Scientific daring, great talent and historical coincidences led to the cracking of the protein puzzle
If the Nazis had not occupied Austria, it is possible that Max Perutz - one of the giants of modern biochemistry - would have managed the chemistry department in the textile factory of his wealthy Jewish family. But Perutz became a destitute refugee in 1938 and settled in England where he began his doctoral studies. He received his training at the Cavendish Laboratory at the University of Cambridge, six of whose scientists received Nobel Prizes in the fields of biochemistry. Together with his student John Kendro, Perutz received the Nobel Prize in Chemistry in 1962.
His enormous contribution to the understanding of the phenomenon of life was summed up by the fact that he managed to crack the protein puzzle. He passed away about a month ago.
The protein is mainly known as one of the nutrients, or as the white substance in a broken egg, and its name in Hebrew is derived from milk. But this substance has a much deeper importance, as implied by its foreign name, protein, from a primary language. Most of the weight of the human body (except for water) is protein, and different proteins are the main building blocks of blood cells, muscles, skin and hair. Special proteins called enzymes are in charge of controlling all chemical processes in the body. Important hormones such as insulin and essential protective components such as antibodies - are also proteins. In short, the proteins are the essence of every living thing.
Organic substances that make up the living body come in many shapes and sizes. A molecule as simple as alcohol in wine has two carbon atoms, six hydrogen atoms and one oxygen atom, for a total of nine atoms. Cane sugar has a more substantial separation and has 45 atoms. But in a protein molecule, even a relatively small one, there are more than a thousand, and in many there are tens or even hundreds of thousands of atoms. But not only the size matters: each protein also has a unique code, as it is built as a long string of units called amino acids, which are like letters in written text. The information needed to build the proteins is stored in the genes, each of which is responsible for the production of a specific protein.
When Kandro and Peretz began their pioneering work, a central puzzle still remained regarding the essence of proteins: how is a long chemical chain, similar to that found in a "dead" plastic material such as nylon, able to bring about the complicated life processes and build cells and organs? To find the answer, it was necessary to find out the detailed structure of a protein, that is, to find the exact spatial position of each and every atom within it. Perutz chose to start this ambitious work with a protein known to everyone - hemoglobin, which gives blood its red color and carries oxygen from the lungs to the various tissues. Separating the hemoglobin was quite a challenge, more than ten thousand atoms, and the work of decoding that began in 1973 lasted about 25 years.
The Cavendish Laboratory at the University of Cambridge is one of the most amazing science sites ever created by mankind. Among the scientists who won Nobel Prizes are Jim Watson and Francis Crick, who deciphered the double helix structure of DNA, and Fred Zenger, who received two Nobel Prizes for methods to find the order of the "letters" in DNA and protein. The young Max Perutz began working with the physicist Sir Lawrence Berg, another Nobel laureate from the same laboratory, who invented a method for deciphering the spatial structure of frogs. The method is called X-ray crystallography, and its development was made possible thanks to an interdisciplinary combination that we see more and more at the beginning of the 21st century, a connection between biology and chemistry, physics, mathematics and computing.
With this method, one must first produce crystals of the material whose structure is to be deciphered. The process of consolidating the large protein powders is not simple and requires special skill. In the next step, the crystal is irradiated with a focused beam of X-rays (x-rays) and the manner in which the rays are scattered in space is monitored, in a process that physicists call diffraction. An example of this is the rainbow colors reflected from the face of a CD, due to the dense dots burned onto the silver surface. And just as the colors may teach about the microscopic model of the burning points, it is possible to get information about the arrangement and structure of the particles in the crystal from the scattering of the X-rays. In this radiation, the wavelength is a thousand times smaller than that of visible light, and thus it is possible to observe the spatial arrangement of the tiny atoms, in a sort of molecular microscope.
When it comes to a small particle, such as that of sugar, it is relatively easy to perform the mathematical analysis with the help of which the exact atomic structure is calculated from the scattering of the rays. But in protein production the task is thousands of meters difficult, and originality and courage were required to start a project of this kind. Perutz had to apply special methods, such as combining "foreign" metal atoms - mercury or gold - in the protein, and the deciphering required experiments with more than a hundred different preparations. Another historical coincidence that made the breakthrough possible is the development of the first digital computers in the XNUMXs and XNUMXs, just in time to complete the decoding of the hemoglobin structure.
At the end of the admirable study, Perutz and his colleagues were confronted with the hemoglobin separation in every exclusion. It turned out that the protein is not a purely random chain. Internal chemical forces give it a very precise three-dimensional structure and give it types of functional capacity, which justify calling it a molecular machine. It was discovered, for example, that the binding of an oxygen molecule to one of four sites on the surface of the protein causes a tiny shift that is transferred by "atomic levers" to the other end of the protein. The "transmitter" generates a structural change in the remote area and a stronger binding of oxygen in the additional sites, a process called allostery. This phenomenon, it turned out, is essential for hemoglobin's ability to bind a lot of oxygen in the lungs and release it efficiently in the tissues.
In fact, during the publication of Perutz's articles in the XNUMXs, the details of the first nanotechnological device were discovered - a sphere measuring a millionth of a centimeter. The modern developments of nanotechnology today aim to apply the same principles, with the help of which the hemoglobin fragment can "automatically" fold into a tiny entity with a defined structure and function, one that fulfills its biochemical tasks with maximum efficiency.
Perutz's work brought about a revolution in the field of molecular biology. In every large research university, also in Israel, there is a unit that implements his methods. In the online databases there are currently thousands of structures of different proteins, with different degrees of accuracy. Also, relying on the information that has already been accumulated, the modern supercomputers make it possible to try to guess the three-dimensional structures of other proteins according to the order of their chemical "beads". In an initiative that is not typical of the world of heavy-headed science, a competition is held every year to predict protein structures. A scientist who is getting close to deciphering some protein with X-rays in the style of Max Perutz informs the organizers of the competition at a later date. All those interested submit guesses based on calculation without seeing the results of the experiment, and the person whose computer program came closest to the truth is highly respected.
An important use of the method developed by Perutz is in the field of discovering new drugs. Most drugs in pharmacies are a kind of "guided missiles" that target a specific protein in the body. Knowing the exact spatial structure of proteins that sit at important junctions in the cell's mechanisms makes it possible today to design drugs with the greatest efficiency. In such a way, for example, some of the components of the AIDS cocktail were developed.
Even today, 50 years later, there are still many challenges in cracking the protein puzzle. For example, only a few of the proteins found in the fatty membrane of the cell and used as "antennas" to transmit intercellular transmissions - have been successfully deciphered. Precisely these proteins, whose importance in the pharmaceutical field is great, are extremely difficult to synthesize, and whoever invents a proven method to do so will gain fame. There is also the important goal of deciphering the structure of all the tens of thousands of proteins encoded in the genome, within the branch called proteomics. It seems that this goal will be achieved in the next decade or two.
When Proutz was working on hemoglobin, some argued against him that a protein is too big a molecule and that with the methods he used he would never succeed in deciphering it. Perutz's persistence and talent proved the critics wrong. In the XNUMXs, such criticism was directed at scientists who proposed to use similar methods to decipher one of the most complicated nuclear devices, the ribosome, which is responsible for building the proteins in the cell according to the genetic information in the DNA. Prof. Ada Yonat from the Weizmann Institute of Science was the first to attack this impossible "machine" containing millions of atoms using the methods invented by Peroz. For her pioneering success, she will be awarded the Israel Prize this year.
Perutz and Yonath's stories emphasize once again the fact that pure basic research, such as involves taking risks, is essential to human development and ultimately pays medical and economic dividends to the nations in which it is conducted.
