This will in general be true in an asymmetric interface (between two
different molecules) if you look at the "accessible" surface, defined
by the locus of a water molecule rolling over the surface. The surface
measured by that method is larger on a convex surface than on a
concave one.
Phil
On 11 Aug 2008, at 11:06, P.J.Briggs wrote:
> 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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