Orientation of Multipass Proteins:
Hydropathy profiles: a characteristic of a given polypeptide, a technique to identify hydrophobic
domains. Each a.a. has a value on the hydropathy index, a measurement of the a.a’s
hydrophobicity/philicity. The more positive, the more hydrophobic. To determin hydropathy, calculate
average hydropathy for 5 a.a. window, slide over, calculate the new set of 5 a.a., to calculate, and thus
produce a plot of the average vs. position graph of amino acid in the polypeptide.
Protein Modification in the ER:
Proteins fold relatively slowly when compared to covalent bond formation. Most protein that enter the
ER are glycosylated, with carbohydrates attached, and many of them assemble with each other to form
a multi-subunit complex. It is important to note that only the correctly folded proteins are allowed to be
secreted from the ER and sent to the Golgi. Enzyme protein disulfide isomerase, which can exist in
reduced form with 2 exposed sulfhydride group or oxidized, with the 2 groups linked. In its oxidized
form, the enzyme will react with cysteine to form a disulfide bridge, becoming reduced in the process.
Ero1 will convert reduced form PDI into oxidized PDI. Exposed protein, with PDI, will open up its
disulfide bond, and form a disulfide bridge in its correct form.
The glycosylation process occurs either N-linked or O-linked. N-linked bonds require a preformed
oligosaccharide to attach to Asn residues of the protein. The carbohydrate is synthesized on Dolichol
phosphate, which is an ER phospholipid. Tenichmycin can block this process. Only Asn residues flanked