User:Ke Xiao/Geobacter pilus models

Pilus Model

The theoretical Geobacter sulfurreducens pilus model shown here, called ARC-1^[1] (), is representative of a cluster of 50 low-energy models with an arrangement of aromatic rings consistent with X-ray diffraction data^[2]. Unlike the docking of crystallographic models into electron density from cryo-electron microscopy^[3][4], these models have chemically realistic interactions between subunit chains. Energy minimization produced subunit interactions with shape complementarity, non-covalent bonds, and very few atomic clashes.

Monomer Chains

This ARC-1 model contains 21 chains of pilA^[5] of Geobacter sulfurreducens. The 21 chains were restrained to have . Amino acids 3-50 are . Modeling was initiated with model 1 of NMR ensemble 2m7g of Geobacter sulfurreducens. The monomers in ARC-1 are only slightly different from the initial conformation:

• : 2m7g model 1, ARC-1 chain K.
• .

Stacked Aromatic Rings

The ARC-1 model (and others of its cluster) are the first chemically realistic pilus models that can account for the electrical conductivity of these pili in terms of a core of stacked aromatic rings. These models are consistent with multiple lines of experimental evidence including X-ray diffraction suggesting stacked aromatics^[1][2].

Each pilA chain contains . In the pilus assembly, .

The aromatic . The core aromatic rings are .

Salt Bridges

80% of the 50 lowest-energy models have a salt bridge between Arg41 and Asp39 in different chains.

• (Arg41:Asp39, sidechain nitrogens and oxygens).
• .