AlphaFold predictions of proteins involved in CO2 fixation
Title: AlphaFold predictions of proteins involved in CO2 fixation
DNr: Berzelius-2024-31
Project Type: LiU Berzelius
Principal Investigator: Guillaume Gaullier <>
Affiliation: Uppsala universitet
Duration: 2024-01-22 – 2024-08-01
Classification: 10601


Rubisco, the enzyme fixing inorganic carbon from CO2 into carbohydrates, evolved at a time when the Earth’s atmosphere contained mainly CO2. The Great Oxygenation Event, caused by the first photosynthetic organisms releasing oxygen into the atmosphere, posed a challenge for Rubisco, as it poorly discriminates between CO2 and O2. Cyanobacteria responded to this change in atmospheric composition by evolving a CO2 concentration mechanism made of bicarbonate importers and carboxysomes. Carboxysomes are large bacterial microcompartments consisting of a protein shell encapsulating Rubisco and carbonic anhydrase (CA). The shell is differentially permeable to small molecules: it keeps O2 out but allows bicarbonate to enter, which is turned into CO2 by the CA, increasing the local concentration of CO2 around Rubisco. Thus, carboxysomes help overcome both the low catalytic efficiency of Rubisco and its poor specificity towards CO2. Understanding the structure and assembly principles of carboxysomes is important not only from a basic research standpoint, but also because it enables the rational engineering of nano bioreactors designed to encapsulate other biochemical reactions of interest. To understand how carboxysomes assemble, our goal is to determine structures of individual complexes reconstituted in vitro from recombinantly expressed components using single-particle cryoEM, and of entire carboxysomes purified from their native cyanobacterial sources, or in situ in intact cells, using cryoET. Protein structure prediction using AlphaFold-Multimer will be of critical help in all of these structural biology projects.