Three developers of a technique to view proteins, viruses and other biological objects have just won the 2017 Nobel Prize in chemistry. The technique requires flash freezing the materials. Now, with some recent advances, scientists can use this technique to peer into structures at the atomic scale.
Jacques Dubochet works at the University of Lausanne in Switzerland. Joachim Frank is a scientist at Columbia University in New York City. Richard Henderson works in England at the MRC Laboratory of Molecular Biology in Cambridge. Together, they contributed to the development of what’s now known as cryo-electron microscopy.
The Royal Swedish Academy of Sciences announced the new winners on October 4. At an awards ceremony in December, the men will receive a medal. They’ll also share a 9-million-Swedish-kronor prize. (It’s worth about $1.1 million.)
Andrew Murray is a systems biologist at Harvard University. He applauds the selection of these winners. Their work “lies at the basis of an incredibly important technique.” The award, he says, goes to people who helped science be able to “see molecules up close and personal.”
Now we can see the intricate details of every drop of our body fluids, Sara Snogerup Linse said at a news conference today. With that, “we can understand how they are built and how they act and how they work together," said Linse. She chaired the 2017 chemistry Nobel committee. “Soon,” she predicted, there will be “no more secrets.”
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Evolution of the technique
The technique allows scientists to map the landscape of molecules. They can see details at scales as tiny as just tenths of a nanometer (billionths of a meter). Such closeup details can help them see how these very small things work.
In the past, structural biologists have relied on two other tools. One of them is nuclear magnetic resonance (NMR) spectroscopy. NMR allows scientists to probe biological molecules in a solution, such as water. But this technique generally could be used only with fairly small proteins. The other is X-ray crystallography. It bounces X-rays off of a crystal to create a 3-D picture of a molecule’s structure. Unfortunately, “A lot of proteins cannot be crystallized,” Murray notes, “So their structures are inaccessible to the prying mind of the biochemist.”
Another technique is electron microscopy (EM). It works well for imaging nonliving things. It fell short, however, when applied to biological molecules.
EM is similar to X-ray crystallography in some ways. The technique maps how the beams deflect off of the material they’ve passed through to sketch out the material’s atomic structure. But the powerful electron beams can incinerate any protein or biological material as they pass through it. This produces fuzzy images. And there’s another drawback. The material being imaged must be in a vacuum (in the microscope). That causes water within biological molecules to evaporate. This further distorts the shapes.
In 1975, to get around these problems Henderson placed bacterial proteins within the electron microscope. To keep them from drying out, he covered their membrane with a sugar-water solution. To minimize damage to the proteins, he also weakened the electron beam. Still, the images were fuzzy, not clear.
But the proteins in his sample happened to be oriented in the same direction. So Henderson put the fuzzy images together. This created one sharper image.
He then turned the membrane this way and that. With each change in direction, he grabbed new images. Depending on how he added them together, he could now see the protein’s structure in three dimensions. This was better than before. But it still didn’t give him atomic-scale details.
Frank’s work helped with that. He was tackling the issue of orientation. Unlike Henderson’s proteins, most molecules do not all line up in the same direction. Frank’s solution, published in 1981, was to create a computer algorithm. He scanned the images to look for any proteins oriented in the same direction. Then the computer program grouped similar ones together. Like Henderson’s combined image, each group that Frank processed was somewhat sharper than before.
Meanwhile, Dubochet was probing how to keep his samples from drying out and becoming damaged. Freezing the samples also wouldn’t work. That’s because ice crystals will distort a molecule’s shape. But if the water cooled superfast to ‒196° Celsius (‒320° Fahrenheit), it would turn solid without forming ice crystals. Instead, it became glass-like, or vitrified. In 1984, Dubochet showed that when he covered viruses with a fine layer of vitrified water, he could be safely image them in an electron microscope.
This was the birth of cryo-electron microscopy, or cryo-EM.
At last, atomic-scale resolution
In 1990, Henderson produced the first cryo-EM image of a protein at the atomic scale. The next year Frank used cryo-EM to view ribosomes (RY-boh-soams). These are particles that help make proteins. But for some time, such images were not all that sharp. Many researchers in fact took to calling this technique “blobology.”
Over time, however, other researchers offered up improvements. Some used better optics or detectors or computing techniques. Sriram Subramaniam is a structural biologist at the National Cancer Institute in Bethesda, Md., In 2015, he reported improving the resolution of cryo-EM images to an ultrafine 0.22-nanometer scale. This rivalled the resolution of the current gold standard: X-ray crystallography.
“We are now at atomic resolution,” says Subramaniam. “Now, we need to apply this to look at larger [structures] to understand how these different molecular machines work.”
Recently, cryo-EM has begun to demonstrate its value. Last year, for instance, it was used to map the structure of the Zika virus. This helped identify possible regions of the virus that could be targeted with a vaccine or other drug.
New types of electron detectors have recently been developed for this type of microscope, notes Michael Rossmann. He’s a physicist and microbiologist at Purdue University in West Lafayette, Ind. He worked on the Zika mapping. With these new advances, he says, “Cryo-EM has revolutionized structural biology, particularly in the last three years.” He describes it as a “resolution revolution.” Next up, he predicts: looking at an entire cell.
Subramaniam also believes there are exciting years ahead. “This is just the beginning.”
algorithm A group of rules or procedures for solving a problem in a series of steps. Algorithms are used in mathematics and in computer programs for figuring out solutions.
atomic Having to do with atoms, the smallest possible unit that makes up a chemical element.
bacterial Having to do with bacteria, single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside animals.
biology The study of living things. The scientists who study them are known as biologists.
cancer Any of more than 100 different diseases, each characterized by the rapid, uncontrolled growth of abnormal cells. The development and growth of cancers, also known as malignancies, can lead to tumors, pain and death.
cell The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.
chemistry The field of science that deals with the composition, structure and properties of substances and how they interact. Scientists use this knowledge to study unfamiliar substances, to reproduce large quantities of useful substances or to design and create new and useful substances. (about compounds) Chemistry also is used as a term to refer to the recipe of a compound, the way it’s produced or some of its properties. People who work in this field are known as chemists.
computer program A set of instructions that a computer uses to perform some analysis or computation. The writing of these instructions is known as computer programming.
crystal (adj. crystalline) A solid consisting of a symmetrical, ordered, three-dimensional arrangement of atoms or molecules. It’s the organized structure taken by most minerals. Apatite, for example, forms six-sided crystals. The mineral crystals that make up rock are usually too small to be seen with the unaided eye.
crystallography A field of science that studies crystals, especially their structure and composition.
distort (n. distortion) To change the shape or image of something in a way that makes it hard to recognize, or to change the perception or characterization of something (as to mislead).
electron microscope A microscope with high resolution and magnification that uses electrons rather than light to image an object.
evaporate To turn from liquid into vapor.
gold standard A common term used to mean the premier currently most reliable standard for judging the quality or authenticity of something.
magnetic resonance The vibration of two magnetic waves in synchrony, allowing one of them to strengthen.
membrane A barrier which blocks the passage (or flow through) of some materials depending on their size or other features. Membranes are an integral part of filtration systems. Many serve that same function as the outer covering of cells or organs of a body.
microbiology The study of microorganisms, principally bacteria, fungi and viruses. Scientists who study microbes and the infections they can cause or ways that they can interact with their environment are known as microbiologists.
microscope An instrument used to view objects, like bacteria, or the single cells of plants or animals, that are too small to be visible to the unaided eye.
molecular biology The branch of biology that deals with the structure and function of molecules essential to life. Scientists who work in this field are called molecular biologists.
molecule An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).
National Cancer Institute The largest of the 21 institutes making up the National Institutes of Health. With a staff of almost 4,000 people, NCI is based in Bethesda, Md. It’s budget of almost $5 billion a year goes to support research — by its scientists and outside researchers — to better understand, diagnose and treat cancers.
Nobel Prize A prestigious award named after Alfred Nobel. Best known as the inventor of dynamite, Nobel was a wealthy man when he died on December 10, 1896. In his will, Nobel left much of his fortune to create prizes to those who have done their best for humanity in the fields of physics, chemistry, physiology or medicine, literature and peace. Winners receive a medal and large cash award.
optics Having to do with vision or what can be seen.
particle A minute amount of something.
physicist A scientist who studies the nature and properties of matter and energy.
protein A compound made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. Among the better-known, stand-alone proteins are the hemoglobin (in blood) and the antibodies (also in blood) that attempt to fight infections. Medicines frequently work by latching onto proteins.
solid Firm and stable in shape; not liquid or gaseous.
solution A liquid in which one chemical has been dissolved into another.
vaccine (v. vaccinate) A biological mixture that resembles a disease-causing agent. It is given to help the body create immunity to a particular disease. The injections used to administer most vaccines are known as vaccinations.
vacuum Space with little or no matter in it. Laboratories or manufacturing plants may use vacuum equipment to pump out air, creating an area known as a vacuum chamber.
virus Tiny infectious particles consisting of RNA or DNA surrounded by protein. Viruses can reproduce only by injecting their genetic material into the cells of living creatures. Although scientists frequently refer to viruses as live or dead, in fact no virus is truly alive. It doesn’t eat like animals do, or make its own food the way plants do. It must hijack the cellular machinery of a living cell in order to survive.
X-ray A type of radiation analogous to gamma rays, but having somewhat lower energy.
Zika A viral disease that can be transmitted to humans via mosquitoes. About 20 percent of infected people get sick. Symptoms include a slight fever, rash and pinkeye and usually fade quickly. A growing body of evidence suggests that the virus could also cause a devastating birth defect — microcephaly. Evidence suggests it may also cause neurological conditions such as Guillain-Barré syndrome.
Journal: M. Adrian et al. Cryo-electron microscopy of viruses. Nature. Vol. 308, March 1, 1984, p. 32.
Journal: A. Bartesaghi et al. 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor. Science. Vol. 348, June 5, 2015, p. 1147. doi: 10.1126/science.aab1576.
Journal: A. Merk et al. Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Cell. Vol. 165, June 16, 2016, p. 1698. doi: 10.1016/j.cell.2016.05.040.
Website: The Nobel Prize in Chemistry. Nobelprize.org, October 4, 2017.