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American architect Louis Sullivan famously said that in building, “form follows function.” So it goes with the machines of life, the myriad cellular structures that keep an organism afloat. Their job determines their shape. Knowing the shape of any given cellular machine, then, provides crucial information about what the structure does—how it works.
A large subfield of biology, structural biology, busies itself with unraveling the shapes of proteins and other cellular machines. In the early 1960s, chemists Max Perutz and John Kendrew discovered they could determine the shape of a protein by shooting x-rays into crystals made from that protein. The pair won the 1962 Nobel Prize in Chemistry for their efforts.
 | | | | |  |  | | | | |  |  | The Ribosome at Work
The ribosome is a molecular factory that translates the genetic information in RNA into a string of amino acids that becomes a protein. The following animation, which is part of HHMI's Biointeractive web site, shows how the ribosome works.
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| | | | |  | | The Award-Winning Work
This slideshow includes pictures of Steitz and his team, as well as an image of the ribosome.
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Nearly a half-century later, the 2009 Nobel Prize in Chemistry was awarded to a trio of structural biologists who decoded the structure of the ribosome—the largest, most intricate of the cellular machines. Steitz earned his third of the prize for decoding one of two halves of the ribosome, the large subunit, while Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology in England won for decoding the smaller subunit, and Ada Yonath of the Weizmann Institute of Science in Israel won for developing basic techniques for studying the ribosome.
Weighing in at more than 150,000 atoms, the ribosome is the engine of life itself, a delightfully intricate cellular gizmo that churns out the billions of proteins that brick-by-biological-brick build bacteria, birds, and biochemists. As the map of the ribosome helped show, the ribosome reaches back to the very beginning of cellular life on Earth, some two billion years ago. Decoding its shape, its structure, afforded a glimpse into that almost-unknowable past Đ and offered a road map to the future of antibiotics.
The first step in determining the structure of any molecule is making a crystal of it, and it's a notoriously tricky trial-and-error process. Yonath made the breakthrough in this regard, publishing in 1980 her recipe for making crystals of ribosomes that power a hardy, salt-loving Dead Sea micro-organism.
Convention in the field of structural biology holds that once someone figures out how to crystallize something, that person gets to take the first stab at solving the structure. But by the early 1990s, it became clear to Steitz that Yonath wasn't having any luck solving the structure of the ribosome, so he decided to jump in, and in 1995 Steitz launched the Yale ribosome project with biochemist Peter Moore and a postdoctoral fellow Nenad Ban.
After a lot of noggin-scratching, the trio eventually learned one reason Yonath wasn't having any luck: the crystals were moody, hypersensitive to salt. A drop in salinity caused some of them to “twin.” That is, the ribosome particles aligned in two distinct patterns instead of one, confusing data collection. “It took more than a year to figure out” how to make untwinned crystals, says Steitz.
As the team worked through that problem, they invented new techniques. At 10 times the size of the biggest molecule anyone had ever solved, the ribosome demanded special treatment. In particular, the Yale team figured out how to replace some light atoms in the ribosome with clusters of heavy atoms. The heavy atoms produce a big signal that can be used as a waypoint, or landmark, in the mapping of the ribosome. The Yale team pioneered this technique of heavy-atom replacement, which proved crucial in the quest to map the ribosome.
As the team generated the first low-resolution images of the ribosome, they double-checked their data against images made by HHMI investigator Joachim Frank. Though fuzzy by x-ray crystallography standards, Frank's electron microscopy images offered proof that the new techniques developed by the Yale team were, in fact, working.
The Yale team drove on. In 1998, they published their first ribosome paper, a low-resolution map of the large ribosomal subunit—the factory half of the machine, the part that actually builds proteins. (The other half, the small subunit, is the foreman—it receives messenger RNA and tells the large subunit what to do.) The team revealed their methods, and the race was on. Other teams working on the ribosome changed course, says Steitz, adopting the new methods his team had developed.
Within a year, the Yale team sharpened the image threefold. They made a trip to the powerful X-ray beam at Argonne National Laboratory in Illinois for final data collection. The data poured in, and the team spent months interpreting it, nearly hand-placing each atom. In early 2000 the team completed a finely wrought 2.4 angstrom-resolution structure of the large ribosomal subunit. “It was extraordinary,” says Steitz. “We had no idea what the ribosome was going to look like.”
Some 31 proteins glued together the outer shell and helped with housekeeping tasks. But deep inside, where the protein-making magic happened, there was nothing but coiled RNA, 3,000 bases of it. Here, laid bare, was the secret of life, or at least one of them: proteins were not built by other proteins, as biologists had once assumed. RNA did the job. For several decades, starting with Francis Crick in 1968, some ribosome researchers had theorized this to be the case, but the Yale structure proved it.
The implications were profound: the ribosome map provided deep support for the theory that the first organisms on Earth were built from RNA. “The ribosome is a prime basis for the ‘RNA world’ hypothesis” of how life began, says former HHMI President Thomas Cech.
And while the ribosomal shell differs from organism to organism, the RNA center, where the protein-building action happens, is nearly identical across every species on the planet. For some two billion years of cellular evolution, the same heart of the machine has been there churning out proteins, building life.
Fortunately, there exist minute differences between bacterial and human ribosomes. Antibiotics exploit these differences, mucking up bacterial ribosomes and killing the bugs. In 2001, Steitz, Moore, and other ribosome scientists launched a biotechnology company to exploit their new knowledge of the ribosome. Rib-X, based in New Haven, Connecticut, now has two new antibiotics in human trials, and many more in the pipeline. All are aimed at overcoming antibiotic resistance, a growing problem that renders some infections impervious to all known antibiotics.
Photo: Michael Marsland/Yale University
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