<i>In Vitro</i>
            Analysis of Bacterial Microcompartments and Shell Protein Superstructures by Confocal Microscopy

Trettel, Daniel S.; Winkler, William E.

doi:10.1128/spectrum.03357-22

Cited by 5 publications

(3 citation statements)

References 59 publications

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“…Alternative morphologies such as sheets of hexamers or arrays of trimeric BMC proteins have been experimentally characterized. Cylinders have been reported in vitro after modifying the ratio of shell components for the Haliangium ochraceum (HO) shell. − While the HO shell is quite small, other BMCs, such as carboxysomes, form large icosahedral structures with large triangular planar facets connected together with vertices . The vertices for the icosahedron are filled by pentameric shell proteins, but the approximately planar facets are thought to be a mixture of hexameric and trimeric proteins analogous to the hexameric and trimeric proteins in HO. , In this study, we design a theoretical and computationally feasible mode of the BMC shell protein in sheet conformation and we compare the dynamics and structure of a small periodic BMC sheet model developed in silico to an equivalent shell fragment derived directly from experimental structures .…”

Section: Introductionmentioning

confidence: 89%

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Raza,

Sarkar,

Chan

et al. 2024

ACS Omega

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Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria that encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We used molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed the overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

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Section: Introductionmentioning

confidence: 89%

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Raza,

Sarkar,

Chan

et al. 2024

ACS Omega

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“…This has also been found in simulations which assume shell proteins demonstrate no spontaneous curvature of their own [motivated by atomic force microscopy studies on shell subunits ( Sutter et al., 2016 ; Garcia-Alles et al., 2017 )] and can essentially trap a growing cargo droplet out of equilibrium ( Rotskoff and Geissler, 2018 ). This, however, may depend on the system of study as shell proteins have been observed to form sheets, nanotubes, and empty icosahedra among other morphologies, sometimes within the same sample ( Ferlez et al., 2023 ), without the need of cargo templating to induce curvature ( Ferlez et al., 2023 ; Trettel and Winkler, 2023 ; Uddin et al., 2018 ; Hagen AR. et al., 2018 ; Noël et al., 2015 ).…”

Section: Modeling the Physical Principles Underlying Carboxysome Asse...mentioning

confidence: 99%

“…The carbonic anhydrase component in both examples is omitted for clarity. (Ferlez et al, 2023;Trettel and Winkler, 2023;Uddin et al, 2018;Hagen AR. et al, 2018;Noël et al, 2015).…”

Section: The Role Of Shell Components In Bmc Assembly and Morphologymentioning

confidence: 99%

Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation

Trettel,

Pacheco,

Laskie

et al. 2024

Front. Plant Sci.

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The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.

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Dynamic structural determinants in bacterial microcompartment shells

Trettel,

Kerfeld,

Gonzalez-Esquer

2024

Current Opinion in Microbiology

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In Vitro Analysis of Bacterial Microcompartments and Shell Protein Superstructures by Confocal Microscopy

Cited by 5 publications

References 59 publications

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation

Dynamic structural determinants in bacterial microcompartment shells

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