Amino Acid Sequence

[ash.bekah]

If I know the Amino Acid sequence for something, how do I go about making the chain, and displaying it? This is one of the sequences for the splice variants of the receptor for the medication Tramadol.

 

1 mdssaaptna snctdalays scspapspgs wvnlshldgn lsdpcgpnrt dlggrdslcp

61 ptgspsmita itimalysiv cvvglfgnfl vmyvivrytk mktatniyif nlaladalat

121 stlpfqsvny lmgtwpfgti lckivisidy ynmftsiftl ctmsvdryia vchpvkaldf

181 rtprnakiin vcnwilssai glpvmfmatt kyrqgsidct ltfshptwyw enllkicvfi

241 fafimpvlii tvcyglmilr lksvrmlsgs kekdrnlrri trmvlvvvav fivcwtpihi

301 yviikalvti pettfqtvsw hfcialgytn sclnpvlyaf ldenfkrcfr efciptssni

361 eqqnstrirq ntrdhpstan tvdrtnhqle nleaetaplp

 

Now, if I want to make a chain of amino acids, what would I use? All of it?

 

I want to do something like this with the protein sequence for Tramadol (mu-opioid receptor) http://fyeahtattoos.com/post/5998856013/its-a-chain-of-amino-acids-spelling-the-word

How would I do it?

Ash

[CharonY]

The letters represent the chain of AA (i.e. the primary sequence). I am not sure what precisely you want. If you want to give structural information (i.e. secondary or tertiary structure) you will be dependent on more information. Of course there prediction and modeling software, but without experimental data they are just predictions and can be rather inaccurate. For the more complex structures different type of notations exist.

[ash.bekah]

CharonY,

 

Sorry for the confusion... Let me give you an example. In the fourth paragraph on this page, the amino acid sequence for this medication is given: http://en.wikipedia.org/wiki/Ziconotide

What I want to know is, how do I figure out the amino acid sequence for the medication "Tramadol" ? I do not want the protein that is part of the human body, that tramadol binds to. I want the amino acid sequence for tramadol. If such a thing exists. I apologize for giving you the wrong info to begin with.

[Natasha]

What you have up there IS your amino acid sequence. Each letter represents an amino acid. For your first amino acid, you have Methionine, or "Met". Next, "D", is aspartic acid. So far, for your first two amino acids, in the format that I think you want them in, you have Met-Asp...

Is that what you're looking for? If you google image "codons", you can find a codon chart that will give you all the information you need to decipher the letters...

[Essay]

There is no "amino acid sequence" for Tramadol. I don't know anything about the drug, but I'd bet it is not a protein.

 

The receptor is a protein (so it has an aa sequence).

 

Thinking of drug receptor interactions as a lock-n-key is helpful, but trying to apply that "mirror image" concept won't work, if it is simply based on using aa sequences to reverse engineer something to fit the receptor... if that is what you were thinking about.

 

...or words to that effect. Does that help, or am I misunderstanding?

 

~

 

P.S.

 

 

 

Theoretically, from the aa sequence, you could predict and map the quantum sensitivities of the receptor/binding site. From that you could "reverse engineer" a mirror image type of drug to manipulate the receptor; but you don't use amino acids to do that sort of "quantum mapping" or design.

 

~

[CharonY]

Yes, tramadol is defintely not a protein.

 

Theoretically, from the aa sequence, you could predict and map the quantum sensitivities of the receptor/binding site. From that you could "reverse engineer" a mirror image type of drug to manipulate the receptor; but you don't use amino acids to do that sort of "quantum mapping" or design.

 

Eh, what? I have never heard "quantum sensitivity" in this context. Nor quantum mapping, for that matter. But predictions of docking sites (if that is what you meant) is notoriously difficult and usually requires additional data to be useful.

Edited January 20, 2012 by CharonY

[Essay]

Yes, tramadol is defintely not a protein.

 

Eh, what? I have never heard "quantum sensitivity" in this context. Nor quantum mapping, for that matter. But predictions of docking sites (if that is what you meant) is notoriously difficult and usually requires additional data to be useful.

Yes, I thought about putting a parenthetical in (about needing to account for "surrounding interactions") also, but I wanted to keep close to the "mirror image" / lock-n-key aspect.

 

You're right, those terms were only meant to be evocative of what is theoretically possible, not practical now (or ever possibly). Posting rapidly, I didn't think to look up the term for the pictures I've seen; but I searched "electronic contour map of binding site" and found this (which I entitled QuantumContours).

 

http://www.scielo.br/scielo.php?pid=s0100-40422007000500016&script=sci_arttext

 

This is the type of thing I was trying to indicate. Sorry if that didn't come across in my hasty metaphorical language. I thought the OP would "get" that --as well as (or perhaps better than) a well researched, technologically accurate, list of points and citations. Thanks for getting me to look up that picture though.

 

~

Edited January 20, 2012 by Essay