How Pore Architecture Regulates the Function of Nanoscale Protein Compartments

Abstract

Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.

Encapsulin cargo loading: progress and potential

“…Future efforts aimed at pore engineering to improve molecular flux across encapsulin shells will likely be able to address this problem and result in fully catalytically active nanoreactors. 22,63,81,82 Conclusions and future challenges Encapsulins offer advantages relative to other nanocages used in bioengineering, including their exclusively proteinaceous nature, biophysical robustness, genetic engineerability, and facile in vivo cargo loading that negates the need for additional methods like cargo-scaffold or cargo-capsid genetic fusions, covalent conjugation, or harsh refolding procedures. 7,40,83,84 Encapsulin research has made substantial progress over the past decade, generating novel insights into shell structure and dynamics, cargo encapsulation mechanisms, biological function, and engineering applications.…”

Tuning properties of biocatalysis using protein cage architectures

“…The diversity of capsid pores has been reviewed comprehensively in a recent work, but their potential as gating systems to alter the selectivity of biocatalysis remains to be fully uncovered. 11 We have probed the porosity of P22 VLPs in the context of a biocatalytic reaction within the cage (Fig. 4(b)).…”

“…While membrane compartments are often heterogeneous and fluidic in morphology, 1 the protein cages usually self-assemble from a limited, defined number of different proteins, resulting in modular structures with high symmetry, high homogeneity in shape and size, and potential to disassemble under altered biophysical or biochemical environments. 11 Pores, formed at the symmetry axes of the assembled protein cage architectures, control the permeability of the compartments, 11 which is different from membrane compartments that are mostly associated with membrane transport proteins. 12 Understanding these properties helps us investigate how the protein cage architectures are utilized in nature to tune biocatalysis, and design biomimetic nanoreactors with different functionalities using the diverse architectures of protein cages.…”

Synthetic Multienzyme Assemblies for Natural Product Biosynthesis

“…Protein cages have been well recognized as scaffolds for polyvalent display of biological entities and recently received tremendous attention in vaccine development [80–81] . The architecture of protein cages; in particular, the pore sizes, can be fine‐tuned to control the stability of the cages and molecular flux in and out of the cages [82–85] . This feature then allowed engineers to encapsulate enzymes inside the cages to segregate metabolic pathways from the rest of the cytoplasm.…”

“…[80][81] The architecture of protein cages; in particular, the pore sizes, can be fine-tuned to control the stability of the cages and molecular flux in and out of the cages. [82][83][84][85] This feature then allowed engineers to encapsulate enzymes inside the cages to segregate metabolic pathways from the rest of the cytoplasm. As enzyme encapsulation by protein cages has been thoroughly reviewed elsewhere, [79] here, we only pick a few examples that are related to multienzyme assemblies.…”