Shortly after winning the 1972 Nobel Prize in Chemistry, Anfinsen turned his attention to interferon. Interferon is a protein generated by human cells that have been transformed by exposure to a virus, a parasite, or the actions of chemicals. The protein stimulates a powerful attack by the body's immune system on viruses and other disease-causing entities. Medical researchers believed that harnessing interferon's power could be a potential boon to fighting disease. Just as the complexities of Staphylococcus aureus stirred his interest in the 1960s, the chemical composition of interferon fascinated Anfinsen because protein chemists knew so little about it.
In 1974, Anfinsen and a team of young laboratory researchers used affinity chromatography to isolate and purify interferon. The purification process enabled them to produce large amounts of the protein, which had been previously available only in miniscule quantities. By 1979, Anfinsen guided a new team of researchers to determine the complete sequence of interferon's amino acid structure. He published the results of this research in 1980 in an important article in the Annals of the New York Academy of Sciences. The potential biomedical implications of this work were enormous. Pharmaceutical companies could produce interferon easily and design drugs that would capitalize on the protein's anti-viral properties. Scientists and physicians in the early 1980s hoped that they might be able to use the protein to treat certain forms of cancer. While interferon has not fulfilled all of these hopes as a "wonder drug," interferon drugs produced through recombinant DNA technology are used to treat tumors and infections, as well as multiple sclerosis, hepatitis C, leukemia, and AIDS-related Kaposi's sarcoma.
After spending a year as a visiting scholar at the Weizmann Institute in Israel, Anfinsen returned to the United States in 1982 to become a professor of biology at The Johns Hopkins University. After 1983, his research agenda was focused on Pyrococcus furiosus, or what he called "hyperthermophilic bacteria." These are microorganisms that thrive at extremely high temperatures, a rare occurrence since most enzymes lose their catalytic properties outside of a relatively narrow temperature range around 25º to 30º Celsius. "These crazy animals," as Anfinsen described the bacteria to a colleague in March 1983, "seem to enjoy life at 350º [Celsius] and 300 atmospheres and should have some fascinating proteins and nucleic acids in them." Like the Staphylococcus aureus he studied in the 1960s, or interferon in the 1970s, the biochemical composition and structure of these unusual bacteria captivated Anfinsen. And to a certain extent, investigating the chemical composition of these remarkable microorganisms was a return to his study of the biochemistry of the malarial parasite Plasmodium knowlesi in the early 1940s. He imagined that biochemists could use these thermophilic bacteria for practical applications, just as he imagined interferon could be a potential breakthrough for cancer patients. At the time of his death in May 1995, he was working on a project sponsored by the National Science Foundation to create enzymes from thermophilic bacteria that were powerful enough to detoxify contaminants, pollutants, and nuclear wastes in the world's oceans.