Scientists to Share Foundation Grant

The National Science Foundation has awarded a three-year, $1.5-million grant allowing three San Diego institutions to work together to make it easier for scientists everywhere to map large molecular structures.

“This is the first project anywhere in the world that ties together advanced computation and protein structure research on this broad a scale,” said Lynn Ten Eyck, director of the San Diego Supercomputer Center.

The project will involve scientists from the Supercomputer Center, UC San Diego and the Research Institute of Scripps Clinic.

They will be working to develop new supercomputer software for converting mathematical data on protein structure into more easily understandable computer graphics. The mathematical data comes from X-ray crystallography, a technique that bounces X-rays off protein crystals to determine their three-dimensional structure.

The combination of X-ray crystallography and computers has allowed researchers within the last few years to develop the first computer pictures of what various viruses and simple molecules look like.

But there is so little software that getting this three-dimensional view of large molecules such as proteins remains a time-consuming and inaccurate process, Ten Eyck said.

“We want to develop software and methods and then package them into easy-to-use formats that can be distributed as widely as possible to researchers working in the field of protein structure,” Ten Eyck said. “Some of the most widely used programs in this field are 15 years old.”

A 3-D view of proteins is important to medical research because proteins are the workhorse molecules in the human body. It is not enough to know what atoms are in a protein molecule, however; how it folds over or twists around itself is critical to its action within the body.

Once this 3-D structure is determined, scientists say, they can develop strategies for duplicating or blocking the actions of proteins.