Dear Hay
Your post prompted me to respond, since I think the issue of symmetry is
extremely important.
I would like to reinstate here what should be obvious to everyone: a
stable asymmetric assembly of proteins in solution is essentially
impossible (or at most very very unlikely), purely because of
topological reasons.
This is beautifully explained in a classic paper now 50 years old:
Monod, Wyman, Changeux (1965) "On the Nature of Allosteric Transitions:
A Plausible Model". The reasoning there is that a homomeric protein in
solution can only associate in 2 ways: isologous (binding with same
surface patches in both monomers, necessarily through a 2-fold axis) or
heterologous (binding through different surface patches in both
monomers). The isologous case is clearly symmetric (C2). Whilst in the
heterologous case the monomers can either assemble infinitely or form a
closed symmetry. The conclusion that follows is that stable
homo-oligomers can only be symmetric.
I especially like this paragraph:
"On the basis of these considerations, it is reasonable to assume that,
if an oligomeric protein possesses a wide range of stability, it
consists of a closed structure where all the protomers use the same
binding sets; which implies, as we have just seen, that the molecule
should possess at least one axis of symmetry."
The paper really explains it a lot better than me, it can be found here:
http://www.pasteur.fr/ip/resource/filecenter/document/01s-00004j-0er/monod-wyman-changeux-1965.pdf
The conclusion in any case is that asymmetry in homomers is, if not
impossible, highly unlikely. So in my opinion asymmetric assemblies
should be proposed with a lot of care, only if experimental data really
is overwhelmingly clear. For instance I don't think that gel filtration
or AUC would be good evidence enough: it really needs to be demonstrated
that the interface that you see in the crystal is the one leading to
oligomerisation (perhaps with a mutagenesis experiment?). Otherwise the
interface in the crystal is most likely simply a crystal contact.
Jose
On 12/12/14 10:15, Hay Dvir wrote:
Dear Jeremy,
Indeed, we also incline to think of it as a monomer in solution, but
still quite un-eased by the extensive interactions in the asu being
merely as a result of a crystallization artifact. As you said, we
may need to rely more heavily on biochemical analysis and since SEC
wasn't clear we are turning now to LS (hope to able to post a more
conclusive update).
Regardless of what our final conclusion would be for this case, we
became rather generally interested to find other similar cases of
*homomeric* assemblies related only by non crystallographic
translation symmetry (or as Engin Qzka pointed out "improper NCS" is
the conventional terminology). So to rephrase our question we are
interested to learn about additional structures of *homomoeric
improper ncs assemblies*.
I truly appreciate ANY open-minded or skeptic thought, profound or
trivial that we get here! They all, definitely those made by Mark
Garavito, contribute to shaping our mind around this riddle.
Thanks for commenting on the skepticism, I brought it up as part of
the discussion but a glitch of my own coffee time haziness might have
slipped in. Perhaps I should try some o-cha instead .. :)
cheers,
Hay
On Dec 12, 2014, at 3:05 AM, Jeremy Tame wrote:
Dear Hay
I suggest that you use analytical ultracentrifugation to determine
the oligomeric state of the protein in solution.
Mass spectrometry and light scattering are also useful, but there are
so many examples of gel filtration proving
erroneous it has questionable value as an analytical technique. For
an example of a dimer interface predicted by
PISA to be real you could look at Yoshida et al, JMB 423, 351 (2012).
The protein is in fact a monomer in solution.
PISA is a fantastic tool, but interfaces in crystals do not always
reflect the solution state. My guess (with the
information I have) is that your protein is probably a monomer too.
With regard to Michael Garavito's reply requesting more information,
I would like to comment that scepticism
is indeed an important god in the pantheon of science, but that that
minor deity open-mindedness also deserves the
occasional nod. 10-fold crystal symmetry is one example, but the list
of "impossible" things now become mainstream
is a long one (continental drift, Earth >100,000 years old, quantum
mechanics....and so on). Bayes theorem cannot
help you discover the truth if you have set its prior probability to
zero. But I haven't my morning o-cha yet either.
good luck
Jeremy
On Dec 11, 2014, at 9:27 PM, Hay Dvir wrote:
Dear all,
We have a structure of a rather tightly packed homotrimer protein in
the ASU with no apparent crystallographic or non-crystallographic
rotational symmetry between monomers.
Attempting to establish the biological assembly, we are very
interested to hear about additional similar cases you might know of.
Thanks in advance,
Hay
---------------------------
Hay DvirPh. D.
HeadTechnion Center for Structural Biology
TechnionHaifa 3200003, Israel
Tel:+(972)-77-887-1901
Fax:+(972)-77-887-1935
[email protected] <mailto:[email protected]>
Websitehttp://tcsb.technion.ac.il
