Can someone assist with how I can determine the presence of the RGD (arganine-glycine-aspartic acid) sequence in a protein without doing the sequencing of the whole protein.
It depends on the protein, if the molecular weight is large then it may not be successful to get proof of RGD motif, however it totally depends in experiment. It may also show presence of RGD. But, if you dont see RGD is sequencing result, you might not be sure, weather it is due to incomplete sequence converage, or it is absent. Sequencing usually covers partial region of a protein and with the help of that identified sequence, you can BLAST. If you have the name of protein, you can search the coding sequence in the gene. If it is a unkown protein, clone the gene and sequence it. There is also possibility to use anti-RGD antibodies and perform western blotting.
Thanks for the response Birendra. I am working with silk fibroin and the molecular weight for the heavy chain is quite large (390kDa). My background is analytical chemistry so I am not experienced in this field. I was also wondering if there are enzymes that target such kinds of linkages?
How about an enzymatic digest followed by mass spectrometry (peptide fingerprint)? Trypsin should cut your RDG well and you should see characteristic peptide sizes on either side.
http://web.expasy.org/peptide_cutter/
Hello Vimbi,
Go to expasy wesite; (http://www.expasy.org/) and search for your protein. there are silk fibroin light and heavy chain sequences available. you can see in one of the heavy chain (P05790), there is no RGD motif present. you can search all other sequences available in database. hope you dont need to sequence your protein.
there are many RGDs in protein accession number (O76786 ) beclonging to Antheraea pernyi (Chinese oak silk moth)..
I will take a look at the website. Some of the species I am working with belong to the same family (Saturniidae) with the A. pernyi and A. assama which have the RGDs. I want to determine what are the similarities and differences between them including the sequences as they have an impact on the applications of the fibroin, which is my ultimate goal.
hello vimbai....
how r u?
do you know how to remove the side chain protecting group from the peptide chain without cleavage of peptide fron solid support?
Hi Rahul,
This is really not my field thats why I actually posted my question! I think you can get more help by actually posting it as a question on its own, I am sure you will get responses from people who are experts in the field.
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