• It is directed against competing microbes like Salmonella and Shigella

• Microcin seems to have different modes of action against different microbes
  • In some, it inhibits gene translation

  • In others, it disrupts cell membranes

• It is produced by removal of a 37-residue prosegment

The first eight residues form a ring, by making a peptide bond between the N-terminal Gly and the side chain carboxyl of Glu8.

• This is why you need to display sidechains to see the ring

Residues 1-8 of Microcin	Space Filling Model

Residues 9-21 then form the "thread" which passes through the "eye" of the ring.

Residues 9-21 Thread the Needle

The thread penetrates so that residues 20 and 21 are through the ring, with residue 19 on the originating side.

Like the knotted peptides, microcin is relatively stable to hydrolysis.

• However, it does fragment in the mass spectrometer

• But residues 18-21 remain threaded through the ring!

What accounts for the stability of the threaded structure?

Steric Interactions of Residues 20 and 21	Charge-Charge Interactions

The steric size of residues 20 and 21 on one side of the ring, and residue 19 on the other, make it likely that cyclization must have occurred after the protein adopts a suitable conformation - they would not fit through a preformed ring.

Some sort of guided folding mechanism is therefore required:

• Possibly the prosegment facilitates the folding and is cleaved after cyclization

• An external chaperone may produce this fold - or both

Finally, note that there are numberous examples of large globular proteins in which the MAIN chain is knotted [Virnau, Mirny, and Kardar, PLoS Comp. Biol., 2006, 2, 1074; Yeates, Norcross, and King, Curr. Opin. Chem. Biol., 2007, 11, 595]. One example:

Trefoil Knot in E. coli Methyl Transferase (1ns5, resi 67-123)

Find protein topology interesting? Here are a few possible topics for papers:

• Wikoff et al., "Topologically Linked Protein rings in the Bacteriophage HK97 Capsid", Science, 2000, 289, 2129

• Boutz, et al., "Discovery of a Thermophilic Protein Complex Stabilized by Topologically Linked Chains", J. Mol. Biol., 2007, 368, 1332

• Mallam and Jackson, J. Mol. Biol., 2007, 366, 650, describe the folding pathways of two trefoil knots