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Posted: 30 June 2006

New online biotechnology system helps scientists engineer more environmentally friendly enzymes

Dr Jens E Nielsen and Barbara Tynan-Connolly, UCD School of Biomolecular and Biomedical Science, investigators from the UCD Conway Institute and the Centre for Synthesis and Chemical Biology, have developed an online system for studying the biology of enzymes.

Dr Jens E Nielsen
Dr Jens E Nielsen

Enzymes are the catalysts in most reactions in living organisms. Without them chemical reactions would happen too slowly to sustain life. Just one malfunctioning enzyme in the human body can result in the development of severe disease.

Humankind has used enzymes indirectly for thousands of years - enzymes are responsible for the fermentation of sugar to ethanol by yeasts, a reaction that forms the basis of beer and wine production. However in our recent history, we have employed enzymes more directly. We have isolated enzymes and genetically engineered them for maximal productivity and optimised properties – enzymes were first used in detergents in 1914 and by the 1960s all major detergent manufacturers were using them. Today, enzymes are also used in the starch industry, the baking industry, the brewing industry, the dairy industry, the rubber industry, and the photographic industry.

By understanding how enzymes function in different environments, researchers can modify their characteristics in desired ways to adopt them for use in industrial processes. Enzymes are an environmentally friendly alternative to traditional chemical processes because they are biodegradable and energy efficient. The industrial enzyme business is expanding steadily due to improved production technologies, engineered enzyme properties and new areas for application. In 2005, the world enzyme market was valued at near US$2 billion.

Before the advent of computational programs, it took years of experiments and laboratory testing for researchers to investigate how an enzyme, and slight variations of it, would function in different environments. Each time a researcher changed the characteristics of an enzyme they had to conduct huge numbers of experiments to record the many possible outcomes. A vast amount of time was needed to conduct these experiments. But now, researchers can significantly reduce the time needed for this investigative process by bringing their research from the laboratory to the computer.

However, in order to take advantage of computer aided design for re-designing the (pH-dependent) behaviour of enzymes researchers would have to install complex computer programs and conduct time-consuming calculations. But now, with the help of the new online system developed by Dr Jens E Nielsen and Barbara Tynan-Connolly from the UCD School of Biomolecular and Biomedical Science, researchers can bypass this complex process and get straight to the heart of the experiment. Using the new online system, researchers can begin to study the biology of their protein at the click of a button.

The new webserver developed by the UCD research team is the first of its kind. ‘Ultimately, researchers will be able to employ online systems like this to design more environmentally friendly and efficient enzymes for use in industrial processes’ says Nielsen. And as prediction programs become a standard part of the protein scientist’s toolkit ‘this online system will be of immense assistance to many researchers.’ It can predict mutations that will change the pH dependence of enzyme activity.

Nielsen was one of four researchers to receive the prestigious Science Foundation Ireland, President of Ireland Young Researcher Award in 2004. The award was valued at €1.2 million over five years.

The pKD server is freely available to researchers worldwide at

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