Polar bears and drunken ribosomes

Professor Ada Yonat from the Weizmann Institute deciphered the structure of the ribosome, the cell's factory for producing proteins, and tells about the bumps, the breakthroughs and the coincidences on the way to one of the most important discoveries in biology

by Dorit Ferns

These days, when genetics permeates almost every area of ​​our lives, it is easy to forget that the main players in the body are actually the proteins. Many of the genes of each of us contain the code that allows the cell to produce the various proteins responsible, in fact, for all the important processes in our body. The genes, i.e. the DNA found in the cell nucleus, do not create the proteins directly, but are first copied into RNA segments, which leave the cell nucleus and enter the cytoplasm where they are translated into proteins.

The processes of DNA replication, transcription into RNA and the translation of RNA into protein underlie the activity of all cells known to us today, and they are carried out through a set of proteins unique to each of them. The first to isolate the protein responsible for DNA replication was Arthur Kornberg, who won the Nobel Prize for his work in 1959. The structure of the reproduction complex was deciphered by his son, Roger Kornberg, who also won the Nobel Prize in 2006. The third side of the triangle, the structure of the ribosome, was deciphered by Ada Yonat, from the Weizmann Institute, who has not yet won the Nobel Prize for her work, but has won many prestigious awards, including the Israel Prize in 2002, the Wolf Prize in 2007, and recently the L'Oréal-UNESCO Prize "For Women in science".

As with other important discoveries in biology, the road to the structure of the ribosome was also full of bumps, mistrust from colleagues and many lucky moments that Yonat knew how to take full advantage of. After a bachelor's degree in chemistry and a master's degree in biophysics at the Hebrew University of Jerusalem, Yonat began her doctoral thesis at the Weizmann Institute of Science, where she began to specialize in protein crystallography, that is, in deciphering the structure of proteins by forming them and irradiating them with X-rays. After completing her doctorate, she studied at the Massachusetts Institute of Technology (MIT) , returned to the Weizmann Institute in 1970, where she still works today.

Crystallography is in fact the only way today that makes it possible to accurately determine the structure of complex molecules. One of the most well-known examples of this is of course the decoding of the DNA structure after its formation by Rosalind Franklin and its crystallographic decoding by Francis Crick and James Watson, who won the Nobel Prize. Deciphering the spatial arrangement of the DNA makes it possible to immediately understand how it replicates, that is, how the genetic information is passed from generation to generation. Yonat also understood the main principles of the process in which RNA is translated into protein immediately after seeing the structure of the ribosome for the first time - but this exciting moment occurred after many years of struggles and experiments.

When Yonat began her journey in the world of crystallography, they mainly knew how to determine the structure of stringy molecules such as nucleic acids and small proteins, or of viruses whose formation is very easy thanks to their polyhedron structure. But the ribosome in bacteria consists of about 50 different proteins, and our ribosomes are even bigger than it. In addition, it is very difficult to crystallize ribosomes because they contain a considerable amount of RNA, which, as we know today, serves as the main active ingredient in this wonderful machine, but does not "like" to crystallize. Not only are ribosomes huge, they also break down quickly and can be found in a variety of spatial arrangements (conformations), for example in structures that allow certain phases of activity versus an inactive structure. All these factors make their formation an awe-inspiring task, since in order to create a crystal, it is necessary to somehow "convince" the ribosomes to be in the same conformation and line up side by side in an orderly three-dimensional pattern.

About a decade before she began her research on ribosomes, Yonat, as a beginning researcher at the Weizmann Institute, was engaged in setting up her laboratory. The head of the department at the time, Gerhard Schmidt, was very supportive in the field of crystallography, and gave the young Yonat an extraordinary honor - her own office, which was a bathroom where the toilet was converted into a chair and the sink was converted into a desk. "Good, a dual-purpose office," Yonat tried to admire. "Not really," answered Schmidt, "we cut off the water flow." Yonat got the courage to try and synthesize ribosomes, an operation that was considered impossible, from an article that described how the ribosomes of polar bears are packaged in dense and orderly cases on top of the cell membrane during hibernation. If the bears can, Yonat thought, then so can I.

In order to understand the activity of ribosomes, Yonat embarked on a journey of almost two decades to determine the structure of the ribosome. The tendency of ribosomes to disintegrate during preparation and formation is the most difficult problem, especially regarding ribosomes produced from the most common bacterium in the world of research, Escherichia coli, which they tried to form before her. Yonat decided to produce ribosomes from bacteria growing in harsh living conditions, assuming that their ribosomes would be more stable, such as bacteria growing in the Dead Sea and thermophilic bacteria (growing at temperatures of about 80 degrees Celsius). Indeed, the ribosomes produced from these bacteria were more stable.

However, the problem of conformation still remained, since most of the ribosomes produced were in inactive states. An article published 20 years earlier by researchers at the Weizmann Institute, Ada Zamir and Ruth Miskin, describing how ribosomes can be returned to their active conformation by heating them in the presence of alcohol, resulted in the long-awaited solution. Happily, Yonat and her group were able to obtain small crystals of the alcoholic ribosomes already 3 months later, but it took more than six years before Yonat was able to obtain suitable crystals for X-ray analysis.

But when the big day came, it turned out that the joy was premature. During the measurement, the X-rays created free radicals that immediately spoiled the fine crystals and did not allow obtaining important information. Yonat assumed that it would be possible to solve the problem by deep cooling which would stop the progress of free radicals and their intensification. But a method for deep, immediate and uniform cooling was not found, because during the preparation for cooling, which takes a few seconds, the biological crystals dry out and are damaged. But Yonat did not despair. A visiting scientist from the USA who was involved in synthesizing a particularly explosive organic molecule encountered a similar problem. "In the few seconds it took to transfer the crystals from the viscous growth solution to the center of the crystallography facility, they were exposed to air and exploded," explains Yonat. To solve the problem, he used to dip the crystals in gear oil." To protect her crystals, Yonat dipped them in gear oil that "wrapped" them and isolated them from the air. Those who survived the "humiliation" were immediately cooled to the temperature of liquid nitrogen, stayed there until the end of the measurement, and were preserved even after many X-ray irradiations.

Within four months in 1986, the entire world of crystallography switched to using this method. The method known today as cryo-crystallography (freeze formation) has since been perfected and is used as the accepted method for determining the structure of crystals of biological molecules and enables the use of problematic crystals, which in no other way are suitable for measurement.

It was one of the most significant breakthroughs in the journey. Yonat started the experiment on Friday evening, and by midnight her group already had the first data on the structure of the ribosome. The next morning she received phone calls from many scientists who called excitedly to ask if it was true - if she really succeeded in collecting crystallographic data from ribosome crystals. The positive answer of Yonat, who was considered the "crazy" of the field, did not satisfy them. "Let us talk to someone reliable," they asked. However, another 10 years passed and additional obstacles had to be overcome before her group was able to solve the structure of the ribosome.

Understanding the structure of the ribosome is important for understanding all forms of life known to us today. But it has another importance: many types of antibiotics damage the activity of bacterial ribosomes. Antibiotics solve many problems, but resistance to them is a serious problem. Revealing the structure of the ribosome allowed Yonat to focus on understanding how antibiotics work and to propose ways to fight resistance to them and develop new types of antibiotics. Another research goal is to try to understand how ribosomes looked and worked in the ancient world, when life was just beginning to form on Earth.

"Today, such studies are extremely rare," Yonat says, because they take a long time and scientists whose promotion is important to them will hesitate to take on such a research topic. This is also the reason that financing such studies, which produce results after more than a decade, is almost impossible. In Yonat's opinion, there is a need for "a committee of experts that will find a way to separate the chaff from the chaff, and locate the important projects that cannot be reached easily, without waving the stick of publicity and personal promotion." Yonat also accepts that the number of students who come to study in Israel has decreased considerably compared to the distant past mainly due to the security situation. It is hoped that Yonat's recommendations will be accepted. We will all just get hired from them.

Dorit Ferns is a doctor of biology, a practitioner of Chinese medicine and a member of the editorial board of Scientific American Israel.