Nobel Prize in Chemistry 2017: Cryo-Electron Microscopy and Its Three Laureates

This note covers the Nobel Prize in Chemistry 2017: who won it, how cryo-electron microscopy lets scientists see the atomic shape of biomolecules frozen in water, how the three laureates' separate discoveries fitted together, how the method developed over several decades, why it matters for biology and medicine, and quick facts for exams.

What was the Nobel Prize in Chemistry 2017 awarded for?

The Nobel Prize in Chemistry 2017 was awarded jointly to Jacques Dubochet, Joachim Frank and Richard Henderson with the citation:

"for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution"

In plain words, the three laureates together built a way of using an electron microscope to take sharp, atom-level pictures of the molecules that make up living things, while those molecules are suspended in water rather than locked into a crystal.

Before this, scientists had very few ways to see what proteins and other large biological molecules actually looked like in their natural, watery state. The method is called cryo-electron microscopy (cryo-EM) because the samples are frozen ("cryo") before being examined.

The official name of this award is the Nobel Prize in Chemistry, awarded each year by the Royal Swedish Academy of Sciences.

Who are the laureates?

Jacques Dubochet

Jacques Dubochet was born on 8 June 1942 in Aigle, Switzerland. At the time of the award he was affiliated with the University of Lausanne, Switzerland, where he held an honorary professorship in biophysics.

He received one third of the prize. Dubochet earned his doctorate in 1973 from the University of Geneva and University of Basel, and worked at the European Molecular Biology Laboratory in Heidelberg from 1978 to 1987 before moving to Lausanne.

His contribution was solving the problem of water: in the early 1980s he found a way to cool water so fast that it became a solid glass-like state instead of forming damaging ice crystals, allowing biomolecules to keep their natural shape inside the microscope's vacuum.

Joachim Frank

Joachim Frank was born on 12 September 1940 in Siegen, Germany. At the time of the award he was affiliated with Columbia University, New York, USA, where he had worked since 2008 as Professor of Biochemistry and Molecular Biophysics.

He received one third of the prize. Frank completed his doctorate at the Technical University of Munich in 1970.

Between 1975 and 1986, working largely in the United States, he developed a mathematical method for taking many blurry two-dimensional electron microscope images of randomly oriented molecules and combining them into one sharp three-dimensional structure.

Richard Henderson

Richard Henderson was born on 19 July 1945 in Edinburgh, Scotland. At the time of the award he was affiliated with the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, where he was Programme Leader.

He received one third of the prize. Henderson earned his PhD at Cambridge University in 1969 and returned to the MRC Laboratory of Molecular Biology in 1973, remaining there ever since.

In 1990 he produced the first three-dimensional image of a protein, bacteriorhodopsin, at atomic resolution using an electron microscope, proving that the technique could in principle rival X-ray crystallography.

What problem were the laureates trying to solve?

For most of the twentieth century, scientists had almost no way to directly see the shape of proteins, DNA and RNA, the molecules that carry out the chemistry of life.

In the 1950s, researchers at Cambridge began using X-ray crystallography, in which molecules are packed into an ordered crystal and bombarded with X-rays, with the diffraction pattern used to work out the structure.

Later, nuclear magnetic resonance (NMR) spectroscopy was added for studying smaller proteins in solution.

Both older methods had real limits. NMR only works well for relatively small proteins. X-ray crystallography needs the molecule to form a well-ordered crystal, and many important biomolecules, especially membrane proteins embedded in the fatty membrane surrounding cells, simply refuse to crystallise.

Richard Henderson experienced this problem directly: while trying to crystallise a membrane protein for X-ray work in the 1970s, one protein was hard to produce in enough quantity and another failed to form crystals at all.

This pushed him towards the electron microscope as the only remaining option, even though electron microscopes were then thought suitable only for dead material.

The electron microscope itself had two long-standing obstacles. First, the powerful electron beam needed for high resolution would destroy delicate biological material, and a weaker beam gave only fuzzy, low-contrast images.

Second, electron microscopy needs a vacuum, and the water surrounding biomolecules would evaporate in that vacuum, causing the molecules to collapse and lose their natural shape. Solving these two problems, contrast and water loss, is the story of this prize.

How did Henderson get the electron microscope to atomic resolution?

Richard Henderson worked with bacteriorhodopsin, a purple, light-capturing protein naturally embedded in the membrane of a photosynthesising organism.

Instead of trying to remove and crystallise the protein on its own, he and a colleague kept it inside its natural membrane and covered the sample with a glucose solution to stop it drying out in the vacuum.

To deal with the destructive electron beam, the researchers exploited the fact that bacteriorhodopsin molecules are packed regularly and all facing the same way within the membrane. The general procedure was as follows:

1. Keep the protein inside its natural membrane rather than isolating it, and protect the surface with a glucose solution so it does not dry out in the vacuum.
2. Use a weak, low-dose electron beam to avoid destroying the sample, accepting that any single image will have poor contrast.
3. Because all the protein copies are regularly packed and identically oriented, use the overall diffraction pattern from many molecules at once to calculate a sharper structural image, in a way similar to X-ray crystallography.
4. Tilt the membrane sample under the microscope and take images from many different angles.
5. Combine these angled views mathematically to build a three-dimensional model of the protein's structure.

In 1975 this gave a rough three-dimensional model showing how the protein's chain wove through the membrane seven times, at a resolution later described as the best protein image an electron microscope had yet produced.

Henderson kept refining the method, travelling to different electron microscopes that each had particular strengths, and in 1990 he achieved a structure of bacteriorhodopsin at atomic resolution, matching what X-ray crystallography could achieve for crystallised proteins.

Draw a strip representing the cell membrane, with a protein chain zig-zagging back and forth through it seven times, as Henderson's 1975 model showed, and label the protein as "bacteriorhodopsin" and the surrounding strip as "membrane".

How did Frank make the method work for molecules without a crystal?

Henderson's success depended on bacteriorhodopsin's unusual, naturally ordered packing. The open question was whether an electron microscope could generate a sharp three-dimensional image of a protein that was simply scattered randomly in solution, at random angles, with no helpful crystal order at all.

Joachim Frank, working largely in New York, spent from 1975 to 1986 developing the mathematics to answer this.

His approach treated each fuzzy, low-dose electron microscope image of a molecule as a faint pattern buried in background noise. The steps in his image-processing strategy were:

1. Take many two-dimensional electron microscope images of individual, randomly oriented copies of the same molecule, each too faint and noisy to interpret on its own.
2. Use a computer program to spot recurring patterns that represent the molecule, separating signal from the noisy background.
3. Sort similar-looking images into groups, since images in the same group are likely to show the molecule from a similar angle.
4. Average the images within each group together, producing a sharper two-dimensional image for that viewing angle.
5. Work out mathematically how the different two-dimensional views relate to one another in three dimensions, and merge them into one three-dimensional structure.

Frank finished the core algorithms for this analysis in 1981 and published the method for combining the angled views into a full three-dimensional structure in the mid-1980s, demonstrating it on the surface of the ribosome, the large molecular machine inside cells that builds proteins.

This image-processing method, applied to any correctly prepared sample, became the mathematical backbone of modern cryo-EM.

How did Dubochet solve the problem of water?

Even with Henderson's imaging trick and Frank's mathematics, there remained the basic problem that most biomolecules exist dissolved in water, and water evaporates in an electron microscope's vacuum, destroying the sample's natural shape.

Earlier attempts to simply freeze samples failed because ordinary freezing forms crystalline ice, and ice crystals scatter the electron beam so badly that the resulting images are useless.

Jacques Dubochet's insight, developed in the early 1980s at the European Molecular Biology Laboratory in Heidelberg, was to cool water so extremely fast that its molecules had no time to arrange themselves into an ice crystal.

Instead, the water solidified while keeping the disordered, liquid-like arrangement of its molecules, a state called vitrified water or glass. The table below sets out how his preparation method worked.

Dubochet published the first clear images of several different viruses prepared this way in 1984, and the technique was soon adopted widely because it was relatively simple and needed only a tiny amount of sample.

Draw a small metal mesh grid holding a thin film of watery solution, an arrow showing it being plunged into a container of liquid ethane cooled by liquid nitrogen, and a zoomed-in box showing the water molecules frozen in a disordered "glassy" arrangement rather than neat ice crystal rows.

How did the discovery unfold?

Why does this discovery matter?

According to the Royal Swedish Academy of Sciences' press release, cryo-electron microscopy "has moved biochemistry into a new era" by letting scientists see biomolecules that were previously invisible, including proteins frozen mid-movement during a biological process.

In the years after the technique matured, it was used to image structures such as proteins that give bacteria resistance to antibiotics, molecular complexes involved in circadian rhythms, and the outer surface of the Zika virus, helping researchers look for possible drug targets.

The committee highlighted several practical advantages. Cryo-EM needs only a small amount of sample, works without the need to grow crystals at all, and can capture moving parts of a process as a kind of molecular film. It is especially useful for membrane proteins, which are common drug targets but are notoriously difficult to crystallise, and for very large molecular machines.

One limitation noted in the background material is that very small proteins are still better studied using NMR spectroscopy or X-ray crystallography rather than cryo-EM.

Overall, the sources describe the achievement as opening up what had been "blank spaces" on the map of biochemistry, letting researchers explore what the sources call life's molecular machinery in close to atomic detail.

How does this connect to what you study?

Cryo-electron microscopy builds directly on ideas met in school science: the structure of proteins and cells in biology, and states of matter and the behaviour of water in chemistry.

Understanding why water forms ice crystals on ordinary freezing, but can be turned into a disordered glass on extremely rapid cooling, touches the same concepts used when studying the particle arrangement of solids and liquids. The award ceremony speech notes that vitrified water is "both liquid and solid at the same time," which is a useful way to picture an amorphous solid for anyone studying states of matter.

Likewise, the basic idea that a protein's three-dimensional shape determines how it works, whether as an enzyme, a membrane channel or part of a virus, connects directly to biology lessons on protein structure and function. A student who has studied how enzymes depend on their folded shape can see why biochemists needed a way to see that shape directly rather than guessing at it.

The idea of a wavelength determining how small an object a microscope can resolve, met in physics lessons on light and waves, also explains why electrons, which have a much shorter wavelength than visible light, let scientists see details as fine as individual atoms, something an ordinary light microscope could never achieve.

Quick facts for exams

The Nobel Prize in Chemistry 2017 was announced on 4 October 2017 and awarded jointly to Jacques Dubochet, Joachim Frank and Richard Henderson by the Royal Swedish Academy of Sciences.

The citation praised them "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." Each laureate received one third of the 9,000,000 Swedish kronor prize. Dubochet was born in Switzerland and was at the University of Lausanne;

Frank was born in Germany and was at Columbia University in the USA; Henderson was born in Scotland and was at the MRC Laboratory of Molecular Biology in Cambridge, UK.

Together their work let scientists see biomolecules, such as proteins, frozen in near-natural, watery conditions at atomic-level detail, a major advance for structural biology and drug research.

Note: Source. The prize facts in this note are from the Nobel Prize's official site, nobelprize.org.

Glossary

• Cryo-electron microscopy (cryo-EM) — a technique that freezes biological samples and images them with an electron microscope to reveal their structure.
• Electron microscope — a microscope that uses a beam of electrons, instead of light, to produce highly magnified images.
• Vitrified water — water cooled so rapidly that it solidifies without forming crystalline ice, keeping a disordered, glass-like arrangement.
• X-ray crystallography — a method of working out a molecule's structure by shining X-rays through a crystal made of that molecule.
• Nuclear magnetic resonance (NMR) spectroscopy — a technique used to study the structure and movement of relatively small proteins in solution.
• Membrane protein — a protein embedded in the fatty membrane surrounding a cell, often difficult to crystallise.
• Bacteriorhodopsin — a light-capturing, purple protein found in the membrane of certain photosynthesising organisms, studied by Henderson.
• Atomic resolution — a level of image detail fine enough to show the positions of individual atoms within a molecule.
• Ribosome — the large molecular machine inside cells that builds proteins, used by Frank to demonstrate his method.
• Diffraction pattern — the pattern formed when a beam, such as electrons or X-rays, scatters off an ordered structure, used to calculate molecular shape.
• Negative staining — an older electron microscopy preparation method using a heavy-metal coating around the sample.
• Electron detector — the component of an electron microscope that records the image; new detectors introduced around 2013 sharply improved resolution.

Common errors and misconceptions

• Misconception: Cryo-electron microscopy was invented by a single person. Correct: It resulted from three separate breakthroughs by Dubochet, Frank and Henderson that were combined together.
• Misconception: The method simply freezes samples the way a freezer does. Correct: Dubochet's technique cools water so rapidly that it forms a disordered glass, avoiding the damaging ice crystals ordinary freezing produces.
• Misconception: Cryo-EM replaced X-ray crystallography and NMR entirely. Correct: The sources note small proteins are still better studied with NMR or X-ray crystallography; cryo-EM is particularly strong for large complexes and membrane proteins.
• Misconception: Henderson's 1990 result worked for any protein straight away. Correct: It depended on bacteriorhodopsin's special, naturally ordered packing in its membrane; a general method for randomly oriented molecules needed Frank's separate work.
• Misconception: The prize was for inventing the electron microscope itself. Correct: The electron microscope already existed; the laureates developed ways to use it on biomolecules in solution at high resolution.
• Misconception: The breakthrough happened all at once in 2017. Correct: The key discoveries date from the 1970s and 1980s, with resolution improving further after 2013; 2017 was simply the year the prize was awarded.

Exam-style questions with model answers

Q1. In which year was the Nobel Prize in Chemistry 2017 announced? [1 mark]

1. It was announced on 4 October 2017.

Q2. Name the three laureates of the Nobel Prize in Chemistry 2017. [2 marks]

1. The laureates were Jacques Dubochet, Joachim Frank and Richard Henderson, who shared the prize equally for developing cryo-electron microscopy.

Q3. What practical problem did Jacques Dubochet solve, and how? [4 marks]

1. Biomolecules in water could not survive an electron microscope's vacuum because water evaporates and ordinary freezing creates damaging ice crystals that scatter the electron beam.
2. In the early 1980s Dubochet solved this by cooling water extremely rapidly in liquid ethane, which was itself cooled by liquid nitrogen.
3. This rapid cooling turned the water into a glass-like, non-crystalline solid called vitrified water, preserving the molecule's natural shape.
4. He demonstrated the method in 1984 by publishing sharp images of several viruses prepared this way, and the technique became widely used.

Q4. Explain how Richard Henderson achieved the first atomic-resolution structure of a biomolecule using an electron microscope. [5 marks]

1. Henderson worked with bacteriorhodopsin, a protein naturally packed in regular, identically oriented rows within its membrane.
2. Instead of isolating the protein, he kept it in its natural membrane and protected it from drying with a glucose solution.
3. He used a weak electron beam to avoid destroying the sample, and because the molecules were regularly packed, used the overall diffraction pattern to calculate structural detail despite the poor image contrast of any single picture.
4. By tilting the sample and imaging it from many angles, he built up a three-dimensional model, first a rough version in 1975.
5. After years of refining the approach on the best available microscopes, in 1990 he achieved a structure of bacteriorhodopsin at atomic resolution, proving cryo-EM could match X-ray crystallography in detail.

Q5. Describe Joachim Frank's contribution to cryo-electron microscopy and explain why it was necessary. [5 marks]

1. Henderson's 1990 result depended on bacteriorhodopsin's unusually ordered, repeating packing within its membrane, which most proteins do not have.
2. The open question was whether randomly oriented, scattered molecules in solution could also be imaged at high resolution without any crystal-like order.
3. Between 1975 and 1986, Frank developed a mathematical method to find faint, noisy traces of individual molecules in electron microscope images and separate them from background noise.
4. He sorted similar images into groups representing similar viewing angles, then averaged each group to get a sharper two-dimensional view.
5. Finally he worked out how these different two-dimensional views related to each other in three dimensions, merging them into a single three-dimensional structure, demonstrated on the ribosome in the mid-1980s.

Q6. Why does the official press release say cryo-electron microscopy matters for biochemistry? [3 marks]

1. The press release states that cryo-electron microscopy "has moved biochemistry into a new era" by letting researchers see biomolecules previously invisible to any imaging technique.
2. It allows biomolecules to be frozen mid-movement, revealing processes in the cell that could not be seen before.
3. This has let scientists image structures such as antibiotic-resistance proteins and the surface of the Zika virus, aiding the search for new medicines.

Q7. What were the limitations of X-ray crystallography and NMR spectroscopy that cryo-EM helped overcome? [3 marks]

1. NMR spectroscopy only works well for relatively small proteins studied in solution.
2. X-ray crystallography requires the molecule to form a well-organised crystal, which many biomolecules, particularly membrane proteins, fail to do.
3. Cryo-EM avoids both limits because it does not need crystallisation and can image large complexes and membrane proteins directly in a near-natural, frozen watery state.

Q8. What was the prize amount for the Nobel Prize in Chemistry 2017, and how was it shared? [2 marks]

1. The prize amount was 9,000,000 Swedish kronor, shared equally among the three laureates, with each receiving one third.

Key takeaways

• The 2017 Nobel Prize in Chemistry honoured Jacques Dubochet, Joachim Frank and Richard Henderson for developing cryo-electron microscopy.
• The citation recognised their work on high-resolution structure determination of biomolecules in solution.
• Richard Henderson showed in 1990 that an electron microscope could reach atomic resolution, using the regularly packed protein bacteriorhodopsin.
• Joachim Frank developed the mathematics, from 1975 to 1986, to turn fuzzy images of randomly oriented molecules into sharp three-dimensional structures.
• Jacques Dubochet, in the early 1980s, solved the problem of water evaporating in the microscope vacuum by vitrifying it into a glass-like solid.
• After 2013, new electron detectors let cryo-EM routinely reach atomic resolution for a wide range of biomolecules.
• The prize amount of 9,000,000 Swedish kronor was shared equally, one third each, among the three laureates.
• Cryo-EM is especially valuable for membrane proteins and large complexes that resist crystallisation, though very small proteins remain better studied by NMR or X-ray crystallography.

Test yourself

Who were the three Nobel Prize in Chemistry 2017 laureates and what did they develop together?

Jacques Dubochet, Joachim Frank and Richard Henderson together developed cryo-electron microscopy for determining biomolecule structures at high resolution.

Where was Richard Henderson affiliated at the time of the award?

Richard Henderson was affiliated with the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, at the time of the award.

What is vitrified water, and who developed the method to create it for cryo-EM?

Vitrified water is water cooled so fast it solidifies into a disordered glass rather than ice crystals; Jacques Dubochet developed this method.

Which protein did Richard Henderson study to reach atomic resolution in 1990?

Richard Henderson studied bacteriorhodopsin, a light-capturing protein embedded in a membrane, achieving an atomic-resolution structure in 1990.

What problem in electron microscopy did Joachim Frank's work solve?

Joachim Frank developed mathematics to merge many fuzzy two-dimensional images of randomly oriented molecules into one sharp three-dimensional structure.

Why can cryo-EM study membrane proteins more easily than X-ray crystallography?

Because cryo-EM does not require the protein to form an ordered crystal, unlike X-ray crystallography, which many membrane proteins fail to do.

What technical change around 2013 improved cryo-EM further?

The introduction of new, more sensitive electron detectors around 2013 let cryo-EM routinely achieve atomic resolution for many more biomolecules.

What example virus did the press release mention as imaged using cryo-EM?

The press release mentioned the Zika virus, whose surface was imaged using cryo-electron microscopy to help search for potential drug targets.