AMBER Archive (2004)

Subject: Re: AMBER: disulfide bonds

From: David A. Case (case_at_scripps.edu)
Date: Mon Jan 12 2004 - 19:54:48 CST

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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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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