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

> An interesting issue, one of identity.  What determines the identity
of
> a molecule, a protein in this case?  
I strongly believe that the identity of a molecule is only dependent on
its physical (chemical) composition.

> If you have a protein that becomes
> phosphorylated, is the phosphorylated protein another one, numerically
> distinct from that non-phosphorylated that was there before?  
Yes, I believe so. However, our databases have traditionally stated
these as qualities of non-modified molecules, which ultimately challenge

> (The
> 'becomes' is somewhat inappropriate here.)  What changes can a protein
> undergo to still be the same protein, and what events make it to
another
> protein?
Identity should be maintained for changes in spatial location or
structural conformation or other non-configurational (atom/bond
composition) qualities that occur during its lifetime. Any event that
changes its configuration would transform it into another protein. 

>what about denaturation?  is the nature (what nature, by the way?) of a
>protein not fundamentally different in its native vs. denaturated
state?
A protein's shape is already highly dynamic from one moment to another,
and this has to do with interactions with the environment (solvent,
heat, etc). The identity of the protein is maintained, and it is simply
reacting to the environmental conditions placed on it. 

> Is it completely arbitrary, i.e., is the identity dependent merely on
> the observer's fiat?  If I remove a page from a book, is it the same
> book, or another book?  Does "fundamentally different" imply
> "non-identical", or merely "discernible"?
The basis for protein identity has traditionally been defined by its
amino acid sequence. It just so happens that we also want to
differentiate sequence identical proteins of different taxonomic origins
because their role/function might also change due to environmental
conditions. 

What do you think?

-=Michel=-