Protein surface interpretation - help

D.K. dk at no.email.thankstospam.net
Tue Oct 5 20:21:05 EST 2004


On Sun, 3 Oct 2004 20:24:30 +0200, "Stefek Borkowski" <stefek at killspam.edu>
wrote:

>Hi,
>Could someone tell me whether I am right or wrong in understanding the idea
>of different protein surfaces, please? Do the values of the surfaces area
>that I have managed to calculate for a 15 kD protein seem reasonable?
>1. van der Waals surface - the bigest area (covers van der Waals atomic
>surfaces), eg. 14,000 squared Angstroms
>2. molecular surface or contact surface covered by a rolling molecule of the
>solvent, eg. 2,000 squared Angstroms
>3. (solvent) accessible surface - described by the trace of the central
>point of a solvent molecule rolling over the protein contact surface, eg.
>7,000 squared Angstroms.
>
>Are the values calculated for a 15 kD protein probable? Is the below true
>for a typical protein:
>molecular surface < accessible surface < van der Waals surface?
>
>Which surface area is best to calculate in order to consider the geometry of
>interacting surfaces
>of proteinous antigen and an immunoglobulin? I would like to calculate
>potential binding sites on a surface of an antigen assuming that the average
>antigen surface covered by a monovalent antibody binding site is approx.
>1500 squared Angstroms.
>Thanks in advance for all your help.

Numbers seem reasonable. CryCo gives SAS for 1flo as 6426 A^2
http://atlantis.weizmann.ac.il/~eyale/cryco/cryst2.cgi?id=1lfo

I always thought of your #2 and #3 definitions as equivalent. That
is, molecular surface = SAS (kinda makes sense, doesn't it?)
IMHO, only it makes real physical sense in general and for what 
you want it for in particular.  I always use CNS to calculate it - it gives
numbers very close to GRASP which is used by many/most.

I suspect that your number for #2 is in reality total area of 
_crystal contacts_ of a single protein molecule with other molecules 
in the crystal lattice. 1749 A^2 in your case, accordidng to CryCo. 

To answer your question, definitely SAS - what is not accesible
for water (those 1.4A), would equally not be accessible by protein
atoms.  

DK




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