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A Change for the better

24.09.2009
Scientists develop a new method for improving the functional characteristics of enzymes

An international team of scientists from the Czech Republic, Germany and Japan have developed a new method for improving the properties of enzymes.

The method has potential for wide application in the chemical, medicinal and food industries. The research has been published in the prestigious scientific magazine Nature Chemical Biology (Martina Pavlova Martin Klvana, Zbynek Prokop, Radka Chaloupkova, Pavel Banas, Michal Otyepka, Rebecca C Wade, Masataka Tsuda, Yuji Nagata & Jiri Damborsky Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chemical Biology 2009;5(10):727-33).

See: http://www.nature.com/nchembio/journal/v5/n10/abs/nchembio.205.html

The modified enzymes can be used, for example, for disposal of highly harmful chemical substances which enter into the environment as a result of human activity and can have a very negative influence on human and animal health. Nature cannot degrade many of these chemicals but, in this work, the scientists have developed an approach that can be applied to remove them efficiently from the environment.

The principle of the discovery is based on genetic manipulation of the enzyme which is starting and accelerating the chemical reaction. "Now we can use genetic modifications for changing the properties of the enzymes so they can faster and more easily dispose of harmful substances in the environment," says Jiri Damborsky, leader of the Protein Engineering Group at the Institute of Experimental Biology, Faculty of Science, Masaryk University.

Up to now, the scientists had focused during the modification of an enzyme's properties on the site in its structure where the chemical reaction happens, the active site. The new method is based on the modification of so-called access tunnels that connect the active site with the surface of the enzyme. "Specialized computational techniques guided the experimental work to engineer these tunnels to alter their accessibility to the degraded substances," notes Rebecca Wade, leader of the Molecular and Cellular Modeling Group at EML Research in Heidelberg.

The scientists applied the approach by modifying an enzyme to degrade the highly toxic substance, trichloropropane (TCP). This colourless liquid is a secondary product of chemical production. It can reside in the soil and groundwater for over 100 years, can contaminate drinking water and is a carcinogen. Using the new approach, the protein engineers developed a modified enzyme capable of degrading this substance 32 times faster than the original enzyme.

But the method has much wider scope for application than just in the fight against harmful substances and in environmental protection. The targeted modification of the tunnels in enzymes can be utilized in different application areas, including biomedicine, and the chemical and food industries.

Press Contact:
Peter Saueressig
Public Information Officer, EML Research
Phone: +49-6221-533245
Email: Peter.Saueressig@eml-r.villa-bosch.de
Tereza Fojtova
Masaryk University spokeswoman
Phone: +420 724517335
Email: fojtova@rect.muni.cz
Scientific contacts:
Jiri Damborsky, leader of the Protein Engineering Group at the Institute of Experimental Biology, Faculty of Science, Masaryk University Phone+420 549493467, mail: jiri@chemi.muni.cz

Rebecca Wade, leader of the Molecular and Cellular Modeling Group, EML Research, Heidelberg. Tel +49 6221 533 247; email: Rebecca.wade@eml-r.villa-bosch.de

How many people participated in the research and how long did it last?
Ten members of four scientific teams participated - biochemists from the Institute of Experimental Biology, Masaryk University, Brno, Czech Republic; physical chemists from Palacky University, Olomouc, Czech Republic biophysicists from EML Research, Heidelberg, Germany and molecular biologists from Sendai University, Japan. Three doctoral students also participated in the research. The project started in 2003 and lasted 6 years.
What is the use of the new method?
The new method makes it possible to change enzyme properties by targeting modifications to tunnels that connect the enzyme's catalytic site with the enzyme's surface. The sites for modifications are selected with the aid of computational methods using specialized software developed by participants in this research. The method can be used for improving the properties of enzymes used in biomedicine, environmental protection, and the chemical and food industries.
Who is financing the research?
The research was financed by the Czech Ministry of Education, the Youth and Sports and Czech Science Foundation, the Klaus Tschira Foundation, Germany, the Ministry of Education, Culture, Sports, Science, and Technology, Japan and the Ministry of Agriculture, Forestry, and Fisheries, Japan and the North Atlantic Treaty Organization,

The Protein Engineering Group at Masaryk University (loschmidt.chemi.muni.cz/peg/) conducts research projects dedicated to fundamental principles of enzymatic catalysis and to development of enzymes for environmental, chemical and biomedical applications. The group has particularly extensive experience in the engineering of enzymes to degrade halogenated compounds.

Masaryk University (www.muni.cz), located in Brno, is the second-largest public university in the Czech Republic and the leading higher education institution in Moravia. At present it comprises nine faculties with more than 200 departments, institutes and clinics. Masaryk University has 41052 students enrolled in regular degree programmes. Recognized as one of the most important teaching and research institutions in the Czech Republic and a highly-regarded Central European university, it has been marked by a strong democratic spirit ever since its establishment in 1919.

The Molecular and Cellular Modeling Group at EML Research (www.eml-research.de/mcm) conducts research on the development and application of computer-aided methods to predict and simulate biomolecular interactions.

EML Research gGmbH (www.eml-research.de) is a non-profit institute conducting research in Information Technology and its applications. There is a strong focus on bioinformatics and computational biology. Research is carried out in close collaboration with universities and other research institutes. EML Research projects are supported by the Klaus Tschira Foundation (KTS) (http://www.klaus-tschira-stiftung.de), as well as by the European Union, the German Ministry of Research and Education (BMBF) and by the German Research Foundation (DFG). EML Research is a partner in the first German Center for Modeling and Simulation in the Biosciences (BIOMS, www.bioms.de). KTS and EML Research are housed in the Villa Bosch in Heidelberg, the former residence of Nobel Prize laureate Carl Bosch (1874 - 1940).

Dr. Peter Saueressig | idw
Further information:
http://www.klaus-tschira-stiftung.de
http://www.eml-r.org/english/press/form/onerror.php?we_objectID=634&pid=563
http://www.nature.com/nchembio/journal/v5/n10/abs/nchembio.205.html

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