Motivation
The implementation of biomolecular modelling methods and analyses can be cumbersome, often carried out with in-house software reimplementing common tasks, and requiring the integration of diverse software libraries.
Results
We present Biobox, a Python-based toolbox facilitating the implementation of biomolecular modelling methods.
Availability and implementation
Biobox is freely available on https://github.com/degiacom/biobox, along with its API and interactive Jupyter notebook tutorials.
Clostridium perfringens is one of the most widely distributed and successful pathogens producing an impressive arsenal of toxins. One of the most potent toxins produced is the C. perfringens b-toxin (CPB). This toxin is the main virulence factor of type C strains. We describe the cryo-electron microscopy (EM) structure of CPB oligomer. We show that CPB forms homo-octameric pores like the heterooligomeric pores of the bi-component leukocidins, with important differences in the receptor binding region and the N-terminal latch domain. Intriguingly, the octameric CPB pore complex contains a second 16-stranded b-barrel protrusion atop of the cap domain that is formed by the N-termini of the eight protomers. We propose that CPB, together with the newly identified Epx toxins, is a member a new subclass of the hemolysin-like family. In addition, we show that the b-barrel protrusion domain can be modified without affecting the pore-forming ability, thus making the pore particularly attractive for macromolecule sensing and nanotechnology. The cryo-EM structure of the octameric pore of CPB will facilitate future developments in both nanotechnology and basic research.
We describe the cryo-EM structure of Clostridium perfringens β-toxin (CBP) in styrene maleic acid (SMA) discs, which represents the membrane-inserted pore form, at near atomic resolution. We show that CPB forms an octamer, which though having a similar conformation to the hetero-oligomeric pores of bicomponent leukocidins, features a different receptor binding region and a novel N-terminal β-barrel. The latter contains an additional selectivity filter and creates a bipolar pore. We propose that the N-terminal β-barrel domain may regulate oligomerization and solubility of the complex and influence channel conductance and monomer stability. In addition, we show that the β-barrel protrusion domain can be modified or exchanged without affecting the pore forming ability, thus making the pore particularly attractive for macromolecule sensing and nanotechnology. The cryo-EM structure of the octameric pore of CPB will facilitate future developments in both nanotechnology and basic research.
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