Medical Biophysics

Dr. Emil Pai illustrates the working of a Molecular String Phone

Sep 27, 2019

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Researchers from Toronto and Hamburg combined their efforts to watch an enzyme at work with unprecedented detail.

Researchers from the laboratories of Dr. Emil Pai (Depts. of Medical Biophysics and Biochemistry, University of Toronto, and the Campbell Family Institute for Cancer Research, UHN) and Dr. Dwayne Miller (Depts. of Chemistry and Physics, University of Toronto, and the Dept. of Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Hamburg) have pieced together a time-lapse movie revealing all the major steps during the catalytic cycle of an enzyme. This is the most detailed depiction of such a process to date.

The communication between the protein units is accomplished via a water-network somewhat akin to a string telephone. This communication is aligned with a “breathing” motion, i.e. a molecular expansion and contraction of the protein. This time-lapse sequence of structures reveals dynamic motions as a fundamental regulatory element in the molecular foundations of life.

Dynamic behaviour is an integral part of the molecular building blocks of life. The motions and structural changes of biomolecules are fundamental to their function. Understanding these dynamic motions at a molecular level, however, is a formidable challenge. How is a protein able to accelerate a chemical reaction, which would take years to proceed without the help of such a molecular catalyst?

To obtain answers to this fundamental question, the researchers turned to an enzyme, made up of two identical parts, that splits the strongest single-bond in organic chemistry: the Carbon-Fluorine bond. Fluorinated carbons can be found in materials such as Teflon or GoreTex as well as in many pharmaceuticals and pesticides. Fluorinated compounds are of particular influence in climate change and their effects exceed those of CO2 by orders of magnitude. Therefore, the ability to potentially control and accelerate the turnover of C-F bonds is of particular interest to climate change moderation and bioremediation.

The researchers used time-resolved X-ray crystallography, a technique that allowed them to take molecular snapshots during the turnover reaction of the natural enzyme at ambient temperatures. This time-lapse movie revealed eighteen time points extending from 30 milliseconds to 30 seconds and covering all key catalytic states that finally lead to breakage of the C-F bond.

The researchers were very excited to see that the enzyme “breathes” during turnover, i.e. it expands and contracts in sync with the various catalytic steps. While this happens, the two halves of the enzyme communicate with each other via a string of water molecules that connects both halves and is part of a larger water network. These interactions allow the two halves to “talk” to each other and to share information about their catalytic state. This is crucial to the enzyme’s function as only one half of the enzyme can be active at a given time, a process that has been named “half-of-the-sites reactivity” and which is postulated for many of Nature’s catalysts but was visualized here for the first time. These dynamic changes have proven crucial to the enzyme’s function and the researchers expect many other enzymatic systems will exploit similar mechanisms to achieve their activity.

View the full research article.