June 1, 2006
SFI PIYRA researcher designs web-based biotech tool

What have biological washing powders, beer and stone-washed jeans got in common? The answer is protein molecules called enzymes. Biological washing powders contain enzymes that remove stains and work at lower temperatures, thus saving energy. In the beer brewing process enzymes are often added to assist in filtration or to improve the fermentation yield of alcohol, and enzymes have also replaced pumice stones in the stone washing of jeans.

Enzymes are biodegradable and have many environmental advantages over more traditional chemical processes. Biotechnology has enabled scientists to design new enzymes for a range of industrial applications using a technique called site-directed mutagenesis, which entails making selective changes to the amino acid sequences of enzymes. Re-designing industrial enzymes using site-directed mutagenesis is time consuming and it often takes years of careful experiments to change the characteristics of an enzyme in the desired way.

Dr Jens E. Nielsen, a CSCB and UCD Conway Institute investigator from the UCD School of Biomolecular and Biomedical Science, has developed an online tool called the pKD web server, which allows researchers to predict the performance of new enzymes with respect to their pH-dependent characteristics using computational methods.

Dr Nielsen was one of the first four recipients of the prestigious Science Foundation Ireland President of Ireland Young Researcher Awards (PIYRA) in 2004. The award is worth € 1.2 million over a five-year period and has provided significant funding for Dr Nielsen's research group which currently consists of 8 researchers.

"The pKD web server will allow scientists to study the biology of their protein at the click of a button without investing large amounts of time in running complicated calculations and installing pKa prediction software," says Dr Nielsen. "pKa prediction programs are becoming a standard part of the protein scientist’s toolkit, and we believe that the pKD web server will be a great help to many researchers."

Scientists use pKa prediction software to determine the pH-dependence of protein characteristics. This helps them to understand how enzymes will function in different environments. For example, it is important that enzymes in biological washing powders work in the pH range of 9 to 10 to maximise their cleaning effectiveness.

The pKD server is freely available online to researchers worldwide at http://enzyme.ucd.ie/pKD

"Our online tool is unique because it is the first that can calculate mutations that will change the pH-dependence of enzyme activity," explains Dr Nielsen. "Ultimately, researchers will be able to use tools like ours to design more environmentally friendly and efficient enzymes for use in industrial processes."

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