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This 4-day course will bring together computational and experimental (bio)chemistry experts who will give comprehensive lectures on understanding and engineering enzyme catalysis. Hands-on practical sessions will be focused on how to use state-of-the-art software and webservers. The five focus areas are (i) the EBI enzyme portal, (ii) MD simulations with GROMACS, (iii) FuncLib and PROSS for protein design using structure and sequence alignments, (iv) CAVER, CaverDock and CaverWeb for analysis and visualization of tunnels, channels and cavities in protein structures (v) DynaComm for the computational prediction of active site and distal mutations for novel function. This will be complemented by lectures on the EVB, QM/MM methods and qFIT for multiconformer modeling. In addition, experimental researchers will give lectures on how these in silico approaches complement their research on enzyme catalysis. Students will be encouraged to work on their own research problems using their own laptops for working with the web-tools that will be covered in the tutorials, either attending in-person or remotely. For some tutorials it could be required to install software on your laptop in order to be able to run a tutorial more efficiently. Please make sure that it is possible to install software on your laptop, in advance of the actual course event. Students will present and discuss their own research results during the poster sessions and short oral presentations. The programme will encourage interactions between students and lecturers and will provide opportunities to establish new professional relationships.
The course will be organized as a hybrid event, allowing for efficient remote attendance as well as in person attendance, if allowed by the COVID-19 restrictions at that time.
Registration – Tuesday, October 19, 2021
Registration will take place between 9:00-9:30 at the Faculty of Biochemistry and Molecular Medicine (FBMM) of the University of Oulu.
Five focus topics
Rossana Zaru - Enzyme Portal: a portal for enzyme resources at the European Bioinformatics Institute (EMBL-EBI) and beyond
Gerrit Groenhof - An introduction into molecular dynamics simulations of proteins
Silvia Osuna - Conformationally-driven computational enzyme design: development and application of correlation-based tools for distal active site mutation
Sarel-Jacob Fleishman - (i) Automated design of proteins for high expression and stability; (ii) Automated design of efficient and functionally diverse enzymes
Jiří Damborský - Engineering ligand access pathways
Six complementary lectures
Birte Höcker - De novo protein design and its experimental validation
Adrian Mulholland - General Introduction on enzyme engineering and on MD-QM/MM calculations for understanding of enzyme-catalyzed reactions
Aleksandra Maršavelski - The EVB method: in silico approach for understanding the mechanism of enzyme catalysis
James Fraser - Ensembles of Ensembles: How multiple conformations exist within and between protein structures
Reinhard Sterner - Analysis of allostery in a multi-enzyme complex by ancestral sequence reconstruction
Mikael Widersten - Pre-steady state and steady-state kinetics of designed enzymes
Student flash presentations
Accepted participants will be asked to provide presentation for a two-minute talk (max 2 slides).
Slide presentations must be in PowerPoint format.
Dimensions: 90 cm x 120 cm (PORTRAIT format).
Design: Text and illustrations should be legible from a 2 meters distance.