Not sure if this is relevant, however as an addendum: a couple of years
ago I looked at some data from a colleague using AREAIMOL and learned
that while it's not intuitively obvious, it is possible that the
calculated accessible surface area buried on one subunit may differ from
that buried on the other subunit in the same interaction i.e. more
surface area may be buried on one subunit than the other.
I think that this effect is simply an artefact of how the accessible
surface is defined, but it does mean that in some cases the simple
division by 2 of the total calculated buried area may not be accurate
for the individual subunits. In the example that I looked at the
differences could be quite significant - in the most extreme case the
split was 60/40 (although in others it was much smaller).
I suppose this is really just a curiosity, but it does add more weight
to the argument for reporting the total change in buried area due to
interface formation.
Best wishes
Peter
Steven Darnell wrote:
> Phil,
>
> I had a follow up conversation regarding this very topic. Here is an
> excerpt:
>
>> The following is from Chothia and Janin (1975) Nature, 256:705-708,
>> one of the early articles regarding buried surface area and protein
>> interfaces:
>>
>> "The surface area buried in the complex is then defined as the
>> accessible surface area of one subunit plus that of the other subunit
>> minus that of the complex."
>>
>> I believe that definition has not changed in 30 years. While I will
>> agree that dividing by 2 approximates the physical area of the
>> interface, this does not represent the total amount of surface area
>> that is no longer accessible to solvent. In terms of desolvating the
>> interface for binding, the latter is more appropriate.
>
> As you point out, PISA appears to be reporting the area of the
> interface, not the total surface area occluded from solvent. Confusing
> indeed.
>
> Regards,
> Steve Darnell
>
>
> Phil Jeffrey said the following on 8/8/08 10:03 AM:
>> Which brings up something about PISA. If I run PISA on pdb entry
>> 2IE3, which I'm familiar with, I get the following numbers from PISA
>> and CCP4's AREAIMOL (surface areas in Angstrom^2) for the A:C interface.
>>
>> >> PISA for 2IE3
>> Automatic A:C interface selection 907.9
>> (a crystal packing interface is larger than this, but this surface
>> is the A:C interface)
>>
>> >> AreaIMol with some editing of 2IE3 to separate the chains
>> Chain A 25,604.4
>> Chain C 11,847.4
>> Total 37,451.8
>> Chain AC 35,576.6
>> Difference 1,875.2
>> Difference/2 937.6
>>
>>
>> For buried S.A. I agree with Steve Darnell's definition. However PISA
>> appears to be reporting half that value, or what it calls "interface
>> area". Potentially confusing.
>>
>> Phil Jeffrey
>> Princeton
--
___________________________________________________
Peter J Briggs, [log in to unmask] Tel: +44 1925 603826
CCP4, [log in to unmask] Fax: +44 1925 603825
http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD
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