A scientific article in which the president of Tel Aviv University, Prof. Yosef Klifter, is a participant, published today in Nature Chemistry, reveals how geometry affects the laws of motion of molecules and other randomly moving particles and leads to the generalization of the laws of Brownian motion formulated by Einstein * The conditions studied in the article apply, among others, in living cells. The insights that emerge from the article have implications for our understanding of the intracellular chemistry that underlies processes such as: transcription and translation of the genetic material and the activity of drugs
A necessary condition for the occurrence of any chemical process is meeting of the molecules participating in it. For example, during the translation of an RNA molecule into a protein, the ribosome must locate the RNA segment and bind to it before the translation process begins. Although the relative proximity of the reactants always has an effect on the length of time that elapses until the end of the encounter step, the extent of the effect depends on the geometry of the medium Intermolecular.
In an article published today (Sunday) in the online version of the journal Nature Chemistry, Tel Aviv University President Prof. Yosef Klefter and researchers from the Department of Theoretical Solid State Physics at the University of Paris-6 explain how this movement can be described that occurs in an environment that is much more complex than the known environments To us and apparently the chemistry in it is different, through the inclusion of the theory of Brownian motion, which Prof. Albert Einstein was responsible for formulating.
Two people are in a huge stadium and decide to meet during a break for a cup of coffee at the cafeteria. Their chance of having time to hold the meeting and also drink the coffee depends on the distance between them and the amount of people inhabiting the stadium. If the duo is sitting in adjacent areas or alternatively if the stadium is almost empty, there are many chances that the meeting will take place during the break. Alternatively, if the stadium is crowded and the pair are far from each other, there is a reasonable chance that the break will end earlier.
The situation that prevails inside a living cell full of proteins and molecules of different types is similar to the situation described above. In the cell, each protein has a role that requires it to meet with other proteins and molecules. One of the examples of a process in which many proteins participate is the copying of the genetic material stored in the DNA molecule into an RNA molecule and later the translation of the RNA molecule into a protein. A key condition for the process to occur quickly and efficiently is that the physical meeting between the many molecules participating in it will occur within a short period of time.
Understanding and analyzing the factors affecting the meeting times challenge contemporary scientists and this is due to the random movement characteristic of the molecules participating in the process.
Basic research on this topic may have implications in many areas related to the chemistry of small and dense environments. Specifically in cells, it may enable a new research tool for examining the way existing drugs work inside the cells, the possibility of developing personalized drugs and, in the more distant future, the possibility of genetic manipulations for gene therapy - by replacing damaged genes with normal genes.
The botanist Robert Brown was the first to discover the physical phenomenon in which tiny particles immersed in a liquid do not stand still but move randomly back and forth. The person who improved the formulation and stood on the microscopic basis for its occurrence was Prof. Albert Einstein, but the phenomenon is still known as "Brownian motion". Brownian motion is also known as diffusion, an example of which is the spread of an ink drop in a glass full of water. The mathematical formulation of the phenomenon allowed scientists to introduce order into randomness, understand the laws of motion of individual molecules and provide an explanation for a wide variety of phenomena. Despite the great success of the diffusion model, experimental observations have been collected over the years on systems in which such random movement occurs whose characteristics cannot be explained by the existing model, this diffusion was called anomalous diffusion. The scientists tried to explain the observed anomaly in two different ways, the purpose of the change. One explanation attributed the anomaly to the basic movement of the molecules, since it is possible that in certain random systems the underlying movement is more complicated and complex than the one described by Einstein. Another explanation held that the randomness governed by the basic mode of movement remains simple and that the reason for the complication is the complex geometry of the intermolecular medium.
The conventional idea holds that due to differences in the characteristics of diffusion (pulsation), the chemistry inside a living cell or in any other complex environment is different from the chemistry occurring in a test tube. Prof. Clifter is a world-renowned expert in the field of random motion of molecules and other nanoscale particles and his research has resulted in for inclusion of the laws of Brownian motion formulated by Einstein.
In their current study, Professor Clifter and his colleagues were able to link fundamental geometric characteristics of the intermolecular medium to the arrival time of a molecule from one point to another. The main conclusion that emerges from the study is that the degree of influence of the initial distance between the reacting substances on the amount of time that passes until they meet is divided into two. In an intermolecular medium known as compact, each molecule moves in a way that allows the presence of sites it has not visited at all, the presence of sites visited more than once is rare. In this medium the effect of the initial distance is small. In a medium that is not compact, the situation is the opposite, each site is checked many times. In this medium, the initial distance is of great importance because a small difference in it may result in an increase in the time required until the meeting by several orders of magnitude. The result may make the meeting irrelevant at all.
The researchers call the phenomenon they discovered: "geometry-controlled kinetics (movement)" and express hope that the conclusions arising from the research will be particularly useful for understanding reactions that occur inside living cells. State-of-the-art measurement devices that allow real-time observation of the movement and formation of individual molecules have revealed that genes undergoing successful transcription are clustered together in a well-defined spatial region. Movement in a cellular environment is known to suffer from the geometric limitations of the interior of the cell and the high density that prevails in it. Could it be that nature has learned to utilize geometry for its needs?
