Atomic View of Photosynthetic Metabolite Permeability Pathways and Confinement in Cyanobacterial Carboxysomes

18 October 2024, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

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 CO2 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 (HCO3-), 3-phosphoglycerate (3-PGA), or ribulose-1,5-bisphosphate (RuBP). Starting from a high resolution cryo-EM structure of a synthetic beta-carboxysome shell, we perform unbiased all-atom molecular dynamics (MD) to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the BMC trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO3- relative to CO2. To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO2-concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics (ARBD) simulations estimate the mean first passage time for CO2 assimilation in a crowded model carboxysome. Despite a relatively high CO2 permeability of approximately 10^-2 cm/s across the carboxysome shell, the shell proteins reflect enough CO2 back towards rubisco that 2650 CO2 molecules can be fixed by rubisco for every 1 CO2 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.

Keywords

Photosynthesis
Permeability
Carboxysomes
Bacterial Microcompartments
Molecular Simulation

Supplementary materials

Title
Description
Actions
Title
Supporting information
Description
Supporting information figures, captions, and derivations.
Actions
Title
Animation S1
Description
The animation illustrates a full synthetic β carboxysome shell (T=4) solvated in a box of water, represented by a clear transparent glass surface to provide visual clarity. For visual clarity, the BMC-H hexamer proteins are shown as iceblue surface representation, while the BMC-P pentamer proteins is shown in orange.
Actions
Title
Animation S2
Description
The animation starts from a full shell representation where CO2 molecules are placed around the synthetic carboxysome shell, before zooming into a specific hexamer within the shell to better show the transitions. For visual clarity, the hexamer is shown as a semi-transparent blue surface representation, while the CO2 molecule is shown as space-filling spheres.
Actions
Title
Animation S3
Description
The animation starts from a full shell representation where O2 molecules are placed around the synthetic carboxysome shell, before zooming into a specific hexamer within the shell to better show the transitions. For visual clarity, the hexamer is shown as a semi-transparent blue surface representation, while the O2 molecule is shown as space-filling spheres.
Actions
Title
Animation S4
Description
The animation starts from a full shell representation where HCO3 – molecules are placed around the synthetic carboxysome shell, before zooming into a specific hexamer within the shell to better show the transitions. For visual clarity, the hexamer is shown as a semi-transparent blue surface representation, while the HCO3 – molecule is shown as space-filling spheres.
Actions
Title
Animation S5
Description
The animation starts from a full shell representation where 3-PGA molecules are placed around the synthetic carboxysome shell, before zooming into a specific hexamer within the shell to better show the transitions. For visual clarity, the hexamer is shown as a semi-transparent blue surface representation, while the 3-PGA molecule is shown as space-filling spheres.
Actions
Title
Animation S6
Description
The animation starts from a full shell representation where RuBP molecules are placed around the synthetic carboxysome shell, before zooming into a specific hexamer within the shell to better show the transitions. For visual clarity, the hexamer is shown as a semi-transparent blue surface representation, while the RuBP molecule is shown as space-filling spheres.
Actions
Title
Animation S7
Description
An animation of a rare event where a RuBP molecule, represented as space-filling spheres, transitions through the BMC-H hexamer protein which is represented in orange only for visualization purposes. Other proteins, where the rare event of RuBP transition were not observed, strictly for this animation are marked in iceblue. It is important to note that the animation only demonstrates a rare transition event for RuBP. It should not be interpreted as observed RuBP transitions are through the represented BMC-H hexamer protein in orange.
Actions
Title
Animation S8
Description
Atomic Resolution Brownian Dynamics (ARBD) simulations of tracking carbon dioxide diffusion in a synthetic carboxysome packed with enzyme Rubisco using Atomic Resolution Brownian Dynamics. The in-silico shell is indicated by a transparent glass surface, encapsulating 160 Rubisco proteins (turbo colors). Carbon dioxide molecules are illustrated as point particles (in white).
Actions

Supplementary weblinks

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.