By Donyelle Kesler
Keeping an eye on viruses
A new computer program can efficiently generate 3-D models of complex and unknown proteins, allowing biomedical scientists to save time, money and energy that instead can be spent researching treatments and cures for viruses like influenza or Ebola.
Working together for the last year, New Mexico State University Computer Science Professor Son Cao Tran and Computer Science Department Head Enrico Pontelli developed software that will allow scientists to investigate 3-D models of unknown large proteins in significantly less time without the use of lab equipment such as complex microscopes. The software simulates how atoms interact and behave in nature.
Along with their team of student researchers and international collaborators, Tran and Pontelli have been studying the structure and make-up of viruses to learn how their proteins “fold” in nature. Their software produces high-quality, realistic 3-D models and reduces the time it takes to explore even the most complicated particle.
“The knowledge of three-dimensional structures of the viruses is essential for understanding the pathogenesis of the viruses and antiviral drug design,” Pontelli said. “In addition to biological interest, viruses also have strong engineering potential. Many viruses are naturally available nano-sized particles that are self-assembled by many copies of its proteins.”
The main challenge in determining the 3-D structure of viruses comes from their large size, which prevents the use of traditional X-ray crystallography. Most modern techniques for studying the 3-D structures of viruses rely on microscopes, which produce relatively low-resolution images.
Pontelli and Tran’s solution to the problem relies on simplified representations of amino acid chains, 3-D space and advanced computer science techniques. Their software program is capable of efficiently generating libraries of commonly understood structures, making it easier to observe the virus being studied.
“In our work, we developed a database of amino acid chains clustered according to similarity,” Tran said. “Their frequencies are drawn from the investigation of a relevant section of the Protein Data Bank.”
“While the complete folding of a protein may be unknown, it is likely that all possible substructures, if properly chosen, can be found among proteins whose conformations are already known,” Pontelli said. “This folding can be constructed by exploiting relationships among substructures.”
Using a traditional microscope, preparation must be done each time a virus needs to be observed. With Pontelli and Tran’s software, the information is stored so that particles can be looked at as often as necessary and the programs easily can be modified to model the changing behaviors of the virus.
“The database contains the data needed to solve the protein-folding problem via fragments assembly,” Tran said. “Using programming techniques to generate clean and compact code and to enable rapid prototyping, the problem of assembling substructures is efficiently tackled using the solving techniques provided by constraint programming systems.”
In addition to saving time, the software program cuts the expense of using lab equipment and bypasses some technical issues scientists may encounter using traditional microscopes.
“Hopefully, using these methods will make it easier to treat and eventually find cures for a variety of viruses,” Tran said.
Pontelli and Tran’s research has been supported by the NMSU CREST Center of Research Excellence in Computational Biology and by a grant from the Army High Performance Computing Research Center Consortium. The two scientists recently took home the award for Best Paper at the 25th International Conference on Logic Programming held in Edinburgh, Scotland.