RE: protein entities (was Re: Rules (was Re: Ambiguous names. was: Re: URL +1, LSID -1)

---- Original message ----
>Date: Thu, 19 Jul 2007 16:29:18 -0400
>From: Michel_Dumontier <Michel_Dumontiercarleton.ca>  
>Subject: RE: protein entities (was Re: Rules (was Re:
Ambiguous names. was: Re:  URL +1, LSID -1)  
>To: Darren Natale <dan5georgetown.edu>,
Michel_Dumontier <Michel_Dumontiercarleton.ca>
>Cc: Eric Jain <Eric.Jainisb-sib.ch>, Alan
Ruttenberg <alanruttenberggmail.com>, Chris
Mungall <cjmfruitfly.org>, Bijan Parsia
<bparsiacs.man.ac.uk>, public-semweb-lifesci hcls
<public-semweb-lifesciw3.org>
>
>
>Darren,
>
>> Also, while we recognize
>> that there are different qualities that can be
ascribed to a basically
>> identical biochemical entity in different
structural conformations or
>> states of ligand binding, we are not attempting (at
least in the
>> beginning) to describe these structural
conformations or bound vs
>> unbound forms.
>
>Indeed, while conformation is an important quality of
molecular
>structure, it does not fundamentally change the nature
of the molecule.
>i.e. a protein in a bound or unbound state should still
be considered
>the same protein. 
>
>Cheers,
>
>-=Michel=-
> 
>
Many post-translational modifications like glycosylation (http://www.functionalglycomics.org/static/index.shtml)i
n proteins fundamentally change the (functional) 'nature' of
the protein (as also the molecular structure of the protein
in case of glycosylation through addition of sugar chains
(glycans)).

Satya Sahoo

Knoesis Center
http://knoesis.wright.edu

> Many post-translational modifications like
glycosylation
> (http://www.functionalglycomics.org/static/index.shtml)i
n proteins
> fundamentally change the (functional) 'nature' of the
protein (as also
the
> molecular structure of the protein in case of
glycosylation through
> addition of sugar chains (glycans)).

Absolutely, but I would go further and state that any
chemical
modification will change the fundamental type, and this will
necessarily
change dispositions to realizing certain functions.

-=Michel=-