Number of codons in a peptide
Since I am coming straight from my physics background, sorry if my knowledge on basic gene sequencing is weak. My problem is - Can I find the number of codons in a peptide using it pdb file and look for the particular codon (717 precise for my peptide) using programs like VMD or PyMol.
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roshanpra •
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The variant (717) refers to the precursor protein APP, while you're just looking at the cleaved amyloid beta fragment. That's why the numbering doesn't match. Which publication are you looking for? I can probably provide you a copy and get sued for copyright issues.
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Codons refer to nucleotides where they (3 nucleotide) code for an amino acid. Are you looking to translate your peptide sequence back into DNA?
No, my peptide contains 40 amino acids and all I have to do is mutate 717 codon from Valine to Isoleucine using either pymol or vmd. Though I can view all these amino acids using both pymol and vmd, I could not find where is 717 codon ?
This doesn't make sense. If your peptide contains 40 amino acids, its template coding sequence consists of 40 codons, and 120 bases. There is no '717' codon or whatever that means, also peptides do not contain codons but consists of amino acids, and codons cannot be seen or manipulated in PyMol. Maybe you are referring to something else here? Not quite sure what.
Thanks for clearing out, that's exactly what I could not figure it out completely. Then, why does the paper stated mutation of 717 codon of beta amyloid (The peptide on which I am working on) http://www.ncbi.nlm.nih.gov/pubmed/1521868
Also, since I am talking about peptide here, I guess I would rather like to say, substitution from Valine to say Isoleucine at 717 codon
You are definitely dealing with a different protein here. Also, amino acid #717 can go from V to I, codon #717 will have to go from
AU[UCA]toGU[UCA]- codons are triplets of nucleotides, not amino acids.Your peptide presumably comes from a longer precursor.
Yes it is, It's from amyloid beta precursor protein.
The paper is dealing with a different protein than you are. What is the identifier of the protein you're working on? Can you give us the full text PDF of this paper? We don't have access to it.
So the codon numbering looks like it's from the coding sequence for the full-length precursor,
and google brings up this page for the mutation you are looking at, V717I: http://www.alzforum.org/mutation/app-v717i-london
Yes this is the reason, I cannot get any more information on the article by Kumar, no abstract or fulltext. To change the corresponding amino acid in your peptide, you should align the peptide sequence to the precursor, and then change the position.