Kevin Gardner wrote:
>> Hi all:
> While my upstairs neightbor Larry (lamoran at gpu.utcc.utoronto.ca)
> brings up an interesting point in this discussion, I think we're on two
> different wavelengths on the definition of domains and motifs. Anyone
> else care to comment?
>> L.A. Moran (lamoran at gpu.utcc.utoronto.ca) wrote:
> : This request brings up another issue that might be worth discussing. Should
> : these DNA binding regions be referred to as "domains" or "motifs"? In the
> : literature on protein structure the word "domain" usually refers to a
> : discrete, independently folding region with a globular structure. Such
> : domains consist of large stretches of primary sequence and they can be
> : recognized as distinct units in the overall structure of a protein. Domains
> : are usually connected by short linker sequences.
>> OK --- looks good so far, although I don't agreed with the term "large
> stretches" of primary sequence. Some domains that don't bind ligands
> are as small as ~50-60 aa (SH3 domain, for example); if metals and/or
> disulfide bonds are present, the size can be smaller.
>> : Domains, as defined by structural biologists, consist of multiple regions
> : of secondary or supersecondary structures.
>> Fine.
>> : Zinc fingers and other zinc containing structures are examples of motifs
> : and not, strictly speaking, domains. They are often part of a large domain
> : within a protein. Motifs are usually short stretches of primary sequence
> : on the order of 20-100 amino acid residues. Domains are larger.
>
Haven't read the whole discussion - sorry if this point has been made.
The distinction between domains and motifs is not related to size, or
number
of residues etc. There is no physical size limit on a motif, it can be
as
small or as large as you want. There are, however, upper and lower
physical size limits on domains (would be quite interesting to discuss
the possible reasons for this, but it's a bit off-topic, so I won't)
A motif is a feature that is commonly recurring. So a Zinc finger could
be
called a motif. But I don't see why it couldn't also be called a
domain. A
good definition of a protein domain is tricky - but something in terms
of a
strong (maybe or maybe not autonomous?) intrinsic propensity to fold to
it's
native form is a good way to think about it.
Gotta go,
Simon
Simon M. Brocklehurst
smb at bioch.ox.ac.uk
OCMS, Dept. Biochemistry
University of Oxford, UK
