Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells.

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Modeling

Background:

• Bacterial microcompartments (BMCs) are protein-bound organelles that enhance enzyme catalysis by encapsulating enzymes.
• Their semi-permeable shells, formed by self-assembling protein tiles (hexamers, trimers, pentamers), regulate molecular transport.
• While icosahedral shells are common, BMC proteins can also form planar sheets or cylinders.

Approach:

• Atomically detailed models of planar BMC protein sheets and curved shell structures were developed using molecular modeling.
• Classical molecular dynamics simulations were employed to animate these models.
• Analyses focused on structural stability, water accessibility, water residence time, and pore geometry.

Key Points:

• No substantial variation in pore structure or solvent accessibility was observed between flat and curved BMC shell geometries.
• Molecular dynamics simulations revealed consistent water interaction patterns across different morphologies.
• Hydroxyl radical footprinting data corroborated simulation findings, identifying residues with long water molecule binding times.

Conclusions:

• Planar and capsular BMC morphologies exhibit similar pore structures and water interaction profiles.
• The findings suggest that planar BMC models can be reliably used to study permeability through BMC pores.
• This interchangeability simplifies future research on BMC protein shell transport mechanisms.