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

van Lun, Michiel (2013). Structural dynamics of ribulose-1,5-bisphosphate carboxylase/oxygenase. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2013:40
ISBN 978-91-576-7819-5
[Doctoral thesis]

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Abstract

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.

Authors/Creators:van Lun, Michiel
Title:Structural dynamics of ribulose-1,5-bisphosphate carboxylase/oxygenase
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2 May 2013
Volume:2013:40
Number of Pages:64
Papers/manuscripts:
NumberReferences
I.Valegård, K., Pearce, F. G., Haslam, R. P., Madgwick P. J., Andralojc, P. J., Kristoffersen, A.K., van Lun, M., Jewess, P., Taylor, T. C., Klein, U., Eilertsen, H. C., Parry, M. A. J. and Andersson, I. Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco. Manuscript.
II.van Lun, M., van der Spoel, D., Andersson, I. (2011). Subunit interface dynamics in hexadecameric Rubisco. Journal of Molecular Biology 411, 1083-1098.
III.van Lun, M., Hub, J., van der Spoel, D., Andersson, I. CO2 and O2 distribution in Rubisco suggests the small subunit functions as a CO2 reservoir. Manuscript.
Place of Publication:Uppsala
Publisher:Dept. of Molecular Biology, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-7819-5
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:X Agricola extesions > X30 Life sciences
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 103 Physical Sciences > Atom and Molecular Physics and Optics
(A) Swedish standard research categories 2011 > 1 Natural sciences > 104 Chemical Sciences > Theoretical Chemistry
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
Agrovoc terms:rubisco, carbon dioxide, bacillariophyceae , x rays, gas exchange, diffusion, dynamic models
Keywords:Ribulose-1,5-bisphosphate carboxylase/oxygenase, rubisco, CO2/O2, specificity, diatoms, protein interface, X-ray crystallography, gas diffusion, molecular dynamics simulations
URN:NBN:urn:nbn:se:slu:epsilon-e-1432
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-1432
ID Code:10380
Department:(NL, NJ) > Dept. of Molecular Biology (until 131231)
Deposited By: Michiel Van Lun
Deposited On:03 May 2013 13:17
Metadata Last Modified:02 Dec 2014 11:00

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