Opinion: Enzymes are a well-oiled industrial machine

The analogy to autonomous cars opens up possibilities for further future research, in which enzymes will be programmed by scientists using methods of artificial intelligence * Article by Prof. Emeritus Sasson Tchaik from the Institute of Chemistry at the Hebrew University

Enzymes are complex and wonderful objects, which are responsible for many essential actions and reactions in nature. In the picture (1A) you can see one such enzyme, which belongs to the family of cytochromes called P450 which him I recently researched with Dr. Kashtrash D. Dubey, of Shivnar University in India, and published in a book called "". The P450 is made up of coils and pieces of protein units. 6 million nanometers), so it is a miniature machine used by our body to carry out essential needs such as maintaining pregnancy, creating essential molecules News, neutralization of toxic molecules and production of bioactive molecules.

In addition to their complexity, the enzymes are characterized by reaction speed and cyclic reaction mechanisms, starting with the reception of the molecule (the raw molecule), which is intended to be changed by the enzyme, the change of the molecule to the final product (the target molecule), then back to the initial state of the cycle, until the entry of the next raw molecule, and God forbid . This process is called the catalytic cycle of the enzyme, (Figure 1B), and it occurs many times (tens of thousands to millions of times) in one second, with each time the target molecule is formed. The greater the number of cycles per second, the more efficient the enzyme. The P450 family is found in all the flora and fauna, and is the engine of chemical synthesis of many of the molecules that make up the biological world around us.

In general, the reaction speed of enzymes is enormous (thousands to millions of times per second) and faster than that of industrial catalysts. The fastest enzyme, called "Catalase", protects cells from antioxidants by converting hydrogen peroxide to oxygen and it reaches a speed of 10 million cycles per second. Another example concerns the enzymes involved in DNA synthesis in the human body. The length of the DNA strands produced by them in one second is equivalent to a speed that is about 12 times the speed of sound. If we combine the length of DNA that is produced for the entire human population, we can say that these enzymes created in one second DNA equal to the length of 247 rotations of the Earth around the Sun.

The catalytic cycle of the enzyme (Figure 1B) is one of the most fascinating aspects of enzymatic activity, functioning autonomously - almost like a machine with internal software. In the depths of the enzyme, there is a flat ring of atoms called a porphyrin that binds an iron ion, thus creating an iron-porphyrin complex which is the site where the reaction of the enzyme takes place (VII in picture B1). The iron binds to the protein on one side of the ring while on the other side the iron binds the oxygen molecule, which is then split into two atoms by electrons and protons supplied to the enzyme. This is how the active molecule is created which performs all the chemical transformations that the enzyme needs to bring about in the raw molecule (picture B1).

The rest of the enzyme consists of helices, loops, and groups of protein units (Figure 1A), which help the iron complex carry out each step of the reaction at the correct timing. The researchers in the current study used a method called molecular dynamic (MD) simulation, which initializes the enzyme at room temperature and follows over time the movements of the atoms or group of atoms. When the enzyme receives a raw molecule, it will break down one of the carbon-hydrogen bonds (CH) and oxidize it (link to COH) while creating a molecule that the organism uses for its needs (for example: creating energy). MD simulation allows the researcher to map out all the essential movements that this little machine makes to complete a cycle, which is seemingly autonomous, just as if the programming by hand had disappeared.

The simulations show that P450 is a nanomachine, exchanging molecules with the outside, using channels and water dams and functioning automatically as soon as the raw molecule enters the enzyme cavity. The rest of the work is done by a protein that provides electrons, some of the atom groups of the enzyme and water molecules that provide us with the correct timing to change the molecule that entered the enzyme at the beginning of the cycle and to produce the target molecule (for example fatty acids that have undergone a change essential to their function in the organism).

During the research, we discovered fascinating results, related to the opening or closing of the enzyme to absorb the raw molecules, closing and opening of water dams used as shuttles for protons, and channels through which the oxidized products exit and provide the enzyme with a signal to activate a new cycle. The more we analyzed the MD pathways, the more it became clear to us that the amazing properties of these enzymes are rooted in the chemistry of weak interactions in crowded spaces. This signal is sensed by the protein coordinating all the stages of the cycle and by the oxidation selectivity of the enzyme. This mode of activity is different from industrial or artificial catalysts created in laboratories.

Since these enzymes are created by specific genes, and assuming that the gene constitutes the activation programming of the enzyme, we assume that all the critical movements of the enzyme (such as closing and opening water dams) are programmed into the enzyme as artificial intelligence. This intelligence reacts to the chemical course of the chemical reaction, and is sensed by the enzyme with the help of the changes in the weak interactions between the enzyme and the raw molecule that undergoes a change. The analogy to autonomous cars is at this point only an idea, but although it has not been proven yet, it opens up possibilities for further future research, in which enzymes will be programmed by scientists using methods of artificial intelligence.

The author of the article is Prof. Emeritus Sasson Tchaik, from the Institute of Chemistry at the Hebrew University of Jerusalem.

More of the topic in Hayadan:

• An interdisciplinary development at the Technion: a cell that produces electricity and hydrogen from spinach leaves using sunlight
• Study: Human Enzyme Extends Mice's Life
• On evolutionary pathways of enzymes and communication between sophisticated bacterial populations