RE: [ccp4bb]: Damaged SS-bond

["Frank Vondelft" <Frank.Vondelft@syrrx.com>]

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One paper (of many, I'm sure) comes to mind:
	Ravelli RB, McSweeney SM. Structure Fold Des 2000 Mar
15;8(3):315-28

Arguments about where the charge goes are probably a bit gratuitous,
because you're looking at an average not only of many million unit
cells, but also of the course of data collection.  What happens when you
calculate maps using data from only the beginning or only the end of the
data collection (if you have enough data for that, of course.)

phx.


> -----Original Message-----
> From: Bart Hazes [mailto:bhazes@ualberta.ca]
> Sent: Wednesday, December 12, 2001 11:28 AM
> To: ccp4 bulletin board
> Cc: Kirsty Dunlop
> Subject: [ccp4bb]: Damaged SS-bond
> 
> 
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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> 
> Dear all,
> 
> We have a protein with an interesting pattern of damage to a 
> disulphide bond.
> A room temperature rotating anode dataset shows only a single 
> conformation.
> Synchrotron datasets show apparently two conformations of the 
> disulphide bond;
> the original and one in which one of the cysteines adopts a 
> different X1
> angle. Fitting the second conformation optimally in our 0.78 
> Angstrom map
> places the sulphur approximately 2.4Angstrom form the other 
> cysteine sulphur.
> Too far for a covalent bond and too short for vanderWaals 
> comfort. The density
> is somewhat elongated and difference density suggest a split 
> conformation in
> the second X1 setting, eg 3 conformations for one cysteine; 
> the original
> disulphide bond, a second disulphide bond with different X1, 
> and a third
> conformation with a sulfur-sulfur distance of ~3.0 Angstrom. 
> Still 3.0 is
> quite a bit shorter than twice the vanderWaals radius of sulphur
> (3.7Angstrom).
> 
> I was hoping some of you with a chemistry background could 
> suggest what may be
> going on. If a disulphide bond is broken by radiation, does 
> one get two
> sulphur radicals, or will one cysteine become negatively and the other
> positively charged? If so, could such an ion pair adopt a 
> shorter "ionic" bond
> than the standard 3.7Angstrom vanderWaals distance? If so 
> would 2.4 or 3.0
> Angstrom be the more likely. It is hard to argue with the 
> density at this
> resolution but still the protein should follow proper 
> stereochemistry. Any
> hints are appreciated.
> 
> Bart
> 
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> Dept. of Medical Microbiology & Immunology
> University of Alberta
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