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<[log in to unmask]>
>> Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
>> To: [log in to unmask]
>>
>> 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<[log in to unmask]>
>>>> Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
>>>> To: [log in to unmask]
>>>>
>>>> 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
>
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