Re: [ccp4bb] do you think it is interesting?

2012-06-20 Thread David Schuller 

On 06/20/12 00:36, Edward A. Berry wrote:

Sorry to come late to this discussion-

I think the actin and tubulin people already reverted "polymer"
to its etymological use- google "actin polymerization"

True. Objections withdrawn.

--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] do you think it is interesting?

2012-06-19 Thread Edward A. Berry 

Sorry to come late to this discussion-

I think the actin and tubulin people already reverted "polymer"
to its etymological use- google "actin polymerization"

Another example of infinite polymers formed by domain swapping
(and the surprises you can get trying to engineer a molecular switch):
http://www.ncbi.nlm.nih.gov/pubmed/22245575
eab

Jacob Keller wrote:

Okay, I wiki'd it, and according to them seems you're right: it says
they are "typically connected by covalent chemical bonds." So either
we revert to the etymological use of "polymer," or move onward to
"myriomer!" (assuming the cross-bred "multimer" is out of the
question!)

JPK

On Mon, Jun 18, 2012 at 10:37 AM, David Schuller  wrote:

On 06/18/12 11:17, Jacob Keller wrote:


  But anyway, what is
wrong with calling her structures "polymers?" Is there a subtle
covalent insinuation to "polymer?"


subtle? No, it's not subtle.


--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Cathy Lawson 
Hi Anna,

Your structure and description remind me very much of our domain-swapped 
crystal structure of trp repressor, also an infinite lattice.
One more example to add to the many that have been pointed out by others.
http://www.pdb.org/pdb/explore.do?structureId=1MI7

Cheers,
Cathy Lawson

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Ethan Merritt 
On Monday, June 18, 2012 02:06:46 pm Alexander Scouras wrote:
> > I'm further racking my brain to figure out a biological implication of this 
> > behaviour, I thought something like plaque formation but I can't find 
> > support in literature.
> 
> 
> There are a variety of domain swapped crystal structures out there, but at 
> least the two I'm most familiar with are regarded as being crystallization 
> artifacts. I think I recall seeing examples where domain swapping was 
> biologically relevant, but my impression is most are red herrings. 

You might be interested in the following paper, which describes
domain-swapped ("domain exchange") dimerization as a control mechanism for 
kinases.

 Activation segment dimerization: a mechanism for kinase 
 autophosphorylation of non-consensus sites.
 Pike, A.C.W.,  Rellos, P.,  Niesen, F.H.,  Turnbull, A.,  Oliver, A.W.,
 Parker, S.A.,  Turk, B.E.,  Pearl, L.H.,  Knapp, S.,  
 Journal: (2008) Embo J. 27: 704

But these are specifically dimeric.  Unlike the case posted here,
there is not a second non-swapped interface that would allow 
formation of an infinite chain.

Ethan



> 
> In the poster child of plaque formation, prion protein formed cys-cross 
> linked domain swapped dimers in some crystals. 
> 
> http://www.nature.com/nsmb/journal/v8/n9/abs/nsb0901-770.html
> 
> However, using PAGE & DLS it was later shown that prion has no preference for 
> dimers when you break down Infectious fibrils. Cross linked dimers definitely 
> out. Any subunits ruled out, in fact. 
> 
> http://www.nature.com/nature/journal/v437/n7056/abs/nature03989.html
> 
> 
> RNaseA is another example, and isn't even a disease associated molecule. 
> Similarly to how we've found that many/most proteins may be converted to 
> amyloid forms by harsh enough conditions, I think some will domain swap, and 
> some authors have pursued domain swapping heavily with RNaseA a as a "model 
> for amyloid formation". RNaseA will swap in major and minor conformations 
> even, though not in the same crystal. Still, that's the first thing you need 
> for an infinite series, is two compatible/simultaneous swapping points. 
> 
> 
> Now, I do think domain swapping, particularly an infinite chain, can be 
> interesting from a bioengineering or biophysical level, if that is what you 
> are interested in. I just want to say that there is a high bar to showing 
> biochemical relevance in the sense of holding any physiological implications. 
> 
> 
> Alexander D. Scouras
> Postdoctoral Fellow
> Alber Lab, QB3
> University of California, Berkeley

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Tom Murray-Rust 
> > I'm further racking my brain to figure out a biological implication of this 
> > behaviour, I thought something like plaque formation but I can't find 
> > support in literature.
>

A good example of domain swaps involved in disease-associated
polymerisation is the polymerisation of serpins; while there is still
some debate about whether this mechanism is actually what happens in
patients in vivo, the formation of polymers via domain swapping is
becoming widely accepted as the new paradigm. Relevant references
include:

Nature. 2008 Oct 30;455(7217):1255-8. Epub 2008 Oct 15.
Crystal structure of a stable dimer reveals the molecular basis of
serpin polymerization.
Yamasaki M, Li W, Johnson DJ, Huntington JA. PMID: 18923394

EMBO Rep. 2011 Sep 30;12(10):1011-7. doi: 10.1038/embor.2011.171.
Molecular basis of α1-antitrypsin deficiency revealed by the structure
of a domain-swapped trimer.
Yamasaki M, Sendall TJ, Pearce MC, Whisstock JC, Huntington JA. PMID: 21909074

Interestingly enough they don't rely on disulfide formation ("normal"
polymers fall apart on an SDS gel but not a native  gel), but they can
be engineered to include disulfides which render the polymers stable
to SDS (on a non-reducing gel). This was actually a really useful tool
in determining exactly which domains of a given molecule swapped into
their neighbour during polymerisation.

Best Regards

Tom

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Alexander Scouras 
> I'm further racking my brain to figure out a biological implication of this 
> behaviour, I thought something like plaque formation but I can't find support 
> in literature.


There are a variety of domain swapped crystal structures out there, but at 
least the two I'm most familiar with are regarded as being crystallization 
artifacts. I think I recall seeing examples where domain swapping was 
biologically relevant, but my impression is most are red herrings. 


In the poster child of plaque formation, prion protein formed cys-cross linked 
domain swapped dimers in some crystals. 

http://www.nature.com/nsmb/journal/v8/n9/abs/nsb0901-770.html

However, using PAGE & DLS it was later shown that prion has no preference for 
dimers when you break down Infectious fibrils. Cross linked dimers definitely 
out. Any subunits ruled out, in fact. 

http://www.nature.com/nature/journal/v437/n7056/abs/nature03989.html


RNaseA is another example, and isn't even a disease associated molecule. 
Similarly to how we've found that many/most proteins may be converted to 
amyloid forms by harsh enough conditions, I think some will domain swap, and 
some authors have pursued domain swapping heavily with RNaseA a as a "model for 
amyloid formation". RNaseA will swap in major and minor conformations even, 
though not in the same crystal. Still, that's the first thing you need for an 
infinite series, is two compatible/simultaneous swapping points. 


Now, I do think domain swapping, particularly an infinite chain, can be 
interesting from a bioengineering or biophysical level, if that is what you are 
interested in. I just want to say that there is a high bar to showing 
biochemical relevance in the sense of holding any physiological implications. 


Alexander D. Scouras
Postdoctoral Fellow
Alber Lab, QB3
University of California, Berkeley

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Remy Loris 

This may be somethng similar

Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet 
structure.

Spinelli S, Desmyter A, Frenken L, Verrips T, Tegoni M, Cambillau C.
FEBS Lett. 2004 Apr 23;564(1-2):35-40.

Remy Loris
Vrije Universiteit Brussel

On 18/06/12 15:49, anna anna wrote:

Hi all!
I'd like your opinion about a structure I solved.
Apart from protein structure itself, I think that my protein xtallized 
in an odd way!
The biological unit is a dimer while the asymmetric unit is a tetramer 
(red cartoon in the figure) resulting from domain swapping between two 
dimers.
The strange thing is that swapping connects infinite monomers and, 
rather than a xtal, my diffracting object seems a multilayer of 
endless linear polymers, a kind of papyrus with greek fret-like 
fibers. The figure shows the orientation of the polymers in each layer.
I'd like to know if some of you have already seen a similar pattern or 
it is weird as I think!
I'm further racking my brain to figure out a biological implication of 
this behaviour, I thought something like plaque formation but I can't 
find support in literature.


All suggestions are welcome!!

Cheers,
Anna

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Lucas 
2012/6/18 Tim Gruene :
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> [...]
>> of monomers is called a multimer, not a polymer.
> [...]
> shiver - what a terrible mixture of languages. 'multi-' has got latin
> origin, whereas both poly and mer have got greek origin, and I don't
> think one should mix these. Please!!! think of a different _GREEK_
> syllable to express what you describe as 'multimer'.

In fact this is quite common. "Automobile", for example comes from
greek "autos" plus latin "mobilis".

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Shiva Bhowmik 
Hi Anna,

Interesting assembly. What is the function of your protein? Is it known if
your protein forms a fibril-like assembly in solution? Moreover, can your
crystal packing be indexed higher symmetry space group?

Cheers,

Shiva

On Mon, Jun 18, 2012 at 9:03 AM, David Schuller  wrote:

> If the original poster could engineer a few disulfides or other covalent
> linkages in there, I would drop my objections, and be even more impressed.
>
>
> On 06/18/12 11:48, Jacob Keller wrote:
>
>> Okay, I wiki'd it, and according to them seems you're right: it says
>> they are "typically connected by covalent chemical bonds." So either
>> we revert to the etymological use of "polymer," or move onward to
>> "myriomer!" (assuming the cross-bred "multimer" is out of the
>> question!)
>>
>> JPK
>>
>> On Mon, Jun 18, 2012 at 10:37 AM, David Schuller
>>  wrote:
>>
>>> On 06/18/12 11:17, Jacob Keller wrote:
>>>
  But anyway, what is
 wrong with calling her structures "polymers?" Is there a subtle
 covalent insinuation to "polymer?"

  subtle? No, it's not subtle.
>>>
>>>
>>> --
>>> ==**==**
>>> ===
>>> All Things Serve the Beam
>>> ==**==**
>>> ===
>>>   David J. Schuller
>>>   modern man in a post-modern world
>>>   MacCHESS, Cornell University
>>>   schul...@cornell.edu
>>>
>>
>>
>>
>
> --
> ==**==**
> ===
> All Things Serve the Beam
> ==**==**
> ===
>   David J. Schuller
>   modern man in a post-modern world
>   MacCHESS, Cornell University
>   schul...@cornell.edu
>

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller 
On Mon, Jun 18, 2012 at 11:03 AM, David Schuller  wrote:
> If the original poster could engineer a few disulfides or other covalent
> linkages in there, I would drop my objections, and be even more impressed.

Ooh, that sounds nice! Could act as a bio-spring, releasable by dtt etc...

JPK







>
>
> On 06/18/12 11:48, Jacob Keller wrote:
>>
>> Okay, I wiki'd it, and according to them seems you're right: it says
>> they are "typically connected by covalent chemical bonds." So either
>> we revert to the etymological use of "polymer," or move onward to
>> "myriomer!" (assuming the cross-bred "multimer" is out of the
>> question!)
>>
>> JPK
>>
>> On Mon, Jun 18, 2012 at 10:37 AM, David Schuller
>>  wrote:
>>>
>>> On 06/18/12 11:17, Jacob Keller wrote:

  But anyway, what is
 wrong with calling her structures "polymers?" Is there a subtle
 covalent insinuation to "polymer?"

>>> subtle? No, it's not subtle.
>>>
>>>
>>> --
>>> ===
>>> All Things Serve the Beam
>>> ===
>>>                               David J. Schuller
>>>                               modern man in a post-modern world
>>>                               MacCHESS, Cornell University
>>>                               schul...@cornell.edu
>>
>>
>>
>
>
> --
> ===
> All Things Serve the Beam
> ===
>                               David J. Schuller
>                               modern man in a post-modern world
>                               MacCHESS, Cornell University
>                               schul...@cornell.edu



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Cale Dakwar 
If we are to strictly adhere to polymer as describing "few", then were do
we stand with DNA/RNA being described as a polymer - a long polymer made up
from repeating units of nucleotides, as has been used in textbooks for
ages?!  Is DNA/RNA too now a myriomer?

Cale

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread David Schuller 
If the original poster could engineer a few disulfides or other covalent 
linkages in there, I would drop my objections, and be even more impressed.


On 06/18/12 11:48, Jacob Keller wrote:

Okay, I wiki'd it, and according to them seems you're right: it says
they are "typically connected by covalent chemical bonds." So either
we revert to the etymological use of "polymer," or move onward to
"myriomer!" (assuming the cross-bred "multimer" is out of the
question!)

JPK

On Mon, Jun 18, 2012 at 10:37 AM, David Schuller  wrote:

On 06/18/12 11:17, Jacob Keller wrote:

  But anyway, what is
wrong with calling her structures "polymers?" Is there a subtle
covalent insinuation to "polymer?"


subtle? No, it's not subtle.


--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu






--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Bosch, Juergen 
isn't a polymer considered a poly-multimer of undefined size ?
And you use multi once you run out with your greek naming scheme say when > 
icosahedron ?

Jürgen

P.S. where are all those greeks to shed some light on us ?

On Jun 18, 2012, at 11:48 AM, Jacob Keller wrote:

Okay, I wiki'd it, and according to them seems you're right: it says
they are "typically connected by covalent chemical bonds." So either
we revert to the etymological use of "polymer," or move onward to
"myriomer!" (assuming the cross-bred "multimer" is out of the
question!)

JPK

On Mon, Jun 18, 2012 at 10:37 AM, David Schuller 
mailto:dj...@cornell.edu>> wrote:
On 06/18/12 11:17, Jacob Keller wrote:

 But anyway, what is
wrong with calling her structures "polymers?" Is there a subtle
covalent insinuation to "polymer?"

subtle? No, it's not subtle.


--
===
All Things Serve the Beam
===
  David J. Schuller
  modern man in a post-modern world
  MacCHESS, Cornell University
  schul...@cornell.edu



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller 
Okay, I wiki'd it, and according to them seems you're right: it says
they are "typically connected by covalent chemical bonds." So either
we revert to the etymological use of "polymer," or move onward to
"myriomer!" (assuming the cross-bred "multimer" is out of the
question!)

JPK

On Mon, Jun 18, 2012 at 10:37 AM, David Schuller  wrote:
> On 06/18/12 11:17, Jacob Keller wrote:
>>
>>  But anyway, what is
>> wrong with calling her structures "polymers?" Is there a subtle
>> covalent insinuation to "polymer?"
>>
> subtle? No, it's not subtle.
>
>
> --
> ===
> All Things Serve the Beam
> ===
>                               David J. Schuller
>                               modern man in a post-modern world
>                               MacCHESS, Cornell University
>                               schul...@cornell.edu



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread David Schuller 

On 06/18/12 11:17, Jacob Keller wrote:

  But anyway, what is
wrong with calling her structures "polymers?" Is there a subtle
covalent insinuation to "polymer?"


subtle? No, it's not subtle.

--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Ian Tickle 
On 18/06/2012, Tim Gruene  wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> [...]
>> of monomers is called a multimer, not a polymer.
> [...]
> shiver - what a terrible mixture of languages. 'multi-' has got latin
> origin, whereas both poly and mer have got greek origin, and I don't
> think one should mix these. Please!!! think of a different _GREEK_
> syllable to express what you describe as 'multimer'.
>
> Cheers,
> Tim

Oligomer, surely, from Gk 'oligos' meaning 'a few'?

-- Ian

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller 
I love "myriomer," but what's wrong with boring old "polymer?"

JPK

On Mon, Jun 18, 2012 at 10:27 AM, Emmanuel Saridakis
 wrote:
> Of course, "oligomer" (pure Greek) usually does that kind of job, but not in
> this specific case, since oligo means few and in this case we have "endless"
> chains.
> I can only think of the neologism "myriomer" for this particular case, if
> you want to stick to Greek. Myrioi can mean 1 or countless, depending on
> where you accent the word!
>
> If that catches on, remember you (probably) saw it here first!
>
> Cheers,
> Emmanuel
>
>
> - Original Message ----- From: "Tim Gruene" 
> To: 
> Sent: Monday, June 18, 2012 5:43 PM
> Subject: Re: [ccp4bb] do you think it is interesting?
>
>
>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> [...]
>>>
>>> of monomers is called a multimer, not a polymer.
>>
>> [...]
>> shiver - what a terrible mixture of languages. 'multi-' has got latin
>> origin, whereas both poly and mer have got greek origin, and I don't
>> think one should mix these. Please!!! think of a different _GREEK_
>> syllable to express what you describe as 'multimer'.
>>
>> Cheers,
>> Tim
>>
>> On 06/18/12 16:21, David Schuller wrote:
>>>
>>> Certainly it's interesting, but I think your description is
>>> inaccurate.
>>>
>>> "Endless linear polymers" - Each monomer is a polymer, but a
>>> collection of monomers is called a multimer, not a polymer.
>>>
>>> I don't suppose there are any knots? That would be really
>>> interesting.
>>>
>>> On 06/18/12 09:49, anna anna wrote:
>>>>
>>>> Hi all! I'd like your opinion about a structure I solved. Apart
>>>> from protein structure itself, I think that my protein xtallized
>>>> in an odd way! The biological unit is a dimer while the
>>>> asymmetric unit is a tetramer (red cartoon in the figure)
>>>> resulting from domain swapping between two dimers. The strange
>>>> thing is that swapping connects infinite monomers and, rather
>>>> than a xtal, my diffracting object seems a multilayer of endless
>>>> linear polymers, a kind of papyrus with greek fret-like fibers.
>>>> The figure shows the orientation of the polymers in each layer.
>>>> I'd like to know if some of you have already seen a similar
>>>> pattern or it is weird as I think! I'm further racking my brain
>>>> to figure out a biological implication of this behaviour, I
>>>> thought something like plaque formation but I can't find support
>>>> in literature.
>>>>
>>>> All suggestions are welcome!!
>>>>
>>>> Cheers, Anna
>>>>
>>>>
>>>
>>>
>>
>> - -- - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v1.4.12 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP
>> o034eyZnadpwyQRGXI4FV9w=
>> =Q5GJ
>> -END PGP SIGNATURE-



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Emmanuel Saridakis 
Of course, "oligomer" (pure Greek) usually does that kind of job, but not in 
this specific case, since oligo means few and in this case we have "endless" 
chains.
I can only think of the neologism "myriomer" for this particular case, if 
you want to stick to Greek. Myrioi can mean 1 or countless, depending on 
where you accent the word!


If that catches on, remember you (probably) saw it here first!

Cheers,
Emmanuel


- Original Message - 
From: "Tim Gruene" 

To: 
Sent: Monday, June 18, 2012 5:43 PM
Subject: Re: [ccp4bb] do you think it is interesting?



-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

[...]

of monomers is called a multimer, not a polymer.

[...]
shiver - what a terrible mixture of languages. 'multi-' has got latin
origin, whereas both poly and mer have got greek origin, and I don't
think one should mix these. Please!!! think of a different _GREEK_
syllable to express what you describe as 'multimer'.

Cheers,
Tim

On 06/18/12 16:21, David Schuller wrote:

Certainly it's interesting, but I think your description is
inaccurate.

"Endless linear polymers" - Each monomer is a polymer, but a
collection of monomers is called a multimer, not a polymer.

I don't suppose there are any knots? That would be really
interesting.

On 06/18/12 09:49, anna anna wrote:

Hi all! I'd like your opinion about a structure I solved. Apart
from protein structure itself, I think that my protein xtallized
in an odd way! The biological unit is a dimer while the
asymmetric unit is a tetramer (red cartoon in the figure)
resulting from domain swapping between two dimers. The strange
thing is that swapping connects infinite monomers and, rather
than a xtal, my diffracting object seems a multilayer of endless
linear polymers, a kind of papyrus with greek fret-like fibers.
The figure shows the orientation of the polymers in each layer.
I'd like to know if some of you have already seen a similar
pattern or it is weird as I think! I'm further racking my brain
to figure out a biological implication of this behaviour, I
thought something like plaque formation but I can't find support
in literature.

All suggestions are welcome!!

Cheers, Anna







- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP
o034eyZnadpwyQRGXI4FV9w=
=Q5GJ
-END PGP SIGNATURE-

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller 
I have been curious and suspicious for a long time about "multimer:" I
always assumed it to be a more homey substitute for "oligomer," as
there seems to me to be no difference in usage, and certainly not in
the etymological sense. I have often heard it used by non-experts who
don't know exactly the meaning of the prefix "oligo-" but do know
"multi-," so they feel more comfortable I think. But anyway, what is
wrong with calling her structures "polymers?" Is there a subtle
covalent insinuation to "polymer?"

JPK


On Mon, Jun 18, 2012 at 9:48 AM, David Schuller  wrote:
> On 06/18/12 10:43, Tim Gruene wrote:
>>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> [...]
>>>
>>> of monomers is called a multimer, not a polymer.
>>
>> [...]
>> shiver - what a terrible mixture of languages. 'multi-' has got latin
>> origin, whereas both poly and mer have got greek origin, and I don't
>> think one should mix these. Please!!! think of a different _GREEK_
>> syllable to express what you describe as 'multimer'.
>>
> I didn't invent the term "multimer," it has been in use for some decades.
> And I am writing English, not Latin or Greek.
>
>
> --
> ===
> All Things Serve the Beam
> ===
>                               David J. Schuller
>                               modern man in a post-modern world
>                               MacCHESS, Cornell University
>                               schul...@cornell.edu



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread David Schuller 

On 06/18/12 10:43, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

[...]

of monomers is called a multimer, not a polymer.

[...]
shiver - what a terrible mixture of languages. 'multi-' has got latin
origin, whereas both poly and mer have got greek origin, and I don't
think one should mix these. Please!!! think of a different _GREEK_
syllable to express what you describe as 'multimer'.

I didn't invent the term "multimer," it has been in use for some 
decades. And I am writing English, not Latin or Greek.


--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Bosch, Juergen 
how about greek-protomers-bands (aka GPB) :-)

Nice picture, you can make decorative art with it and sell it.

Jürgen

On Jun 18, 2012, at 10:43 AM, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

[...]
of monomers is called a multimer, not a polymer.
[...]
shiver - what a terrible mixture of languages. 'multi-' has got latin
origin, whereas both poly and mer have got greek origin, and I don't
think one should mix these. Please!!! think of a different _GREEK_
syllable to express what you describe as 'multimer'.

Cheers,
Tim

On 06/18/12 16:21, David Schuller wrote:
Certainly it's interesting, but I think your description is
inaccurate.

"Endless linear polymers" - Each monomer is a polymer, but a
collection of monomers is called a multimer, not a polymer.

I don't suppose there are any knots? That would be really
interesting.

On 06/18/12 09:49, anna anna wrote:
Hi all! I'd like your opinion about a structure I solved. Apart
from protein structure itself, I think that my protein xtallized
in an odd way! The biological unit is a dimer while the
asymmetric unit is a tetramer (red cartoon in the figure)
resulting from domain swapping between two dimers. The strange
thing is that swapping connects infinite monomers and, rather
than a xtal, my diffracting object seems a multilayer of endless
linear polymers, a kind of papyrus with greek fret-like fibers.
The figure shows the orientation of the polymers in each layer.
I'd like to know if some of you have already seen a similar
pattern or it is weird as I think! I'm further racking my brain
to figure out a biological implication of this behaviour, I
thought something like plaque formation but I can't find support
in literature.

All suggestions are welcome!!

Cheers, Anna





- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP
o034eyZnadpwyQRGXI4FV9w=
=Q5GJ
-END PGP SIGNATURE-

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Tim Gruene 
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

[...]
> of monomers is called a multimer, not a polymer.
[...]
shiver - what a terrible mixture of languages. 'multi-' has got latin
origin, whereas both poly and mer have got greek origin, and I don't
think one should mix these. Please!!! think of a different _GREEK_
syllable to express what you describe as 'multimer'.

Cheers,
Tim

On 06/18/12 16:21, David Schuller wrote:
> Certainly it's interesting, but I think your description is
> inaccurate.
> 
> "Endless linear polymers" - Each monomer is a polymer, but a
> collection of monomers is called a multimer, not a polymer.
> 
> I don't suppose there are any knots? That would be really
> interesting.
> 
> On 06/18/12 09:49, anna anna wrote:
>> Hi all! I'd like your opinion about a structure I solved. Apart
>> from protein structure itself, I think that my protein xtallized 
>> in an odd way! The biological unit is a dimer while the
>> asymmetric unit is a tetramer (red cartoon in the figure)
>> resulting from domain swapping between two dimers. The strange
>> thing is that swapping connects infinite monomers and, rather
>> than a xtal, my diffracting object seems a multilayer of endless
>> linear polymers, a kind of papyrus with greek fret-like fibers.
>> The figure shows the orientation of the polymers in each layer. 
>> I'd like to know if some of you have already seen a similar
>> pattern or it is weird as I think! I'm further racking my brain
>> to figure out a biological implication of this behaviour, I
>> thought something like plaque formation but I can't find support
>> in literature.
>> 
>> All suggestions are welcome!!
>> 
>> Cheers, Anna
>> 
>> 
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP
o034eyZnadpwyQRGXI4FV9w=
=Q5GJ
-END PGP SIGNATURE-

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread David Schuller 

Certainly it's interesting, but I think your description is inaccurate.

"Endless linear polymers" - Each monomer is a polymer, but a collection 
of monomers is called a multimer, not a polymer.


I don't suppose there are any knots? That would be really interesting.

On 06/18/12 09:49, anna anna wrote:

Hi all!
I'd like your opinion about a structure I solved.
Apart from protein structure itself, I think that my protein xtallized 
in an odd way!
The biological unit is a dimer while the asymmetric unit is a tetramer 
(red cartoon in the figure) resulting from domain swapping between two 
dimers.
The strange thing is that swapping connects infinite monomers and, 
rather than a xtal, my diffracting object seems a multilayer of 
endless linear polymers, a kind of papyrus with greek fret-like 
fibers. The figure shows the orientation of the polymers in each layer.
I'd like to know if some of you have already seen a similar pattern or 
it is weird as I think!
I'm further racking my brain to figure out a biological implication of 
this behaviour, I thought something like plaque formation but I can't 
find support in literature.


All suggestions are welcome!!

Cheers,
Anna





--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] do you think it is interesting?

2012-06-18 Thread Jacob Keller 
Wow, that's very cool! Can you divulge what the function of the
protein is? One thinks of some kind of mechanical spring...

JPK

On Mon, Jun 18, 2012 at 8:49 AM, anna anna  wrote:
> Hi all!
> I'd like your opinion about a structure I solved.
> Apart from protein structure itself, I think that my protein xtallized in an
> odd way!
> The biological unit is a dimer while the asymmetric unit is a tetramer (red
> cartoon in the figure) resulting from domain swapping between two dimers.
> The strange thing is that swapping connects infinite monomers and, rather
> than a xtal, my diffracting object seems a multilayer of endless linear
> polymers, a kind of papyrus with greek fret-like fibers. The figure shows
> the orientation of the polymers in each layer.
> I'd like to know if some of you have already seen a similar pattern or it is
> weird as I think!
> I'm further racking my brain to figure out a biological implication of this
> behaviour, I thought something like plaque formation but I can't find
> support in literature.
>
> All suggestions are welcome!!
>
> Cheers,
> Anna
>
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***