AMBER Archive (2004)

Subject: Re: AMBER: disulfide bonds/ Engineered

From: bishop (bishop_at_tulane.edu)
Date: Tue Jan 13 2004 - 08:20:19 CST

While what David said is absolutely true, I would like to add
that if one is trying to engineer disulfide bonds into an existing
protein I have found that the amino acids with a Ca to Ca distance of
less than 7angstrom is a good first pass selection criteria.

For two (anti)parallel or twisted helices you'll find a regular pattern
of a.a. that meet this condition.

Just my $0.02
Tom

David A. Case wrote:

> On Mon, Jan 12, 2004, Wen Li wrote:
>
>>I am going to perform an MD simulation on a crystal structure which
>>includes several CYS residues in two connected helices. The CYS residues
>>in the two helices are about 3 - 3.5 angstroms away one another in the
>>crystal structure. Should these CYS' be considered to form disulfide
>>bonds? What is the proper distance cutoff for determining disulfide bonds?
>>
>>
>
> If the two sulfur atoms are less than 2.5 Ang apart, and the coordinates
> are expected to be reasonably good, there is almost certainly a disulfide
> bond. For a distance greater than 3 Ang and (again) good coordinates, the
> bond is probably missing.
>
> But it is best not to use such rules if you can avoid them, since inaccurate
> coordinates can creep into structures. "Real" PDB files (i.e. from the RCSB)
> will indicate where these bonds are, (and where they are not). Otherwise, you
> have to try to find out how the crystals were prepared, and try to go from
> there. It is likely that the nature of these residues is commented upon in
> the paper describing the crystal structure (if there is such a paper...)
>
> Also, given the distances you cite, make sure there is not a missing metal
> atom, i.e. that the two cysteine residues are not coordinated to a common
> metal ion. For example, the cysteine sulfurs in a zinc finger structure are
> about 3.8 Ang. apart. (The values you cite are actually quite unusual: too
> long to be a disulfide bond, but really quite short if both cysteines are
> reduced...)
>
> ...good luck..dac
>
> 

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