Molecular exclusion limits for diffusion across a porous capsid

Ekaterina Selivanovitch,Trevor Douglas,Benjamin Lafrance

doi:10.1038/s41467-021-23200-1

Ekaterina Selivanovitch, Trevor Douglas + Show 1 more

Open Access

https://doi.org/10.1038/s41467-021-23200-1

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Abstract

Molecular communication across physical barriers requires pores to connect the environments on either side and discriminate between the diffusants. Here we use porous virus-like particles (VLPs) derived from bacteriophage P22 to investigate the range of molecule sizes able to gain access to its interior. Although there are cryo-EM models of the VLP, they may not accurately depict the parameters of the molecules able to pass across the pores due to the dynamic nature of the P22 particles in the solution. After encapsulating the enzyme AdhD within the P22 VLPs, we use a redox reaction involving PAMAM dendrimer modified NADH/NAD+ to examine the size and charge limitations of molecules entering P22. Utilizing the three different accessible morphologies of the P22 particles, we determine the effective pore sizes of each and demonstrate that negatively charged substrates diffuse across more readily when compared to those that are neutral, despite the negatively charge exterior of the particles.

Highlights

Molecular communication across physical barriers requires pores to connect the environments on either side and discriminate between the diffusants
We demonstrate that the biochemically determined effective pore sizes for P22 particles are comparable to the pore size calculated from the available cryo-EM structures, after the side chain electron density is taken into account the effective pore sizes appear much larger than the P22 model, suggesting that the capsid might be dynamic and undergo a “breathing” mechanism
P22 virus-like particles (VLPs) were prepared with encapsulated alcohol dehydrogenase-D (AdhD) enzymes from Pyrococcus furiosus, using previously established methodologies[32]

Summary

Introduction

Molecular communication across physical barriers requires pores to connect the environments on either side and discriminate between the diffusants. These data suggest that after NADHNeg3.5 and NADH-Neg2.5 for PC and EX, respectively, the diffusion of substrates across the capsid was inhibited and have approached the size limitations of the pores.

Results

Conclusion