.”

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