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, [EMAIL PROTECTED] Tel: +44 1925 603826
CCP4, [EMAIL PROTECTED] Fax: +44 1925 603825
http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD
