SUPR
Alphafold-assisted enzyme discovery and characterization
Dnr:

NAISS 2023/22-1323

Type:

NAISS Small Compute

Principal Investigator:

Johan Larsbrink

Affiliation:

Chalmers tekniska högskola

Start Date:

2023-12-12

End Date:

2024-12-01

Primary Classification:

10601: Structural Biology

Allocation

Abstract

This project would deal with predicting structures of enzymes and other proteins related to deconstruction of complex biomass. I run a research group focused on enzyme discovery and biochemical characterization, and we also perform structural biology using X-ray protein crystallography. The various project goals associated to this proposal deal with finding and using enzymes for improved biomass utilization (e.g. biofuels), as well as improved health by breaking down microbial polymers. We have gotten some promising results from Alphafold already, though on a web based "light" version, and would like to run the full version without those limitations. The work would entail structure prediction of our various enzyme targets, which range from small carbohydrate-binding domains, to large multidomain enzymes comprising several catalytic and non-catalytic domains, as well as large (up to ca 3000 amino acid residues long) proteins for which most of the protein has no annotated function or homology to studied proteins. If the project is granted, I would then like to add group members (PhD students and postdocs) to it so they can run their own proteins through the pipeline.