Understanding the cell’s massive molecular machine: the ribosome

The Prize:

The 2009 Nobel Prize in Chemistry awarded jointly to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath “for studies of the structure and function of the ribosome.”

The Science:

The central dogma of molecular biology has remained essentially the same for decades: DNA encodes RNA which in turn encodes protein. Every cell’s genome has the information in it to perform all cellular activities, but the genetic information has to be transcribed into RNA, the blueprint molecule, in order to be used. That RNA can then be decoded and used to build the proteins which carry out the enzymatic, structural, and signaling functions crucial to life.

RNA and DNA are chemically very similar, but RNA is usually single-stranded, whereas DNA has two strands. The DNA genome stays in the nucleus, but RNA (or mRNA for message RNA) can be exported anywhere in the cell where its cognate protein is required. The decoding of the mRNA blueprint into a functional protein, a process called translation, requires the ribosome, a massive molecular machine.

The ribosome is a large complex of specialized RNAs, known as rRNAs, and proteins that assemble into two subunits, small and large. Together, the small and large subunits make up the functional ribosome, one of the largest complexes in the cell. In cells that produce a lot of protein, there are millions of ribosomes. Despite its productivity, the ribosome is remarkably accurate: only once in every 100,000 reactions will a ribosome incorrectly “read” the DNA encoding it.

The current understanding of this process, DNA to RNA to protein, has been shaped largely by information gleaned through structural biology. Structural biology is the study of the three-dimensional chemical structure of a biological molecule. Scientists discover a molecule’s structure through a number of methods including nuclear magnetic resonance spectroscopy, X-ray crystallography, and electron microscopy.

Structural biology shed light on the structure of DNA (Nobel 1962) and that of proteins (Nobels in 1962, 1964, 1972, 2002, 2003, 2006), but up until 2000, no one had any idea what the ribosome looked like at the atomic level.

Due to its large size (millions of atomic mass units!), the structural biology techniques most suitable for solving the structure of the ribosome are X-ray crystallography and electron microscopy. Although both methods can give us valuable information about a biological molecule, to date, crystallography has provided the greatest amount of detail, or what scientists call resolution. Structural biologists are always striving for structural information at the highest resolutions, resolutions at which they can visualize biological molecules at the atomic level. This information is available at resolutions around 3Å, or three one-hundred-millionths of a centimetre.

In the late 1970s, Ada Yonath decided to use crystallography to try to solve the atomic structure of the ribosome. At that time this goal was considered ambitious for a number of reasons. Crystallography works by concentrating a beam of X-rays on a crystal and analyzing the diffraction pattern as the electrons in the crystal scatter the incoming X-rays. Each “dot,” or reflection, in the pattern holds structural information for every atom in the crystal. Solving a structure by crystallography has two major prerequisites.

First, the molecule you want to study has to crystallize. Today, scientists manipulate conditions such as salt concentrations and temperature to achieve this, but crystallization is not always possible and it is virtually impossible to predict the conditions that will allow it.

Second, once one has a suitable crystal that diffracts X-rays well, there is a “phase problem.” The complex math required to convert the diffraction pattern into an atomic resolution structure requires one to know the “phase angle” of every reflection, which must be calculated and is not experimentally determined. The common trick for solving the phase problem is to introduce heavy atoms into the crystal, but this does not work in the case of ribosome crystalization, since the ribosome is so large that it binds to too many heavy atoms for proper analysis. Although Yonatz was able to “grow” many suitable crystals of the large subunit of the ribosome in the early 1980s, the phase problem stood in her way.

Thomas Steitz’s group solved this phase problem by approaching it from a different angle. The group used a lower-resolution cryo-electron microscopy structure of the large subunit as a starting point. In the years after this initial discovery, Steitz’s, Yonath’s, and Ramakrishnan’s groups published structure after structure of the ribosome. Each successive structure came closer to reconstructing the entire ribosome, but none reached atomic level resolution.

It wasn’t until 2000—20 years after Yonath crystallized the large subunit—that a high-resolution picture of the ribosome was revealed. Steitz and his collaborators published the structure of the large subunit at 2.4Å, and Ramakrishnan’s and Yonath’s groups published structures of the small subunit at 3Å and 3.3Å, respectively. Since then, others have solved the high-resolution structure of the entire ribosome, small and large subunit alike.

The Significance:

The structure of the ribosome revealed much about the chemistry and biology of translation. It showed the world how the ribosome can read the mRNA sequence and decode it into the unique amino-acid sequence that makes up a protein.

Knowing the structures of the ribosome in complex with mRNA, incoming amino acids, and the nascent protein chain at various stages of protein production has allowed scientists to infer the chemical reactions that govern translation. The structure has also helped guide researchers in designing experiments to test ribosome function and to understand how the ribosome performs its duties so faithfully.

All three of the Nobel laureates have solved structures of the ribosome in complex with antibiotics that target the ribosome. This has improved our understanding of the ribosome and provided insight into the development of new antibiotics for use in the antibiotic-resistance race against bacteria.