BIOGATE project - “Rational design and engineering of enzyme gates”
Enzymes are the catalysts of Nature. Many of them have sophisticated mechanisms that open and close the access of molecules to important regions, such as the catalytic site. These are called molecular gates. There are different types of gates, depending on the flexible elements that control them (e.g., single residues, several residues, secondary elements, or entire domains). These gates of enzymes are nowadays still not well understood and they deserve more attention and systematic methodologies for their study.
In the BIOGATE project we want to find the methodologies to investigate enzyme gates which can be applicable to a wide range of systems. That involves identifying the key elements and how they are orchestrated together.
Main goals: Deliver a methodology for studying enzyme gates. After identifying the gating elements, our goal is to modify the existing gates in order to improve the catalytic activity, selectivity, and even stability of those enzymes.
Study of enzyme gates
In this project we aim at finding how the gating mechanisms are formed, and how their building blocks work together. Our model enzymes are the haloalkane dehalogenases (HLDs), which have important biotechnological applications, namely in the degradation of toxic halogenated pollutants the synthesis of enantiopure compounds, biosensors, etc.
Using different computational tools, such as molecular dynamics simulations and tunnel calculation (CAVER), we study the proteins of interest and the dynamics of their tunnels. This allows us to understand the operating mode of the existing gates. The simulations supply important clues for understanding the relationship between the gate dynamics and the catalytic activity.
Engineering the enzyme gates
Once the gating mechanisms have been understood, our aim is to engineer them and modify some of the gate-forming elements in order to optimize their efficiency. For that, in silico mutagenesis is performed on the model proteins, and the new systems are studied in order to track the effects of the mutations on the tunnel properties. Hence it may be possible to predict important properties of the new systems before preparing them in the lab.
The applications of gate engineering can be very varied. For instance, gates can be introduced de novo in some enzymes in order to rationally control their specificity or enantioselectivity.
Read the public article:
"SoMoPro Project - BIOGATE – Rational design and engineering of enzyme gates", published in the RECETOX Newsletter, vol.3 (3), 2015 (page 5).
Acknowledgements and disclaimer:
This project is currently running at the Loschmidt Laboratories, which are part of RECETOX.
It is financed by the SoMoPro II programme. It acquires support from the People Programme (Marie Curie actions) of the Seventh Framework Programme of EU according to the REA Grant Agreement No. 291782. The research is further co-financed by the South-Moravian Region. What is presented herein reflects only the author’s views and the Union is not liable for any use that may be made of the information contained therein.