Trying to find a disulfide bond in a protein?

Question

I'm looking at the protein bovine rhodopsin.

I'm suppose to find out how far the closest disulfide bond is from the methionine end of the protein.

Currently i'm using .... i'm not sure what the site is actually called, but if you google genbank its the first hit.

Using the CN3D program. It shows me 3d view of the molecule and then spits out the amino acid sequence.

Is there a way i can look at the sequence to figure out where this bond is?

Err...do i look for the closest cystein...and assume thats where the disulfide bond occurs...with another cystein.. I'm a chemical engineer not biochemist....i think i learned somewhere years ago that cysteins form the bonds.....but i'm having no luck googling that.

Answer 1

Here is a link to a paper regarding the structure of bovine rhodopsin. Table 3 shows a 2-D representation of what you need to know and more.

The first cys is involved in the formation of the disulfide bond, but there are more than just two cysteines in the peptide. Check out the table.

http://www.columbia.edu/cu/biology/courses/g4008x/readings03/readings1/Rhodopsinstrucutre.pdf

Answer 2

The disulphide bonds will be at the cystein residues, though it may not necessarily be at the first one you see along from methionine.

Still, if there are only two cystein residues you don't have a lot of choice, presuming the disulphide bond is internal to the molecule. If there is only one cys residue then the molecule is probably a dimer.

Take a good hard look at the 3-D structure and see if /where the molecule kinks together. That might be a clue if there are more than two cys residues.

(I'm not a biochemist either, just had to handle a fair bit of this stuff recently)