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It Wasn’t Always Crystal Clear

Hear from a Nobel-winning crystallographer and her story on polar bears and sending crystallization experiments to space.

With grey, curly hair that strikingly resembles the structure of ribosomes, it was fitting Professor Ada Yonath won the 2009 Nobel Prize in Chemistry for her work in illuminating how ribosome function based on their structure.

Ribosomes exist in the cells of all organisms. They turn information held in DNA into proteins necessary for life, a process that is known as “translation of the genetic code”. Yonath explains, “Ribosomes are clever. They can read a language of four letters. They hardly make mistakes. They can work in every cellular environment, even in the lab, under conditions similar to those of the dead sea, hot spring, and the North poles.”

The structure of the ribosome remained a mystery until Yonath found a way to use the the complicated method known as crystallography. She says, “The procedure is physics, it requires high level math, the question is biological, and the answer is expressed in chemistry. My first contribution was to crystallise the ribosome which had been tried previously by many, all of whom failed.”


Early Life

Yonath was born in 1939 in Jerusalem, Israel into a poor family. Her childhood memories were centered around her father’s medical conditions and her constant desire to understand the world around me. Her father passed away when she was 11. To lift some burden off her mother who had to provide for Ada and her younger sister, she had several jobs as a cleaner, dishwasher, baby sitter as well as giving mathematics and chemistry tuition to help supplement the household expenses. Yonath recalls that books kept her occupied in her tough childhood.


Yonath was curious from a young age. “I was curious about the way things work, and I wanted to understand how the world functions.” To satisfy this curiosity, at five years old, she tried to measure the height from the floor to the ceiling in her balcony, by piling furniture like tables and chairs and climbing on top of them, when she fell into the backyard and broke her arm. Fortunately, she recovered from it and her curiosity survived.

She did not always know she wanted to study science. “My parents did not have formal education. I did not even know that there is a profession called scientist! I did not think that science could be a paid profession as I considered it as a hobby.” In fact, she wanted to be a writer.

After high school, she served compulsory army service in the “top secret office” of the Medical Forces, where she was exposed to clinical and medical issues. She then enrolled to the Hebrew University of Jerusalem.

She graduated with a bachelor’s degree in chemistry in 1962, and a master’s degree in biochemistry and biophysics in 1964. In 1968, she obtained her Ph.D. from the Weizmann Institute of Science for X-ray crystallographic studies on the structure of collagen. She continued working on fibrous proteins (muscle) in her first postdoctoral year at the Mellon Institute in Pittsburgh, Pennsylvania before moving to the Massachusetts Institute of Technology (MIT) to study the structure of a globular protein, staphylococcus nuclease.

In 1970, Yonath returned to the Weizmann Institute where she initiated and established what was for nearly a decade, the only protein crystallography laboratory in Israel.

She was always curious about the process of protein biosynthesis. Ribosomes are found in all living organisms, from yeast, bacteria, to mammals, and are essential to life. In all cells, ribosomes produce proteins that are responsible for a vast array of tasks. Proteins transport oxygen from the lungs to the rest of the body, control the sugar level in blood, build hair and nails, produce energy and more. Yonath says ribosomes are very intelligent, “DNA is a code of four letters, and proteins are made up of amino acids which come in 20 forms. So, the ribosome is a very clever machine that reads one language accurately and operates in another.”

To understand protein synthesis, she had to determine the three-dimensional structure of the ribosome, which are the cells’ factory for translating the instructions written in genetic code into proteins – and thus revealing the mechanics guiding the process.

But she did not work on ribosomes structures until a few years later.


The Polar Bears

How Yonath came to work on ribosomes was a result of her observation that ribosomes readily deteriorate. She assumed that this is the reason for the other’s failures to crystallize. Then, while recovering from a brain concussion from a bicycle accident in 1979, she read a lot including an article on the North pole polar bears.

Yonath says during the winter, the polar bears hibernate. In spring, their metabolism begins to be active again. She read that the polar bears ribosomes were packed in an orderly manner in the inner side on their cell membranes, and assumed that the tight packing is protecting from deterioration for months. “The logical way to explain this phenomenon, was to suggest that at the end of the winter, when they get up from their winter sleep, they need lots of active ribosomes for their normal life. So, I thought that this is the way that they preserve active ribosomes, by close-packing them.”

Assuming that this was a natural strategy to maintain ribosomal activity for a long time, after her recovery in 1979, she started working on ribosomes from organisms that live under harsh conditions. She studied hardy bacteria living under extreme conditions from the Dead Sea, hot springs and nuclear facilities’ waste. Since ribosomal instability was the main obstacle, using bacterial strains that could tolerate high temperature or high salt levels, seemed to Yonath the right thing to do.


Faced With Disbelief

When Yonath started her work to map ribosomes, most scientists were certain she would fail, because many researchers were unable to even obtain the ribosomal crystals that were needed to study their structure.

She persevered and succeeded in obtaining crystals from the hardy bacterial strains. However, after six years of constant crystals improvements, she found out that the crystals decayed in the X-ray beams used for data collection.

She compared this step to climbing Mount Everest only to discover that at the peak, a higher Everest stood in front of her.

She reasoned that the cause was breaking the chemical bonds between the ribosomes followed by motions of the “freed” atoms within the sensitive ribosomal crystals. This led her to invent a procedure to minimise the crystals’ internal energy, thus reducing the motion.

She dipped the crystals in oil before snap-freezing them to cryogenic temperatures (– 185°C), to minimize the crystalline structure’s disintegration under the X-ray bombardment. This technique is called cryo-bio-crystallography, which was essential for the mapping of the ribosome structure and became routine almost instantly after discovery, and this is now routinely used worldwide in structural biology.

Yonath fondly recalls the day in 1987 when her team conducted the experiment, as one of the rare Eureka moments. She says it is only second to the great pleasure she had when seeing her first high resolution structure a dozen years later.

In the mid-1990s, once she proved the feasibility of ribosome crystallography, several scientists initiated parallel efforts to map the ribosome. At the end of the 1990s, Yonath as well as those who used her innovation succeeded in breaking the resolution barrier, thanks to improvements in the crystals, in the facilities for detecting the X-ray diffraction and in ways to determine the diffraction phases. Using X-ray crystallography to map the position for each and every one of the millions of atoms that make up the ribosome, Yonath published the first complete three-dimensional structures of both ribosomal subunits of the bacterial ribosome, simultaneously alongside two other fellow Nobel Laureates in 2000 and 2001.


New Antibiotics

The findings published in Nature in 2001, helped pave the way for clinical applications in improving existing antibiotic drugs or designing novel ones.

Mapping and understanding the structure of the ribosome was a long discovery that took Yonath over two decades, despite the ridicule she received from the international scientific community. She doubted herself many times and harboured thoughts of giving up but encouraged herself to find the answers to the questions she posted two decades ago.

Yonath says mapping the ribosomes was only the beginning, and that her quest to understand them was far from complete. Owing to the vital role played by ribosomes in life, they are targeted by many antibiotics that bind to their functional sites. Armed with new insight into ribosomal structure, she moved on to reveal what these structures could tell about ribosome actions and how antibiotic drugs block those actions in bacterial ribosomes. Because ribosomes translate the genetic codes into protein in the same way in all cells, but they have slightly different structures in microbes, when compared to eukaryotes, such as human cells, many antibiotic drugs work by targeting their actions.

Each antibiotic has only one attachment site and resistance can occur quite easily. Yonath’s efforts are aimed at finding new sites on the ribosome specific to the pathogenic (disease causing) ones to which she is designing new antibiotics using the three-dimensional structures of the ribosomes of harmless and pathogenic bacteria, as determined by her crystallography. She found that the antibiotics bind in specific sites, most of which are located on the periphery of the ribosome, very far from the functional centers, which are targeted by the clinically used antibiotics, thus can block them and prevent the ribosomes from manufacturing proteins.

Research in this area is still ongoing.


Growing Crystals in Space

For about a decade, Yonath also worked with the European Space Agency (ESA) on several crystallography experiments. She explained that when she was growing crystals on Earth, they were always either stuck to the bottom, or to the ceiling of the crystallization chambers. They were very thin, and too fragile to be used for crystallography. She then sent ribosome samples into space, on 12 space missions, to assess crystallisation in zero-gravity. In essence, without gravity, the crystals are expected to float and not stuck to something.

The experiments in space proved futile. ESA was working alongside NASA around the same period, and they had about 30 labs participating in growing crystals for almost two decades. Eventually, Yonath found only one crystal that grew thick enough, but that also broke upon entering Earth, so the research was discontinued.


The Everest Beyond the Everest

Yonath says that science is demanding thus setbacks are expected, whether they are funding issues, failed experiments, or doubts about the feasibility of research.

In fact, on the day she received the Nobel Prize call from Stockholm, Sweden, Yonath was still discussing budget issues with the National Institutes of Health (NIH).

Her best advice for scientists in their early careers? Don’t ask for advices.


More Questions Than Answers

Post-Nobel, Yonath is the Martin S. and Helen Kimmel Professor of structural biology at the Weizmann Institute of Science in Israel, where she is working on the translation of the genetic code, and the antibiotics that hamper it. Yonath is grateful for the prize although she says it should not be the only thing scientists should focus on, “(winning the Nobel Prize is) the highest recognition, I can’t see myself working for it. I work only to satisfy my curiosity. Nevertheless, I appreciate it very much.”

Yonath now has more questions than answers about ribosomes, “How did these first ribosomes come into being? How did they begin to produce proteins? How did they preserve well through evolution into the sophisticated protein factories we see today in living cells?” And she says, “I was called crazy for years, but I was encouraged by seeing modest signs of progress in our work. Being a scientist is a joy. You ask a question that really interests you, and you work on answering it. That is like working on your hobby”.

With the prize and recognition, she says her grey curly hair has a new saying in Israel now, “Curly hair means a head full of ribosomes”. [APBN]

This article was derived from the Global Young Scientists Summit held from 20 to 25 January 2019 in Singapore. The interview was conducted by Lim Guan Yu.