Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Area of Science:

• Biochemistry
• Structural Biology
• Microbiology

Background:

• Bacterial microcompartments (BMC) are protein-based organelles found in many bacteria.
• BMC shells, composed of BMC hexamers (BMC-H), act as nano-reactors, encapsulating enzymes.
• BMC-H exhibit varied assembly behaviors, forming either flat or curved structures.

Purpose of the Study:

• To investigate the bending propensities of BMC hexamers (BMC-H).
• To understand the structural basis for BMC-H assembly into curved or flat structures.
• To identify key residues influencing BMC-H curvature for potential biotechnological applications.

Main Methods:

• Comparative analysis of crystal structures of BMC-H in tiled arrangements.
• All-atom molecular dynamics (MD) simulations.
• Reconfiguration of planar-behaving hexamers for simulation.

Main Results:

• Two major BMC-H assembly modes identified, correlating with experimental observations of flat vs. curved structures.
• MD simulations confirmed that BMC-H curvature is robustly triggered by specific crystal arrangements, mimicking reconstituted BMC shells.
• Hexamers' lateral positioning, not their intrinsic identity, primarily determines bending propensity.
• An interfacial lysine residue was identified as crucial for PduA spontaneous curvature.

Conclusions:

• BMC-H bending is primarily dictated by their arrangement and lateral positioning within the shell structure.
• Understanding these assembly mechanisms can inform strategies for controlling BMC size and shape.
• This research advances the understanding of BMC biogenesis and their potential as nano-reactors.