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Doctoral thesis, 2013

Structural dynamics of ribulose-1,5-bisphosphate carboxylase/oxygenase

Van Lun, Michiel


Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) assimilates carbon dioxide (CO2) from air into biomass. Due to its slow turnover, the reaction is a rate-limiting step in photosynthetic carbon fixation. The carboxylation reaction catalyzed by Rubisco is subject to inhibition by oxygen (O2) in a competing, non-productive reaction that reduces the efficiency of the enzyme by up to 50%. This makes Rubisco a target for engineering to increase crop yield. The specificity of Rubisco for CO2 over O2 is a measure how well the enzyme is able to suppress the unwanted oxygenation reaction and varies between organisms. The specificity of Rubisco from several marine algae surpasses that of crop plants. Diatoms with high CO2 specificity from the arctic waters around Svalbard have been cultured, the Rubisco protein has been isolated and characterised, and the crystal structure has been determined. The holoenzyme structure is similar to the structure of Rubisco from plants, but the fold of the small subunits differs and has a shorter βA-βB loop and carboxy- terminal extension that extends into the solvent channel, that appears to provide extra stability to the holoenzyme. The holoenzyme is a hexadecamer consisting of 8 large, catalytic, and 8 small subunits (L8S8) with a mass of 500 kD. The dynamics of the interaction between the subunits in this large protein will likely influence catalysis and CO2/O2 specificity. In order to examine the interface communication between subunits, molecular dynamics simulations have been performed on Rubisco enzymes from different organisms and with different holoenzyme structures, showing that the number of contacts and the size of the interaction area differ significantly in the different complexes examined. Single-residue mutations that affect specificity in Rubisco from the unicellular green alga Chlamydomonas reinhardtii also influence the protein dynamics and interactions across the subunit interfaces. The migration of the gaseous substrates, CO2 and O2 in and around Rubisco, was investigated using molecular dynamics simulations. The results indicate that at equal concentrations of the gas, Rubisco has a preference for binding CO2 over O2. Amino acids with small hydrophobic side chains are the most proficient in attracting CO2, indicating a significant contribution of the hydrophobic effect in the interaction. On average, residues in the small subunit bind approximately twice as much CO2 as do residues in the large subunit, suggesting the small subunit may function as a reservoir for CO2 storage.


Ribulose-1,5-bisphosphate carboxylase/oxygenase; rubisco; CO2/O2; specificity; diatoms; protein interface; X-ray crystallography; gas diffusion; molecular dynamics simulations

Published in

Acta Universitatis Agriculturae Sueciae
2013, number: 2013:40
ISBN: 978-91-576-7818-8, eISBN: 978-91-576-7819-5
Publisher: Department of Molecular Biology, Swedish University of Agricultural Sciences

Authors' information

Van Lun, Michiel
Swedish University of Agricultural Sciences, Department of Molecular Biology

UKÄ Subject classification

Bioinformatics and Systems Biology
Atom and Molecular Physics and Optics
Theoretical Chemistry

URI (permanent link to this page)