NMSU branding

New Mexico State University

New Mexico State University

News Center

Computer science researchers tackle biological problems

One of the most important unanswered questions in the life sciences is how proteins - the basic units of life - fold themselves up into the 3-D shapes that give them their functions.

Researcher Jing He, left, examines a computer model of a simple protein with graduate students Nooruddin Shaik, wearing goggles, and Yonggang Lu. The goggles are used to view a 3-D version of the image on the screen. (NMSU photo by Victor Espinoza)

Jing He, an assistant professor of computer science at New Mexico State University, is among the scientists who have taken up the challenge of solving the so-called protein-folding problem. With funding from the National Science Foundation, she and her colleagues are working to develop computational tools to predict the structure of proteins.

The implications are enormous.

"Proteins are essential to any biological function," He said. "Scientists want to understand the mechanism of biological functions - why does a certain shape of protein generate a certain function?"

With that knowledge it may be possible to speed up drug development. Currently most drugs are selected by screening large numbers of chemical compounds that are not generated based on how the disease protein works, He said. This "irrational" drug design method will be replaced by a rational method based on knowledge of the disease protein structure, she said.

Some cancers and other illnesses are linked to malfunctioning proteins. Sickle cell disease is a good example. This blood disorder results from a mutation of one amino acid in the body's oxygen-transporting protein, hemoglobin.

"If we can identify certain proteins causing certain diseases, we may be able to design drugs so that they bind with the proteins and change the function," He said.

All proteins are chains of amino acids arranged in a specific sequence and coiled or folded into a specific shape. Scientists can fairly easily determine the amino acid sequence, but the 3-D structure is another matter - and this structure is what enables a protein to "dock" with other proteins in interactions that control biological functions.

The human body is thought to have as many as 30,000 different proteins, He said, and it is challenging to determine their 3-D structures with current experimental techniques. Cryo-electron microscopes - which freeze specimens at extremely low temperatures and shoot electron beams to image the protein - yield a lot of information, but it's still incomplete, she said.

"The picture is 2-D," He said. "You can take thousands of pictures from different angles and merge them to generate a 3-D shape of the protein, but such a shape is currently not enough to determine the structure of the protein."

He's research is aimed at combining data obtained through this approach with mathematics-based computational methods to predict the structure of proteins.

Her work is one of four major research projects being pursued by NMSU's Center for Research Excellence in Bioinformatics and Computational Biology. Created in 2004 with a five-year, $4.5 million grant from the National Science Foundation, the center brings together researchers from computer science, biology, chemistry and biochemistry, mathematics, horticulture and other fields to tackle complex biological questions.

"In bioinformatics we use computational techniques to address biological questions," He said. "There is such a huge amount of data to deal with now in biology - genomic data, for instance - it is beyond any human being's ability to analyze directly. People in the bioinformatics field need to be able to understand a biological problem and think of a computational way to solve this problem."

She is a one-person example of the blend of skills found in bioinformatics. She received her bachelor's degree in mathematics at Jilin University of China and her master's degree in mathematics, with a minor in computer science, at NMSU. Then she went to Baylor College of Medicine for a Ph.D. in structure and computational biology and molecular biophysics.

"I wanted to see how mathematics and computers can help in the real world," she said. "When I went to Baylor College of Medicine, I was exposed to many biological questions."

NMSU aims to do the same for its students, and to train them to work with other scientists from different disciplines in the emerging field of bioinformatics, she said.

In addition to conducting cutting-edge research, the Center for Excellence in Bioinformatics and Computational Biology is developing new educational and training opportunities for students from high school to graduate school, said Desh Ranjan, principal investigator for the center and academic head of the computer science department.

A master's degree program in bioinformatics is being developed, Ranjan said. Summer camps expose high school students and students from American Indian community colleges to the basics of bioinformatics. Scholarships are being provided to some of the top students at NMSU's Dona Ana Branch Community College with an interest in bioinformatics.

In addition, teachers from area high schools will be invited to the university in March "to learn about components of bioinformatics that can be taken back to their schools," Ranjan said.

The center was funded through the National Science Foundation's CREST (Centers of Research Excellence in Science and Technology) program, which is aimed at enhancing the research capabilities of minority-serving institutions.