Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Journal Article · 05 November 2024 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.2402277121 · OSTI ID:2475888

Sarkar, Daipayan  ^[1]; Maffeo, Christopher  ^[2]; Sutter, Markus  ^[3]; Aksimentiev, Aleksei  ^[4]; Kerfeld, Cheryl A.  ^[5]; Vermaas, Josh V.  ^[6]

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1. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824
2. Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
3. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
4. Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
5. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
6. MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO ₂ in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate ( ${\text{HCO}}_3^{-}$ ), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic $\beta$ -carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to ${\text{HCO}}_3^{-}$ relative to CO ₂ . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO ₂ -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO ₂ assimilation in a crowded model carboxysome. Despite a relatively high CO ₂ permeability of approximately 10 ⁻² cm/s across the carboxysome shell, the shell proteins reflect enough CO ₂ back toward rubisco that 2,650 CO ₂ molecules can be fixed by rubisco for every 1 CO ₂ molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

• Sponsoring Organization: USDOE
• Grant/Contract Number: FG02-91ER20021
• OSTI ID: 2475888
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 45 Vol. 121; ISSN 0027-8424
• Publisher: Proceedings of the National Academy of SciencesCopyright Statement
• Country of Publication: United States
• Language: English