Ada Yonath and the "Impossible" Ribosome Crystals

For most of the twentieth century, the ribosome was too large, too irregular and too fragile to be turned into a crystal good enough for X-rays. Ada Yonath, an Israeli crystallographer at the Weizmann Institute of Science, decided to try anyway. Her patient work, which began around 1980, produced the first ribosome crystals, then the techniques that made them usable, and finally atomic views of how antibiotics jam the bacterial protein-synthesis machine. In 2009 she shared the Nobel Prize in Chemistry with Venkatraman Ramakrishnan and Thomas Steitz. She was the first Israeli woman to win a Nobel Prize and the first woman in 45 years to win the Chemistry prize. This post explains what she did and the chemistry behind it.

The Scientific Problem Before the Discovery

Cells make proteins on ribosomes. A bacterial 70S ribosome contains a 30S subunit (about 21 proteins and a 16S rRNA of about 1,500 nucleotides) and a 50S subunit (about 30 or more proteins and 23S and 5S rRNA). Together the complex has a mass of around 2.5 million daltons. To know how it works, scientists needed an atomic structure, and the main method for large molecules was X-ray crystallography.

Crystallography needs a crystal: billions of identical molecules arranged in a repeating lattice, so that the X-ray scattering from each adds up into sharp spots. A ribosome has moving parts and a large surface of charged RNA, so getting an ordered lattice seemed hopeless. When Yonath began, many senior scientists considered the idea close to absurd. Even if crystals formed, X-rays damage biological crystals within minutes, destroying the order before enough data can be collected. Two problems had to be solved: growing the crystals and surviving the radiation.

The Discovery: Step by Step

1. Choosing extreme organisms. Rather than the usual E. coli, Yonath looked at bacteria that live in harsh conditions, such as the thermophile Geobacillus stearothermophilus (called Bacillus stearothermophilus in older papers) and the salt-lover Haloarcula marismortui from the Dead Sea. Their ribosomes are naturally stable. Working with Heinz-Günter Wittmann in Berlin, she obtained the first microcrystals around 1980.
2. Improving crystal quality. Over years, her group varied salts, precipitants, temperature and ribosome states to get larger, better-ordered crystals.
3. Cryo-crystallography. To stop radiation damage she pioneered flash-cooling the crystal in a stream of cold nitrogen, around 100 K, so that free radicals formed by X-rays could not diffuse. This approach, now routine in protein crystallography, was a major technical breakthrough and helped all later ribosome structures.
4. Phasing with heavy-atom clusters. She introduced dense clusters of heavy atoms, such as a tungsten cluster, attached to the ribosome as markers, to help work out the phases of the diffraction pattern and to locate features at low resolution.
5. From low to atomic resolution. By around 2000, her group had a 3.3 Å structure of the 30S subunit and related work on the 50S subunit. At the same time, Ramakrishnan solved the 30S structure and Steitz the 50S structure. Yonath's group then produced structures of ribosomes with antibiotics bound, using Deinococcus radiodurans 50S subunits as well.

The Chemistry Behind It

X-ray crystallography follows Bragg's law:

nλ = 2d sin θ

where λ is the X-ray wavelength, d is the spacing between lattice planes and θ is the angle of diffraction. Measuring many reflections gives the electron-density map from which atoms are placed. The resolution is limited by how ordered the crystal is. Cooling reduces thermal motion and radiation damage, so higher resolution data become possible.

Chemically, the ribosome is an RNA-rich machine held together by hydrogen bonding, base stacking, and Mg²⁺ ions that neutralise the negative phosphate backbone. Yonath's structures showed how antibiotics exploit this. For example:

• Macrolides (like erythromycin) bind in the nascent peptide exit tunnel of the 50S subunit and block the growing chain.
• Chloramphenicol and related drugs bind near the peptidyl transferase centre and interfere with peptide-bond formation.
• Aminoglycosides (like streptomycin or gentamicin) bind the 30S subunit near the decoding centre and cause misreading of the genetic code.
• Tetracyclines block the A site so aminoacyl-tRNA cannot enter.

Her group also showed that the ribosome's structure suggests the peptide bond is made in a pocket that positions substrates, supporting the findings of Steitz and Moore on the ribozyme nature of the ribosome. Further, she proposed that the ribosome's two-fold symmetrical region near the active site might be a remnant of an ancient RNA dimer, a hypothesis about the origin of life that remains discussed and is not settled.

Applications Today

• New antibiotics. Knowing how drugs fit in the ribosome helps design molecules that overcome resistance, an urgent task in India and the world. Yonath's group continued to study how resistance arises and why certain antibiotics are selective for bacteria.
• Selectivity. Small differences between bacterial and human ribosomes explain why many antibiotics have low toxicity for patients.
• Cryo-cooling in every crystallography lab. Almost all macromolecular X-ray structures in the Protein Data Bank today are collected on cooled crystals, a direct legacy of her technique.
• Basic biology. Ribosome structures explain accuracy of translation, tRNA movement and the evolution of protein synthesis.

Exam Corner

• Nobel Prize in Chemistry 2009: Ramakrishnan, Steitz and Yonath, for studies of the structure and function of the ribosome.
• Yonath produced the first ribosome crystals (about 1980) and developed cryo-crystallography for fragile biological crystals.
• Bragg's equation nλ = 2d sin θ is the basis of X-ray diffraction; know how to use it in numerical problems.
• Macrolides block the 50S exit tunnel; aminoglycosides cause misreading at the 30S decoding site; tetracycline blocks the A site.
• Extremophile organisms (thermophiles, halophiles) give stable ribosomes useful for crystallisation.

Common Misconceptions

• "Cryo-crystallography is the same as cryo-electron microscopy." No. Yonath's method freezes a crystal for X-ray diffraction; cryo-EM images frozen non-crystalline particles with electrons and was recognised by the 2017 Chemistry Nobel Prize.
• "Antibiotics kill by attacking the cell wall only." Many, like those she studied, inhibit ribosomes; penicillins attack the cell wall.
• "Her ribosome was from humans." The structures were from bacteria and an archaeon, which is also why the drugs studied can target bacteria selectively.

FAQ

Why use Dead Sea or hot-spring bacteria?

Their ribosomes are adapted to extreme salt or heat and are more rigid and stable, which helps them form ordered crystals.

What is the phase problem?

Detectors record intensities of diffracted X-rays but not their phases. Without phases you cannot calculate electron density, so methods such as heavy-atom derivatives are needed.

Did Yonath share the prize with the other two ribosome scientists?

Yes. The three laureates solved complementary parts of the ribosome and the prize was shared equally.

How does this link to my syllabus?

It connects X-ray diffraction (physical chemistry), nucleic acids and protein synthesis (biochemistry) and drug action (medicinal chemistry), all common themes in JAM, NET and GATE.

Published by ABC Chemistry — IIT-JAM | CSIR-NET | GATE Chemistry Coaching. Visit abcchemistry.com