How long is a protein sequence?

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Sun Dec 12 08:39:52 EST 2004

Stefek Borkowski wrote:

> Is "clipping the leading Met away" a 
> general phenomenon, concerning all proteins? If not, how do I know the final 
> length of the protein? Are there some dadabases on the net to check it or 
> somrthing? I have happened on some papers using different numbering, i.e. 
> including the first Met and not including. Maybe it goes this way that a 
> part of protein in the cell is with the leading Med and some is not... If 
> so, what kind of numbering system is correct? 

No, it is unfortunately a bit more complicated than that. The number of
amino acids clipped depends on the kind of protein. For example those
that are imported into organelles may have signal sequences at the
N-terminal end, which are clipped away after transport (see e.g. "Import
of proteins into mitochondria" or "Formation of collagen" in any of the
cell biology or biochemistry textbooks). This info should however be
contained in protein databases like BRENDA. 

Note that since proteins crystallised are often produced in bacteria by
genetic engineering, and bacteria do not clip, crystal structures
(PDB-fiels) often contain the complete N-terminus. I have often wondered
how this might affect the result...

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