A Generic Self-Assembly Process in Microcompartments and Synthetic Protein Nanotubes.

Ismail Uddin,Martin J Warren,Richard W Pickersgill,Stefanie Frank

doi:10.1002/smll.201704020

Abstract

Bacterial microcompartments enclose a biochemical pathway and reactive intermediate within a protein envelope formed by the shell proteins. Herein, the orientation of the propanediol-utilization (Pdu) microcompartment shell protein PduA in bacterial microcompartments and in synthetic nanotubes, and the orientation of PduB in synthetic nanotubes are revealed. When produced individually, PduA hexamers and PduB trimers, tessellate to form flat sheets in the crystal, or they can self-assemble to form synthetic protein nanotubes in solution. Modelling the orientation of PduA in the 20 nm nanotube so as to preserve the shape complementarity and key interactions seen in the crystal structure suggests that the concave surface of the PduA hexamer faces out. This orientation is confirmed experimentally in synthetic nanotubes and in the bacterial microcompartment produced in vivo. The PduB nanotubes described here have a larger diameter, 63 nm, with the concave surface of the trimer again facing out. The conserved concave surface out characteristic of these nano-structures reveals a generic assembly process that causes the interface between adjacent subunits to bend in a common direction that optimizes shape complementarity and minimizes steric clashes. This understanding underpins engineering strategies for the biotechnological application of protein nanotubes.

Highlights

Bacterial microcompartments enclose a biochemical pathway and reactive dehydrogenase
Modelling the orientation of PduA in the 20 nm eric bacterial microcompartment protein nanotube so as to preserve the shape complementarity and key interactions seen in the crystal structure suggests that the concave surface of the PduA hexamer faces out
This orientation is confirmed experimentally in synthetic nanotubes and in the bacterial microcompartment produced in vivo

Summary

Synthetic Protein Nanotubes

A Generic Self-Assembly Process in Microcompartments and Synthetic Protein Nanotubes. Modelling the orientation of PduA in the 20 nm eric bacterial microcompartment protein nanotube so as to preserve the shape complementarity and key interactions seen in the crystal structure suggests that the concave surface of the PduA hexamer faces out. The subunit orientation demonstrated for PduA nanotubes and the PduA hexamer in the propane-diol utilization microcompartment shell agrees with the recent crystal structure of the Haliangium ochraceum microcompartment shell.[22] This remarkable crystal structure of the small microcompartment shell has concave surface of the subunits facing out and the bend angles between hexamers are consistent with those predicted from our in silico modeling of PduA nanotubes This knowledge can be used to engineer specific protein– protein interactions to either target proteins more accurately to the lumen of microcompartments or to the outside of the filament scaffolds. To present nanobodies and enzymes on the outside, we know to label the concave surface of these structures; and to place biochemical pathways within the lumen, they should be introduced on the convex side of the subunits forming these nanostructures

Experimental Section

Conflict of Interest