01. 03. 2019

The internationally respected Journal of the American Chemical Society has published a significant discovery by fifteen Czech scientists who have been studying enzymes or, more specifically, the mechanisms which can significantly improve their efficiency. Experts from the Loschmidt Laboratories at the Masaryk University together with scientists from J. Heyrovsky Institute of Physical Chemistry of the CAS have been working on this research for more than six years. They expect their results will find a good use in biotechnological or pharmaceutical industry.

Teams of Jan Sýkora from the Heyrovsky Institute and of Zbyněk Prokop from Loschmidt Laboratories have had one main objective: to understand the ways in which enzyme dynamics can influence the course of chemical reactions. Specifically they focused on dehalogenase – a bacterial enzyme capable of breaking down toxic molecules with chlorine and bromine into less-toxic alcohols.

Dehalogenase enzymes are quite large molecules. The actual chemical reaction, which transforms the substrate compounds to final products, takes place in a so-called active site. This site is adjusted to the molecules entering the reaction, and it has been supposed that its properties have a strong impact on efficiency of the enzyme. In many cases, however, these active sites are buried deep in the molecule of the enzyme, and the substrate molecules have to get there first.

“The molecules enter the active site via a system of tunnels and gates which can influence their passage. So far, scientists have not deemed the shapes and properties of these tunnels and gates to be of any particular importance. We have, however, focused precisely on these transport pathways whose shape and dynamics influence which molecules can get inside or out, thus changing the efficiency of those enzymes,” explains one of the co-authors of the study, Piia Kokkonen, a pharmaceutical chemist of Finnish descent, who currently works in the Loschmidt Laboratories.

Switching between two states

A high activity of the dehalogenase enzyme led scientists to a theory that the enzyme can change between two forms, each of them being suitable for a particular phase of the reaction – specifically an open form, which enables efficient transport to the active site, and closed form, suitable for chemical transformation of the substrate into the final product. The scientists managed to discover rapid switching between these two states; in other words, the dynamics responsible for the high activity of the scrutinised enzyme.

“This is similar to a Swiss army knife with multiple instruments which can be swapped very quickly. Thanks to this, various tasks necessary for chemical transformation are becoming quite fast and effective,” says Jan Sýkora, one of project leaders from the Heyrovsky Institute.

More efficient pharmaceuticals

Scientists from both groups have cooperated on experiments and computer simulations to show how changes in enzyme structure can influence dynamics of the entry gates, therefore having impact on enzyme activity, as well. It was Kokkonen herself who has used computer simulations to describe both of these states on molecular level.

“Enzymes are proteins composed of individual amino acids. In computer simulation, we change one or more of these, and subsequently our colleagues in laboratories have to prepare this modified protein, clear it and test it, because changes in amino acids can change shape and dynamics of enzymes, resulting also in a change of their properties,” Kokkonen elaborates.

According to Sýkora, the research should now focus on other enzymes and, if possible, find a way of introducing such dynamic behaviour of the “gates” into other varieties, thus improving their activity, as well. Kokkonen hopes that the published results may serve as a basis for further development of enzymes which shall find use in preparation of efficient pharmaceuticals.

Prepared by: Milan Pohl, Department of Media Communication of the Head Office of the CAS, and Veronika Zelenková, J. Heyrovsky Institute of Physical Chemistry of the CAS
Photo: J. Heyrovsky Institute of Physical Chemistry of the CAS