Computational biotechnology: prediction of competitive substrate inhibition of enzymes by buffer compounds with protein-ligand docking.

Karen T Schomburg, Inés Ardao, Katharina Götz, Fabian Rieckenberg, Andreas Liese, An-Ping Zeng, Matthias Rarey

ZBH, Center for Bioinformatics, Universität Hamburg, Hamburg, Germany.

Journal of biotechnology 2012 Nov 15

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In vitro enzymatic activity highly depends on the reaction medium. One of the most important parameters is the buffer used to keep the pH stable. The buffering compound prevents a severe pH-change and therefore a possible denaturation of the enzyme. However buffer agents can also have negative effects on the enzymatic activity, such as competitive substrate inhibition. We assess this effect with a computational approach based on a protein-ligand docking method and the HYDE scoring function. Our method predicts competitive binding of the buffer compound to the active site of the enzyme. Using data from literature and new experimental data, the procedure is evaluated on nine different enzymatic reactions. The method predicts buffer-enzyme interactions and is able to score these interactions with the correct trend of enzymatic activities. Using the new method, possible buffers can be selected or discarded prior to laboratory experiments. Copyright © 2012 Elsevier B.V. All rights reserved.

Citation

Karen T Schomburg, Inés Ardao, Katharina Götz, Fabian Rieckenberg, Andreas Liese, An-Ping Zeng, Matthias Rarey. Computational biotechnology: prediction of competitive substrate inhibition of enzymes by buffer compounds with protein-ligand docking. Journal of biotechnology. 2012 Nov 15;161(4):391-401