[BiO BB] RE: [Cheminformatics] RE: [BioInformatics Group] alingment matric score for 22 amino acids; Amino acids Cystine and Hyrooxyproline

[#JIA YIYU#]

Hi Screenu,

Thank you very much for your helps! 

I was confused because I got the 22 number from the textbook "Molecular Biology in Medicine" by Thimothy M. Cox & John Sinclair. This textbook is first pritned in 1997. In page 25, it is said "However, as there are only some 22 amino acids some of the 61 codons specifying amino acids are redundant ...".

I was confused because that book is newer than the textbook, which I learnt before.  And after i carefully count the number of amino acids in its genetic code table. There are only 20 amino acids there!

Thanks a lot!

	Jia Yiyu


-----Original Message-----
From: VB Sreenu [mailto:sreenu at cdfd.org.in]
Sent: Friday, January 30, 2004 5:26 PM
To: cheminformatics at yahoogroups.com
Cc: BioInformaticsGroup at yahoogroups.com
Subject: Re: [Cheminformatics] RE: [BioInformatics Group] alingment matric score for 22 amino acids; Amino acids Cystine and Hyrooxyproline


Hi Jia,
cystine and hydroxyproline were considered as unusual amino acids in the 
proteins
before the discovery of post translational modifications. That is the 
reason they were
established in old biochemistry books as extra amino acids.

Genetic code is not 100% universal. As u said, organelle genetic code is 
different from organisms
genetic code. selenocystine was found in the organism's proteins (single 
letter amino acid code is "U").

some examples are (all from E. coli only)

formate dehydrogenase-N, nitrate-inducible, alpha subunit [Escherichia 
coli K12]
ac number 16129433.
formate dehydrogenase-O, major subunit [Escherichia coli K12]
ac number is 16131734
selenopolypeptide subunit of formate dehydrogenase H [Escherichia coli K12]
ac number 16131905

from those examples it is very clear that selenocystine should have a 
crucial role
in the function of formate dehydrogenase. (I dont have information on this)

you can calculate a substitution matrix including selenocystine 
proteins. But that might
not be statistically significant. Because available selenocystine 
containing proteins
are very few.

regards

Sreenu
-----------------------------
VB Sreenu
Research scholar
Laboratory of Computational Biology
CDFD, Nacharam, Hyderabad-76 India



#JIA YIYU# wrote:

>Hi,
>
>Thank you for your information. But I still feel strange that why only Cystine and Hyrooxyproline are particularly point out because there are not only two modified amino acids. 
>
>About Selenocystine, its condon is UGA, which is normally reconganized as stop condon (except in chondriosome). So is Selenocystine found in particular organism or organelle ? May I have more detail information about it?
>
>Best regards!
>
>	Jia Yiyu
>  
>


 #JIA YIYU# wrote:

>  
> Hi there,
>  
> Anybody would kindly point out where the protein alingment matrix 
> score for 22 nmino acids can be found?
>  
> According to some old biochemistry textbook, all known proteins and 
> enzymes are all produced from only 20 amino acids. But some new books 
> declare that there actually 22 amino acids discovered so far.  Have 
> these 22 amino acids been popular accepted? It seems the extra two 
> amino acids are Cystine and Hyrooxyproline. Any expert would like to 
> give out more information on them?
>  
> Thanks in advance!
>  
> Best regards!
>  
>      Jia Yiyu
>  
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