Protein surface interpretation - help

Stefek Borkowski stefek at killspam.edu
Tue Oct 5 16:05:05 EST 2004


Dr Engelbert Buxbaum wrote:
> Stefek Borkowski 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.
>
> If you told us how you calculated these values, we could comment on
> the methods used rather than the results, which would probably be more
> useful to you.

Dear Dr. Buxbaum,
Thank you so much for offering your help. So again, I would like to
calculate the surface
of Rat Liver Fatty Acid Binding Protein (PDB file name: 1LFO).
It is a relatively small protein - approx. 15
kD molecular mass. I have a reliable literature value of the antibody
monovalent
binding surface area, that is equal to 1500 squared Angstroms, which is the
average value (true for all antibodies), I believe. My main goal is to
determine the number of potential binding sites (epitopes) on my protein
surface (that could be, just theoretically, simultaneously! and monovalently
bound by antibodies)
- this value is going to be an average, as I cannnot an won't model
antibodies specific to all possible epitopes!
Being a lay person at protein modelling and all, I used free software to do
the job (2 for Linux: spock, asv and 1 for Windows: ccp4). Once I had
installed the stuff, I managed to make the calculations. It took just a few
seconds actually, but the results are not all clear to me. Some nomenclature
seems misleading. Below I am enclosing summary of the results by each
software for comparison and some additional questions of mine.
The fundamental question for me, however, is whether the solvent accessible
surface area of a protein is the right choice to calculate the number of
potential antibody binding sites (i.e. the sites that can be bound at the
same time, skipping considerations of spatial hinderance between
antibodies). In other words, could the accessible surface be assumed as the
one interacting with antibody? If this assumption were true then I would be
happy just calculating this: approx. 7000 (the output value for solvent
accessible area - see below)
divided by 1500 is equal to approx. 4 or 5 possible simultaneous binding
sites on my protein.
I hope I have made myself clear now  Do you think it would be
possible for you to find a few minutes of your precious time and have a
closer look at the output of my calculation files. They are not that big at
all - just text files of about dozen kilobytes. If you kindly agreed I would
be eager to send you them as attachments. Maybe it would also help if I sent
you the original PDB file with the crystal structure of the protein of
interest - approx. 120 kB?
Thanks again for any help you can offer.
Sincerely,
Stefek
P.S. Below is the summary from the output of my calculating software.
######################
SPOCK
van der Waals surface area:
   Fractional surface area: 0.47 - what is that "fractional surface area" by
the way?!
   Total surface area: 14619

Accessible surface area
   Fractional surface area: 0.07
   Total surface area: 7905 - again, what is that "fractional surface area"
here?!

van der Waals volume: 10116 cubic Angstroms

Molecular volume: 17567 cubic Angstroms - why does the program calculate
molecular volume and on the other hand I cannot find an option to calculate
molecular surface area ?!!! :( Maybe it is so rarely considered important
that I shouldn't
bother about it either?!

Accessible volume: 27063 cubic Angstroms

Probe radius: 1.4 Angstrom

At least in the case of SPOCK the values of protein volumes seem doubtless



######################
ASV

S =12923 - just by comparison with spock I can get that this regards to the
van der Waals surface
V =10555 - and this regards most probably to van der Waals volume

This software, as far as I can gather, cannot calculate the solvent
accessible volume :(


######################
CCP4

ANALYSIS OF ACCESSIBLE AREAS BY RESIDUE
TOTAL AREA:     6534 - guess that is the solvent accessible surface area -
roughly resembles that of SPOCK

ANALYSIS OF CONTACT AREAS BY RESIDUE
TOTAL CONTACT AREA:     1965 - that small !!!???

And now what is that "CONTACT AREA"?! Is it the same as "molecular area"? If
so, is such a huge difference between solvent accessible area and molecular
area possible then?! Looks improbable...

Any comments highly appreciated. Thanks :)
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