Authors:

Philip Mancino

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About Paper:

Although the importance of microcompartments is widely recognized in structural biology and bioengineering, methods that do not account for structural heterogeneity prevent a full understanding of ultrastructure and function. Modern methods such as cryo-electron microscopy work to combat this issue and better characterize the underlying structure of samples. Recent work done by the Metskas Lab utilizes cryo-electron tomography to image 𝛼-Carboxysomes, a microcompartment facilitating carbon fixation in many cyanobacteria and chemoautotrophs (Metskas et al., 2022). The lab investigates the structure of the Carboxysome shells using the positions and orientations of the internal Rubisco enzymes to extrapolate information about the Carboxysome-a highly generalizable method. Here, we use standard methods of computational biophysics to reverse engineer the analyses of the Metskas Lab into reusable form via MATLAB programming. We solve for the Carboxysome structure by using the Quickhull algorithm to approximate the location of the shell, and compute local and global orientations using vector and tensor analysis. We also compute the volume, Rubisco concentrations inside and on the shell, Euler angles, among other parameters and visualizations. The module was able to exactly reproduce the analyses of the Metskas Lab, and was able to perform computations that were previously impractical, such as the inner Rubisco concentration. The module can easily be expanded to include further calculations, such as Polymerization Affinity computations, local concentrations of Rubisco for arbitrary volumes, and solutions for the missing-wedge effect to aid with tomogram reconstruction. With proper documentation, the release of the module can serve in general structural analyses of beyond the Carboxysome.

Source:

Purdue University / 2023

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Co-authors:

Philip Mancino