Collaborations, and even new facilities with new tools, took hold. “Because I had one foot in the medical faculty, I started interacting collaboratively with a variety of scientists around the medical school,” says Harrison. “The dean asked me to help lead a small center for structural biology in the medical school to try to enhance its presence. I decided that one of the things this new center should do was spearhead a modest initiative in cryoelectron microscopy.”

It wasn’t long before, as Davies recalls, “the findings started coming out in torrents.”

In 1987, just one year into the initiative, Don Wiley at Harvard University answered a central question in immunology. For decades, scientists had wondered how the immune system could tell the difference between normal healthy cells and infected cells. They knew that a molecule called the major histocompatibility complex (MHC) played a role in tagging the unhealthy cells. But how did MHC flag down the passing T cells that would trigger an immune response? Using x-ray crystallography, Wiley and his student Pamela Björkman, who later became an HHMI investigator, showed that MHC contains a deep groove—perfect for cradling a short piece of protein, much like a hotdog in a bun. He surmised that MHC uses the groove to present foreign peptides to the T cells, which recognize the non-native bits of protein as a signal to act.

The Major Histocompatibility Complex
The major histocompatibility complex (MHC) contains a deep groove that is perfect for cradling a short piece of protein (red), much like a hotdog in a bun. The molecule uses the groove to present foreign peptides to passing T cells, which recognize the non-native bits of protein as a signal to trigger an immune response.
Credit: David Goodsell & RCSB Protein Data Bank

X-ray crystallography also proved to be an extremely powerful tool for obtaining information that could be used in fighting viruses. “There was an intense focus on HIV at the time,” says Harrison. “This was only shortly after the discovery of the virus that causes AIDS; there were no adequate drugs, and there was still a scramble to understand as much as possible about the virus and its properties to assist in thinking about therapeutics.” Wiley and Harrison decided to use the flexibility provided by HHMI funding to devote some of their joint effort to work on HIV.

Viruses usurp normal cellular processes to slip inside a cell and hijack its molecular machinery. One of the weapons that allows HIV to gain entry into a host cell is a molecular complex called gp120/gp41. The virus uses the complex to clamp onto a cell surface molecule called CD4. Wiley and Harrison focused their efforts on this entry process. Their work revealed some of the radical changes in shape that gp120 and gp41 undergo when the complex binds to CD4. Conformational changes in gp120 alert gp41 that it is time to go through its own transformation, which, in turn, launches a series of events that lead to the membrane fusion necessary for the virus to enter the host cell. Other HHMI investigators contributed crucial components of this picture, notably Wayne Hendrickson and his student Peter Kwong. According to Harrison, these early HHMI-based structural studies have become one of the foundations underlying current work on HIV vaccines.

Another of HIV’s armaments is reverse transcriptase. This enzyme allows the virus to merge its genome with that of its host, tricking the unsuspecting cell into producing new virus particles to invade neighboring cells. Fortunately, reverse transcriptase has a fatal flaw—it isn’t normally found in human cells, making it an ideal target for drugs. But the enzyme mutates very rapidly—another strategy that results in a very elusive quarry.

In the late 1980s, Steitz began work on solving the structure of reverse transcriptase bound to the experimental drug nevirapine. When nevirapine was discovered, it fit snugly into a pocket on reverse transcriptase where it easily blocked the enzyme’s activity. It wasn’t long, however, before reverse transcriptase mutated, making the drug useless. Steitz’s crystal structure uncovered the reason why. Several parts of the pocket had changed shape, and the drug could no longer bind and inhibit the enzyme’s activity. Luckily, several other areas of the pocket were unaltered, and they were used to create a new version of nevirapine.

HIV Reverse Transcriptase
Tom Steitz solved the structure of reverse transcriptase bound to the experimental drug nevirapine (yellow) and revealed why the drug no longer blocked the enzyme’s activity. Several parts of the pocket had changed shape, and the drug couldn’t bind to reverse transcriptase.
Credit: Tom Steitz

But How Does It Fold?

A phenomenon that puzzled structural biologists for decades is how a string of amino acids can fold into an orderly three-dimensional shape like Pauling and Corey’s alpha-helix. Brian Matthews, who became an HHMI investigator at the University of Oregon three years after the program started, set about answering this question. Using a protein called phage T4 lysozyme, he methodically substituted each of its amino acids with a different amino acid and then compared the resulting three-dimensional structures using x-ray crystallography.

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