Transport of Sugars

Original Settings

Ligand (Use Trimer complex)

The porin shown has three sugar molecules bound inside the pores as well as four magnessiums bound on the external surface of loop 9. The function of these magnessiums is to indirectly help sugar binding by changing the protein conformation to optimize hydrogen bonding to the sugar. The first thing that occurs is that a calcium ion binds to loop 9 of each monomer. This binding aids sugar binding to the protein.

The next step is when the sugar enters through the mouth and binds to the surrounding residues.

Barebones Active Site

Tyr, Arg, and Asp residues play a major role in binding of sugars. Loop 3 folds into the lumen of the pocket thus restricting the pore size and reducing it to roughly 8.5 X 11 Angstroms. It is the size of the pore that is partially responsible for the selectivity of the protein. It is also found through mutation experiments that residues ASN 192 and ASP 201 are the main side chains responsible for the pore size. Their absence causes the most dramatic decrease in sucrose transport.

Important binding residues (wait for ligand)

Original Settings

Protective loops covering channel entrance

The greasy slide: Once the protein enters the pore, a set of six aromatic rings provide binding sites so that together, they provide a sort of slide that the sugar uses to go through the pore and exit on the inside. Here the six rings are highlighted in various colors around the sugar molecule.

Aromatic residues lining channel

Trp capping aromatic path

Ionizable residues from the channel lining are assumed to replace the hydration shells of diffusing molecules and convey sugar specificity to the channel.

Ionizable residues

References

Most of the material is from these two great sites on Porins.

http://biology.kenyon.edu/BMB/Chime/porins/pormast.htm

http://mcdb.colorado.edu/courses/3280/chime/porin/2frmcont.htm