Protein surface interpretation - help

Stefek Borkowski stefek at killspam.edu
Wed Oct 6 11:34:20 EST 2004


D.K. wrote:
> 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

Thank you so much DK. Your answer is very convincing. Now I am much more
confident that my calculations make sense. The SAS area seems the most
rationale to be used in my analysis. I am not going to bother about the
contact area as it looks useless for my considerations. Thanks for the link
to CryCo - it really gives in no time an on-line and moreover free
calculation of SAS, confirming my results obtained by offline software. You
have done a real perfect job for me. Lots of thanks again!!! May you have a
nice day and every success in the future! :)
Warm greetings from still sunny Poland (quite unusual for this time of
year!).
Yours,
Stefek




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