I used "introduction to protein structure" branden &tooze as a source
(nice book!). If I remember correctly the same story appears in
biochemistry textbooks.
The very same definition, put it in extreme terms, will allow us to call a entire fiber of "proteins" in the cell as one protein (think about filaments, etc), something that I've seen nobody doing. I guess that the definition is kind of loose, but is not going to help us, in terms of our software, to call a PROTEIN to something that has a big number of chains. I would slightly prefer complex[1].protein[1] than protein[1].chain[1], but not enough to discuss it too much.
>
> Perhaps not the best source, but wikipedia says:
>
> In biochemistry, quaternary structure is the arrangement of multiple folded
> protein molecules in a multi-subunit complex.
>
> 1 protein = 1 chain.
> more chains = complex.
>
>>
>> and let me put two more cents:
>> PDB format does not define any hierarchy. it is a set of atoms. if we
>> want to build an hierarchy out of PDB it should clearly follow from
>> the format. So the best way is to have 4 levels that are well defined
>> by the corresponding PDB fields:
>> Atom, Residue, Chain, Root
>> I think all other assumptions are only assumptions and a good source for
>> bugs.
>>
>
> The problem is that root is not well defined either. We can agree on how to
> define it, but please please please avoid the name UNIVERSE. Otherwise I'm
> going to decorate all my universes with decorators called God.
>
>> On Thu, Oct 8, 2009 at 6:41 PM, Keren Lasker <">> wrote:
>> > sounds good to me
>> > On Oct 8, 2009, at 6:35 PM, Daniel Russel wrote:
>> >
>> >>
>> >> On Oct 8, 2009, at 6:32 PM, Keren Lasker wrote:
>> >>
>> >>> ok - if you mean that Chain should not be part of the Hierarchy, I
>> >>> guess
>> >>> it makes sense, as usually protein == chain.
>> >>
>> >> To make things clear, I'm using the IMP names, so CHAIN, PROTEIN are
>> >> HierarchyTypes and Chain is a decorator. So there would not be a CHAIN
>> >> hierarchy type, but a PROTEIN could be a Chain (if it has a chain
>> >> designator). Sounds a bit icky...
>> >>
>> >>> On Oct 8, 2009, at 6:15 PM, Keren Lasker wrote:
>> >>>
>> >>>> for me more then one chain is an assembly ( or complex)
>> >>>> I would leave Chain because in modeling sometimes people takes
>> >>>> domains
>> >>>> from different places ( with different chain ids) and this
>> >>>> information might
>> >>>> be useful.
>> >>>> On Oct 8, 2009, at 6:13 PM, Daniel Russel wrote:
>> >>>>
>> >>>>> Does it make sense to talk about a protein which consists of more
>> >>>>> than
>> >>>>> one chain? I've heard people use the words that way (and there are
>> >>>>> google
>> >>>>> hits, but not a huge number), but it was suggested that this is a
>> >>>>> misuse of
>> >>>>> the words. It would make the atom hierarchy a bit simpler to say a
>> >>>>> protein
>> >>>>> is a single chain and has HierarchyType PROTEIN (and to remove the
>> >>>>> CHAIN
>> >>>>> type).
>> >>>>>
>> >>>>> Authoritative answers? Votes?
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