Researchers at Tel Aviv University have developed a three-dimensional model of a protein that crosses the cell membrane. will aid in healing

The scientific journal Molecular Cell publishes today, Friday, September 24, 2004, a study by a group of researchers including Dr. Nir Ben-Tal and PhD student Sheral Fleishman from Tel Aviv University together with two researchers from abroad, Vincens Unger and Mark Yeager.

Avi Blizovsky

The scientific journal Molecular Cell publishes today, Friday, September 24, 2004, a study by a group of researchers including Dr. Nir Ben-Tal and PhD student Sheral Fleishman from Tel Aviv University together with two researchers from abroad, Vincens Unger and Mark Yeager.

The study presents a computational model that makes it possible to predict how protein molecules crossing cell membranes look like. This is of great importance in understanding the molecular basis for the phenomena of communication between a cell and its environment and gaining new insights into various diseases. The important ones were partly performed in parallel processing, on powerful Octane model workstations made by Silicon Graphics.

Each cell is wrapped in a membrane that is a kind of protective wall that prevents dangerous substances from entering, but the cell must take in nutrients and oxygen, get rid of waste materials and communicate with its neighbors. Therefore, a way must be found in which only the essential substances for the cell will enter and substances that the cell wishes to get rid of will leave.

"Think about a group of cells in a tissue," says Dr. Ben-Tal in response to our question. "The cells are in physical contact with each other through these membranes, for example in the heart muscle. With each beat of the heart, all the muscle cells must contract in a coordinated manner. An uncoordinated contraction will impair the pumping efficiency of blood. Therefore, we must find a way for the cells to tell each other 'now we are doing this'. The connexin is one of the proteins responsible for this coordination."

How is this done?
"In order for the action to be carried out jointly, there must be a transfer of information from cell to cell. When a cell receives a signal that tells it to contract, it must transmit this signal to its neighbors in the tissue quickly so that they all carry out the command in a coordinated manner. Cell membranes make it difficult to transfer information, since the signal must pass through two membranes - one for each cell. This protein - connexin creates a channel connecting two adjacent cells, literally a hole in the membranes, which allows information to pass through the hole using small molecules. In this way, each cell in the tissue 'knows' about what is happening in its neighbors. "

The connexin is an example of one protein from a large family of transmembrane proteins. Transmembrane proteins play a central role in the communication between the cell and its environment. Defects in transmembrane proteins cause a wide variety of diseases in humans, including many types of cancer. Knowing the three-dimensional structure of a protein usually helps to understand the molecular basis of its action under normal conditions and in diseases. However, determining the structure of transmembrane proteins at high resolution is extremely difficult, and in many cases requires years of work. Alongside this, there are low-resolution structures of several transmembrane proteins, but these structures do not provide molecular detail of the protein, so it is not possible to learn from them directly about the effect of mutations on the structure, to plan and explain biochemical and biophysical experiments.

Gap junction channels composed of the connexin proteins connect neighboring cells, and play a critical role in the coordination between cells in many tissues, for example, during the heartbeat. Mutations in these channels are the main cause of inherited deafness, and are even involved in the degenerative nerve disease Charcot-Marie-Tooth (Charcot-Marie-Tooth) and the rare skin disease erythrokeratodermia variabilis (EKV). The structure of the canals was experimentally determined at low resolution in 1999 by Vincenzo Unger of Yale University and Mark Yeager of the American Scripps Research Institute. Many transmembrane proteins consist of helices packed against each other, and the structure showed the location of the helices that make up the gap junction channel. However, because of the low resolution, the structure did not provide an explanation for the effect of many disease-causing mutations, and did not shed new light on the properties of the channel as they are known from several decades of biochemical and biophysical experiments.

Ben-Tal: "Mutations in transcellular proteins of the connexin type are associated with diseases, including several types of deafness and skin diseases. The model that Sharel proposed explains the effect of almost 30 such mutations. In general, the molecule is built as a case of helices close together, as can be seen in the drawing. What stabilizes the structure is the interface between these coils. We found that about 30 mutations identified in patients, and characterized as causing diseases such as congenital deafness, are located in these interface areas. Any such mutation disrupts the structure of the protein. If the protein does not take its normal structure, it is easy for it not to be able to perform its function properly. It is difficult to predict exactly what each of these mutations will cause - there will be those that actually break down the protein, and the broken down protein will be digested by enzymes; In other cases, the mutations will cause a slight deformation of the structure so that the channel will be blocked or its permeability to certain critical molecules will change. In any case, these changes may lead to a malfunction of the protein, damage to communication between neighboring cells, and as a result of these, to disease."
This is the first time that such a significant amount of mutations in these channels has been explained by a single study. Based on the structural model, Ben-Tal and Fleishman presented a program for experimental research to examine the accuracy of the model, and to learn more about the relationship between structure, activity and diseases in this protein. The experiments are carried out in the laboratory of the Abraham Foundation (Tel University) and in the laboratories of Ted Bergello and Vito Versalis from the Albert Einstein College of Medicine in New York. Preliminary results from the two experiments confirm the model.
And what are you preparing to explore next?
Ben-Tal: "Now that we have developed the method, we are working on additional proteins. In our sights, the EmrE protein that serves as a pump that removes toxic compounds from the bacterial cell. This pump plays an important role in the resistance of bacteria to antibiotics, so it is important to understand its three-dimensional structure. Another protein we will investigate will be the GABA receptor that is activated in nerve cells in response to the neurotransmitter GABA. The receptor is of great medical importance as it is the intermediary in the introduction of anesthetics - sedatives and pain relievers, such as Valium."

How long did the development take?
Fleishman: "We started the building prediction project about four years ago, but a major part of that time was devoted to the preparation, verification and refinement of the methods. From the moment the tools were ready, another six months of work was required to adapt them to the specific case of the connexin. After we calculated the structure, we invested a lot more work, with the help of our research partners, to understand the meaning of the structure in relation to the biochemical and clinical information, and to establish and verify it."