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
--
Steven Darnell
Department of Biochemistry
University of Wisconsin-Madison
Madison, WI USA
