Observed “live”: Water is an active player in enzymes

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In biologically active enzyme-substrate combinations, such as those found in drugs, water plays a more crucial role than previously thought. The surrounding water acts like a "glue" to hold a substrate in the right place of an enzyme. In addition, the dynamics of the water are slowed down. Researchers at the RUB led by Prof. Dr. Martina Havenith (physical chemistry), in close cooperation with scientists led by Prof. Dr. Irit Sagi from the Israeli Weizmann Institute observed and proved the slowdown in water dynamics “live” for the first time. The researchers report on their results in "Nature Structural & Molecular Biology".

What role does the solvent play?

Enzymes are natural substances that accelerate and control metabolic processes in the body. For example, they are of central importance for the immune system because they control the balance between activating and inhibiting defense reactions and play a major role in inflammatory reactions. It has long been known that enzymatic functions occur at very different speeds in different solvents. So far, however, the contribution of the solvent - in biological processes it is water - has not yet been clarified at the molecular level.

Two new techniques combined

The groups of Prof. Havenith and Prof. Sagi at the Weizmann Institute's Institute of Structural Biology have combined two newly developed experimental techniques to directly demonstrate the importance of water for enzymatic functions. The study focused on matrix metalloproteases (MMP). They are located outside of our cells in what is known as the extracellular matrix, where they perform central tasks on a molecular level as message brokers, managers or maintenance units. By breaking down the extracellular matrix, the MMPs are actively and directly involved in the remodeling of our tissue, for example in embryo or tumor growth and in wound healing. The numerous possible areas of application make this family of enzymes a starting point for drug development. "However, the mechanism for activating the matrix metalloproteases is not yet sufficiently known at the molecular level, which makes synthetic reproduction difficult," says Prof. Havenith.

Exact analysis of all "players"

For a precise understanding of the activation process, the researchers have for the first time carried out a comprehensive analysis of all the "players" involved: the matrix metalloprotease as the "enzyme vehicle", its activating substrate - the "key molecule" - and the water as the solvent that occupies most of the reaction environment. In the experiment, the scientists examined the binding of the substrate to the MMP. With the help of time-resolved X-ray spectroscopy, they were able to characterize the structural changes in the vicinity of the active enzyme center (here: the zinc atom) with atomic resolution. With the help of kinetic THz absorption spectroscopy (KITA), they recorded the changes in the rapid water movements over time.

Consider water in drug development

For different MMP-protein combinations, there was a clear correlation between the fluctuations in the water network, the structural changes and the function. Molecular dynamics simulations provided an explanation for the observations: As long as the substrate has not yet arrived at the "right place" of the enzyme, the water dynamics, ie the change of partners in the water molecules (the "terahertz dance" of water) is still fast . Simultaneously with the docking of the substrate to the active center, the water movement in the area is significantly slowed down. The water acts there like a kind of viscous glue that holds the substrate in place. This change in the THz dance of the water with the formation of the enzyme-substrate bond is only observed with biologically active enzyme-substrate combinations. "The slowing down of the water dynamics, which was investigated for the first time, therefore seems to be an essential part of the functional control," says Prof. Havenith. "It will therefore be crucial in the future to take the role of water into account in the development of drugs, for example to combat tumors."

“Solvation Science@RUB”

This work is integrated into the "Solvation Science@RUB" focus, the topic of the ZEMOS research building recommended by the Science Council for funding, from which the RUB's RESOLV cluster of excellence application also emerges. In chemistry, chemical engineering and biology there is an immense number of publications that consider solvents to be inert

describe (passive) media for molecular processes. Beyond this traditional view, however, the active role of the solvent is becoming increasingly evident. New experimental and theoretical methods now allow the investigation, description and systematic manipulation of the structure, dynamics and kinetics of complex solvation phenomena at the molecular level. "It is therefore time to develop a uniform model with predictive power for solvation processes," says Prof. Havenith. This is exactly the goal of "Solvation Science@RUB".

Title Shot

Grossman M, Born B, Heyden M, Tworowski D, Fields G, Sagi I, Havenith M: Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site. Nature Structural & Molecular Biology, Advance Online Publication (AOP), doi: 10.1038/nsmb.2120 http://www.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb.2120.html

Source: Bochum [RUB]