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Kyrobio Masterclass on Computational Enzyme Engineering

KTN are project partners in EU project, Kyrobio. The objective of KYROBIO project is to broaden the toolbox of single enantiomer chiral chemicals that are produced by industry in Europe using biotechnological routes. The main target is applications of lyase enzymes to selectively synthesize molecules with multiple chiral centres applying enzymatic carbon-carbon and carbon-nitrogen bond formation as the key technical platforms. Synthetic biology will then be applied to improve fermentation processes in order to generate better enzymes. 

An emerging trend in molecular enzyme engineering for white biotechnology is the use of computational methods to streamline mutant design and library construction. Especially in cases where the use of multiple rounds of high-throughput screening is not feasible, computational methods can provide an attractive tool for biocatalyst development. Within KyroBio, the integration of computational methods in directed evolution is intensively explored, aiming at enhanced enzyme stability and control of substrate recognition.

In work package 3, Partner BioProdict (Nijmegen, the Netherlands) is developing structure- and sequence-alignment databases (3DM) that integrate structural knowledge, genetic information and literature data to steer protein engineering projects. The BioinfoBank Institute (Poznan) explores different docking protocols to examine substrate binding. Other partners (Technical University of Stuttgart, University of Graz) use protein structures and bioinformatics tools in various enzyme engineering projects. The University of Groningen explores the use of homology modeling, docking simulations, molecular dynamics, and computational design for enzyme engineering, and organized in April 2015 a course called "Computational Approaches for  Discovery and Engineering of Enzymes for Biocatalysis and Synthetic Biology".

The Kyrobio masterclass took place in the Linnaeusborg, the modern Biology building of the University of Groningen on the Zernike campus, shown below.

This 1-week Kyrobio masterclass  (April 20-24) aimed to make students and post-docs familiar with the use of computational and bioinformatics tools for enzyme engineering. The improved accessibility of many tools brings them within reach of the wet biochemistry and organic chemistry labs. The program consisted of morning lectures by various speakers who presented the basic principles of computational methods and recent highlights from their own research. Speakers were affiliated to Kyrobio or similar projects (BE-Basic, MicroB3, P4FIFTY) aimed at biocatalyst development. Prof. Jiri Damborsky (Univ. of Brno) explained enzyme tunnel engineering, and Dr. Marnix Medema (Univ. Wageningen) discussed bioinformatics tools for exploring non-ribosomal peptide synthesis. Prof. Nick Turner from the University of Manchester gave a well-attended open lecture explaining the great opportunities and future prospects of biocatalysis to a mixed audience of biochemists and organic chemists. Dr. Rene de Jong (DSM) presented the use of modern computational methods in an industrial setting.

The afternoon sessions of the masterclass course students did computer exercises on docking, computational design of stabilizing mutations, and molecular dynamics simulations. These were given by Dr. Marcelo Masman and Dr. Hein Wijma, University of Groningen. A review on the use of the 3DM databases, again in combination with computer training, was given by Tom van den Bergh from BioProdict.

In a participant presentation session, students presented successes and pitfalls of their own research projects, which raised a lot of discussion and mutual interest. The enthusiasm and motivation of the 30 participants made this a really useful and pleasant course, as also apparent from the evaluation results. It will certainly trigger the organizers to plans such a masterclass more often, and we hope to welcome teachers and participants again in the pleasant city of Groningen.

For more informatioln on this project, please visit their website

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