Today’s post was prepared by ES-Cat ESR Paul Zurek
Hello everyone!
I am back from the Netherlands! All the ES-Cat ESRs met and took part in a seminar on computational approaches for enzyme design last summer. I found the topic to be really interesting; it is important to make biocatalysis and protein engineering more efficient and cheaper, so that people can easily use it. Strong computational tools would be ideal for that reason. From my point of view, there are a lot of approaches right now that work decently and could help enable more biocatalysis!
In the seminar, we focused on a few approaches and methods than can be used and had more detailed practicals in molecular docking and molecular dynamics simulations. We learned how they were applied in the CASCO workflow for designing enantioselectivity from Dick Janssen [1] and heard about the efforts to make computational protein engineering tools more accessible and easy-to-use by Jiri Damborsky [2].
In my PhD work I plan to apply these methods, as I am interested in studying the evolvability of proteins. I would like to figure out what characteristics make a good starting point for protein engineering. It will be necessary to verify findings and test to see flexibility and the sampling of so-called sub-states over the course of evolution. I am really liking Silvia Osuna’s recent work on the importance of allosteric regulation of conformational sub-states over the course of directed evolution [3]. We have seen mutations distal from the active site playing crucial role in enzyme activity, so it does make a lot of sense to look more into the dynamics of evolutionary intermediates. Now that I have the tools necessary to look into protein dynamics from the workshop, I’ll be able to investigate potential changes in flexibility in my evolutionary trajectory!
After the insightful ES-Cat seminar, I stayed in Groningen for an additional week to participate in the BioTrans 2019 conference. It was nice to see a lot of the discussed tools being applied to difficult to assay reactions during the talks and poster session of the conference. Also, I finally saw a talk by Frances Arnold, who won the Nobel Prize in Chemistry 2018 for her seminal work on directed evolution. It was a great talk, rather conceptual and inspiring.
We did also have the time to explore Groningen on our own. We rented bikes and went for a ride around lovely Groningen on the weekend. Waterways and lush greens everywhere. I really do like that water focused life style the Dutch have mastered for themselves. We even had time to ride up to almost the North Sea!
ES-Cat 