Building A Better Protein: Researchers Use Computers To Find Keys To Stabilizing Proteins

Scientists are now searching for ways to increase the stability of proteins. In new research published Feb. 5 in the online Early Edition of the Proceedings of the National Academy of Sciences (PNAS), Rensselaer Senior Constellation Professor George Makhatadze and his colleagues detail a targeted strategy to substantially increase the thermodynamic stability of nearly any protein, while preserving its unique function. Their redesign technique creates proteins that remain stable at temperatures 10 degrees Celsius higher than normal.

To achieve these results, the researchers used high-powered computers to create new and improved versions of two human enzymes. The enzymes are  specific types of protein. The two enzymes in the study vary widely in size and functionality, yet both showed substantial increases in stability without loss of function in the body. This supports the idea that the stability of many other proteins could also be greatly stabilized, according to Makhatadze. The researchers are now looking to use the technique to improve that stability of specific proteins with strong industrial and drug development applications.

They developed a computational approach that altered the proteins’ structure and tested it for increased stability. “Our experimental validation of computational results is actually motivated by Thomas Edison, who wrote, ‘Until man duplicates a blade of grass, nature will laugh at his so-called scientific knowledge,’” Makhatadze said.

“There are several viable approaches to optimize proteins,” Makhatadze added. “Many researchers seek to optimize the protein by changing all types of physical interactions within the computer model at once. Instead, we felt that if we could understand one interaction, we could then use it to our advantage to build on the algorithm and then experimentally prove that that property really exists in the real protein system.”

The interaction the researchers focused on was the surface charge of the protein. The investigation of the importance of protein surface structure is a growing area of research within the field. In fact, a 2006 paper in the journal Biochemistry, published by Makhatadze supporting the importance of protein surface structure on stability, was the one of the top five most cited and downloaded papers from the journal that year.

In addition to important potential industrial applications, Makhatadze also believes the research sheds some light on the evolution of proteins. The researchers compared the mutations that they made within the proteins in order to optimize the protein’s performance with the mutations naturally occurring in the proteins from the evolutionary distant organisms.  Instead of seeing more mutations along with increased performance as with most evolutionary adaptations, the researchers saw that less frequent mutations resulted in a more stable protein. “This suggests that the stability of proteins might not be evolutionarily important,” he said.  “It appears that as soon as the protein is able to function in given conditions and is stable at a given temperature, anything above that is not really necessary.”

The research was fully funded by the National Science Foundation (NSF). Makhatadze was assisted in his research by post-doctoral researcher Mayank Patel, graduate student Jiajing Liu, NMR Core Director Scott McCallum, and Assistant Professor of Biology Chunyu Wang, all of Rensselaer, as well as former graduate student Alexey Gribenko, who is currently a member of the faculty at the University of Texas Medical Branch. In addition, the structure of one the proteins used in the study, acylphosphatase (AcPh), was actually solved at Rensselaer using the sophisticated nuclear magnetic resonance (NMR) core within the Center for Biotechnology and Interdisciplinary Studies (CBIS).