[RASMB] V-bar calculation for mAb

[John Philo]

Sumit,
 
Yes you could manually calculate the weight average of light and heavy
chain, but remember it is only the total AA composition that matters, and
for vbar purposes there is no distinction whatever between intra- versus
inter-chain disulfides. Thus the best thing to do is to simply merge
together the 2 sequences (using Notepad for example) and treat the entire
antibody as a covalent dimer of the single fused chain (the order of light
versus heavy is irrelevant). Once SEDNTERP sums the combined sequence, tell
it yes convert all the cysteines to disulfides, and then click the 'make an
oligomer' check box so it converts it to a dimer. Presto!
 
That will give you the right vbar for the polypeptide portion, but does not
deal with the carbohydrates which presumably are present.
 
John

  _____  

From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] On
Behalf Of sumit goswami
Sent: Tuesday, March 22, 2011 12:22 PM
To: rasmb at server1.bbri.org
Subject: [RASMB] V-bar calculation for mAb


Hello all,
             I was trying to calculate v-bar of a mAb using SEDNTERP. I have
the sequence of heavy chain (HC) and light chain (LC) seperately as
expected. It seems to be little complicated. Because there are HC-HC and
LC-LC disulfide linkages too.The question is how do I deal with that? Should
I calculate the v-bar of Fab and Fc seperately and then calculate an weight
avergae of them? 
 
With regards,
Sumit
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