So, that was my previous question.
Em 29-07-2010 14:14, Phoebe Rice escreveu:
You don't have to keep the same number of symmetrical
contacts.
---- Original message ----
Date: Thu, 29 Jul 2010 14:13:56 -0300
From: Fred<ccp4bb.l...@gmail.com>
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISCMAIL.AC.UK
Clarifying... That's happened because I was talking about
the symmetry
of the SAXS envelop/particle. I understand that if you
consider the
symmetry of the whole particle, say a tetramer of identical
subunits,
you can have the 4-fold axis when asking for 222 symmetry
envelop, which
gives you a 422 envelop. I disagree with you
statement "there is no
fundamental reason that a tetramer has to have any
particular symmetry".
Thinking only in the low resolution envelop, that's not
true. Try to
arrange 4 spheres in a non-symmetrical way keeping the same
number of
reciprocal contacts.
Em 29-07-2010 13:17, Phoebe Rice escreveu:
It sounds like you're missing something fundamental about
222 symmetry, but I may be misunderstanding you - there IS
no fourfold. In fact, I think it is more common for the
subunits within tetramers to be related to one another by
three mutually perpendicular twofolds than a fourfold
(e.g.
the favorite classic hemoglobin has no fourfold anywhere).
And there is no fundamental reason that a tetramer has to
have any particular symmetry.
Phoebe
---- Original message ----
Date: Thu, 29 Jul 2010 13:04:02 -0300
From: Fred<ccp4bb.l...@gmail.com>
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISCMAIL.AC.UK
Of course, 222 has not a 4 axis, otherwise it would be a
4-
fold axis.
But that's the output of the program. P4 exp. model has
a 4-
fold axis
along the longest axis, while the P222 MODEL has a 4-fold
axis along the
smallest, which doesn't make any sense. Can you imagine
something build
up with 4 identical subunits and 222 symmtry, but
without a
4-fold axis
at the molecular level (I mean at the envelop resolution
level)?
Em 29-07-2010 12:32, Vellieux Frederic escreveu:
Hi,
To quote you: "even my P222 experimental envelop does
have a 4-fold
axis" - this is not suprising, a particle with 222
symmetry does not
have 4-fold symmetry. There are 3 mutually perpendicular
2-fold axes
that intersect at the origin (of the "particle", of the
molecule) [and
for the nomenclature, these axes are named the P Q and R
axes].
Fred.
Fred wrote:
Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the
symmetry of
the tetrameric particle (point symmetry) at the
molecular level not
at the atomic level. This question has arisen because I
have
collected some SAXS data of my protein in solution and
I
don't have a
molecular model to superpose to the experimental
envelop. Others
experimental data, gel filtration and NAT-PAGE, suggest
a tetrameric
particle. On the other side, P1, P2, P222 and P4
experimental
envelops are quite different. So, I am not sure which
symmetry to
take. Considering the native state (no ligands at all),
4 identical
subunits and that the interface of oligomarization have
to be
conserved, I would take P222 or P4. However, I can be
able to imagine
such spacial arrangement without a 4-fold axis at the
molecular
level. Indeed, even my P222 experimental envelop does
have a 4-fold
axis.
I appreciate if you could add some more comments on
this.
Thanks in advance,
Fred
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry& Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/0
1_Faculty_Alphabetically.php?faculty_id=123
RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry& Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
