User:Eric Martz/5eon

The biological unit of 5eon (restore initial scene) is a crystallographic structure of 6 alpha helices assembled into a fiber with a hydrophobic core^[1]. The individual peptides are synthetic and were designed to assemble in this manner, with a hydrophobic core rich in phenylalanine. The crystal structure has a resolution of 1.7 Å (very good), and an Rfree of 0.22, which is average for this resolution, indicating that the model is reliable.

The aromatic rings of Phe pack in the core. The Phe rings (dark gray) are surrounded by hydrophobic sidechains of Ile (light gray).

The surface of the fiber is mostly charged Lys+ and Glu- sidechains, with an occasional Trp or Gln, interspersed with Ala (spheres).

Charges

The peptides were designed to form salt bridges between chains in the hexamer, assuming the peptides are parallel in the hexamer. Surprisingly, the peptides are anti-parallel in the hexmer that formed. This precluded salt bridges within the hexamer. The authors note that this shows that the energetics of the hydrophobic core are dominant, with the salt bridges being unnecessary.

The charges form helices of opposite charge on the surface, reminiscent of Xiao's theoretical model of the Geobacter sulfurreducens pilus. Terminal charges on the chains were blocked (see below). Unlike Xiao's model, none of these form salt bridges (a few opposite charges are water-bridged).

Cation-pi interactions involving Phe cannot form since Phe is buried and Lys is on the surface. A few cation-pi interactions may form between Trp on the surface and Lys.

Salt Bridges Between Hexamers

The arrangement of rows of alternating negative and positive charge on the surfaces of the hexamers suggests that salt bridges might form between hexamers, stabilizing the protein crystal. In fact, there is

only one salt bridge

between each pair of hexamers, as shown in the crystallographic unit cell.

Sequence and Blocked Termini

The peptide sequence is constructed from 4 copies of heptad

E L/F K A I A Q/K/W

The amino-terminal Glu is acetylated, removing its positive charge. The C-terminal Lys is amidated, removing its negative charge. Here is the sequence of one complete peptide (29 amino acids) showing the heptad repeats.

ELKAIAQ EFKAIAK EFKAIAW EFKAIAQ K