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Researchers Solve Mystery of Mutations in Antibodies

Research groups at The Scripps Research Institute (TSRI) in La Jolla, California, and The Ohio State University in Columbus, Ohio, have discovered a new role for many of the changes that occur to antibodies as they mature to fight disease. According to the study, not only does the immune system optimize antibodies to bind to foreign substances like viruses, it also optimizes them to be more stable. The discovery could change the thinking on how the immune system protects us from foreign substances, and might eventually help make better antibody-based drugs.

The work, recently reported in the online Early Edition of the Proceedings of the National Academy of Sciences of the U.S.A., was led by Peter G. Schultz at TSRI and Thomas J. Magliery at Ohio State. Two other senior researchers from TSRI, Ian A. Wilson and Vaughn V. Smider, along with their colleagues, were authors on the study.

Humans naturally produce a collection of antibodies, called the germ-line repertoire, that gets activated when foreign substances are detected. That detection causes immune cells to optimize antibodies to a mature form that is more effective in fighting a particular invader. It has been known for some time, partly from earlier work by Schultz, that many of the mutations that occur in affinity maturation do not help the antibodies bind better to the foreign substances.

Now, the group led by Schultz and Magliery showed that many of those other mutations are there so that the antibody remains stable. They also showed that many of the mutations that improve the binding actually destabilize the molecule, suggesting that these other peripheral mutations might be required for the proper function of antibodies.

“We mainly have thought of antibodies as being very stable molecules that are tolerant of the mutations needed to make them into better binders,” said Magliery. “But what we know now is that many of the binding mutations lead to instability, and that many of the peripheral mutations that looked unimportant really compensate for the destabilizing ones.”

Much of the experimental work was done by Feng Wang, a colleague of Schultz who is now a scientist at the new California Institute for Biomedical Research, Calibr, in La Jolla. The antibody stability measurements were carried out by graduate student Shiladitya Sen in Magliery’s lab, which has pioneered methods for high-throughput measurements of protein stability.

In collaboration with Wilson, who studies the structures of proteins using a technique called X-ray crystallography, the team was able to show that an antibody with only the destabilizing mutations in the binding site disturbed networks of nearby atoms that are likely to be important for stability. Exactly how the further-away peripheral mutations stabilize the mature antibodies is not yet clear.

The discovery may suggest that the immune system actively works to keep antibodies stable, although only a hint about how it might do that was demonstrated in this study.

Besides shedding new light on how the immune system functions, the discovery could also lead to better drugs. “So-called biologics, which are mostly antibody-based drugs at this point, often suffer from problems with aggregation or storage because of instability,” said Magliery. “Studying these peripheral mutations might help solve that problem.”

Schultz is a professor in the Department of Chemistry, holds the Scripps Family Chair and is a member of the Skaggs Institute for Chemical Biology at TSRI and the director of Calibr. Magliery, now a professor of chemistry and biochemistry at Ohio State, did his graduate training with Schultz at the University of California, Berkeley.

The research was supported by two grants from the National Institute of General Medical Sciences (NIGMS), part of the Nationals Institutes of Health (grant numbers GM062159 and GM083114), as well as by The Skaggs Institute for Chemical Biology at TSRI.

 For more information on the paper, “Somatic hypermutation maintains antibody thermodynamic stability during affinity maturation,” by Feng Wang, Shiladitya Sen, Yong Zhang, Insha Ahmad, Xueyong Zhu, Ian A. Wilson, Vaughn V. Smider, Thomas J. Magliery, and Peter G. Schultz, see

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“What we know now is that many of the binding mutations lead to instability, and that many of the peripheral mutations that looked unimportant really compensate for the destabilizing ones.”
—Thomas J. Magliery