Scientists have revealed the detailed structure of the enzyme diacylglycerol kinase

Scientists have succeeded in deciphering the detailed structure of an ultra-tiny cellular nanomachine using the most powerful X-ray source on Earth

[Translation by Dr. Nachmani Moshe]
Scientists have been able to decipher the detailed structure of an ultra-tiny cellular nanomachine with the help of the most powerful X-ray source on Earth.

The scientists were able to decipher the structural map of this nanomachine - the enzyme diacylglycerol kinase - using a special method of crystallography. Using the method, the scientists were able to understand how this important enzyme performs its vital cellular functions - while receiving answers to questions that have remained unanswered for over 50 years. Kinase is a general name for a group of enzymes responsible for the activation of processes in the cell through the phosphorylation of molecules. These enzymes play an extremely important role in the processes of metabolism, cellular signaling, protein regulation, cellular transport, secretion of substances and many other cellular pathways that are all responsible for the healthy functioning of the body. These enzymes are responsible for coordinating the conversion of energy from certain molecules to a defined substrate, influencing their activity, reactions and their ability to bind to other molecules.

The enzyme Diacylglycerol kinase, which is the focus of the said research, has a role in the synthesis of the cell wall of bacteria. It is a small enzyme that is integrated within the cell membrane and it is the one that coordinates a particularly complex reaction: its fatty base is hydrophobic in nature (repelling water) and is therefore inside the fatty cell membrane, while the molecule with which it reacts, ATP, is completely soluble in water. The exact mechanism of this reaction of the enzyme remained a mystery for decades, until the publication of the study in question. "The mechanism by which this tiny nanomachine, which is less than ten nanometers in size, joins two separate materials together at the membrane interface has been revealed with the help of the detailed molecular crystal structure. This is the smallest kinase enzyme known, and the ability to observe the shape of its crystal structure helps us answer questions that have been formulated over 50 years research," said Professor Martin Caffrey, from Trinity College University's Department of Structural and Functional Biology in Ireland.

The ability to understand how this tiny machine works at the molecular level was made possible by the use of one of the most efficient X-ray sources on Earth, the one located at the Linear Accelerator Center at Stanford University. The lead researcher explains: "This device produces bursts of x-ray beams at a rate of femtoseconds. With the help of such fast bursts, we were able to obtain structural information about the enzyme before it breaks down." The tiny kinase is one of the research targets of the Center for Membrane Proteins within the Infectious Diseases of Arizona State University, designed to reveal the molecular basis of viral and bacterial proteins involved in diseases as well as human proteins that protect the body from attackers. In the future, the scientists hope to expand their work so that even videos depicting the activity of these nanomachines are obtained, so that we can see how the chemistry itself works at the atomic level and in real time. The research findings were published in the scientific journal Nature Communications.

 

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