Is it possible the solution structure of SAXS, NMR and EM neglect the
existence of a very small percentage conformation of the molecule due to
the overwhelming signals from the majority conformations? But this state of
the molecule is trapped and enriched by the crystallization condition.
Nian
O
I feel compelled to throw a few references into the ring.
NFAT is a protein where you get a good sampling of snapshots:
1. Folded up as a monomer when interacting with partner proteins:
http://www.ncbi.nlm.nih.gov/pubmed/9510247
http://www.ncbi.nlm.nih.gov/pubmed/16873067
2. Extended as a
Dear Crystallographers,
thanks for all of the responses and conversation. I have culled
together the various references which have been sent on the BB and
which I have come up with, and posted them below. Worthy of special
mention, I think, is the first one (Lange et al), in which 46 (!)
different
Another good lesson here:
2.
The SAXS solution structure of RF1 differs from its crystal structure and is
similar to its ribosome bound cryo-EM structure.
Vestergaard B, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede
M, Svergun DI, Ehrenberg M.
Mol Cell. 2005 Dec 22;20(6):929-3
2012_02_11
Dear All,
Two really striking examples of "Intrinsically Flexible Proteins" are:
(1) Adenylate kinase: Vonrhein, Schlauderer & Schulz (1995) Structure 3, 483
“Movie of the structural changes during a catalytic cycle of nucleoside
monophosphate kinases”
http://portal.uni-freiburg.de/str
3:25 PM
To:
Subject: [ccp4bb] Crystal Structures as Snapshots
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins can be considered freeze-frame snapshots of actual
conformations assu
ncoln, NE 68588
(402) 472-3626
mwilso...@unl.edu
Jacob Keller
Sent by: CCP4 bulletin board
02/10/2012 03:37 PM
Please respond to
Jacob Keller
To
CCP4BB@JISCMAIL.AC.UK
cc
Subject
Re: [ccp4bb] Crystal Structures as Snapshots
Isn't calcium-calmodulin one of the archetypical examp
> >
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Nat
> > Echols
> > Sent: Friday, February 10, 2012 10:35 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Crystal Structures as S
pporting the
>> physiological crystal structures
>>
>>
>> -Original Message-----
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
>> Echols
>> Sent: Friday, February 10, 2012 10:35 PM
>> To: CCP4BB@JISCMAIL.AC.UK
Along the lines of Roger's second point, there was a very nice paper a few
years back that found very good agreement between the conformational ensemble
sampled by ubiquitin in solution (by NMR) with the ensemble of conformations
observed in a large number of crystal structures:
Lange OF, Lakom
t; George
>
> PS There are lots of solution NMR structures as well supporting the
> physiological crystal structures
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
> Echols
> Sent: Friday, February 10, 2012 10:35 PM
&
On Friday, February 10, 2012 12:51:03 pm Jacob Keller wrote:
> Interesting to juxtapose these two responses:
>
> James Stroud:
> >How could they not be snapshots of conformations adopted in solution?
>
> David Schuller:
> > How could that possibly be the case when any structure is an average of a
The contrast seems to boil down to the semantics of the word "snapshot".
In my definition, I assume that the uncertainty of a structure is an intrinsic
quality of the structure and thus included in the meaning of "snapshot". Part
of that uncertainty comes from averaging.
James
On Feb 10, 2012
solution NMR structures as well supporting the
physiological crystal structures
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nat
Echols
Sent: Friday, February 10, 2012 10:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Crystal Structures as S
So the implication is that some of these treatments might allow the protein to
overcome energetic barriers that are prohibitive in solution--after the protein
is already in the solid state and not in solution any more?
Another view is that crystallization is a result of stabilizing conformations
Interesting to juxtapose these two responses:
James Stroud:
>How could they not be snapshots of conformations adopted in solution?
David Schuller:
> How could that possibly be the case when any structure is an average of all
> the unit cells of the crystal over the timespan of the diffraction
> e
I believe the most justifiable assumption one
can make is that crystal structures are likely to represent the
least soluble conformations of a protein under the conditions of
crystallization (which might be a broad range of conditions,
including physiological). Th
On 02/10/2012 03:25 PM, Jacob Keller wrote:
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins can be considered freeze-frame snapshots of actual
conformations assumed in solution. In a
Hi Jacob,
Lorena Beese has a few systems where snapshots of reaction mechanisms
have been looked at structurally.
Here are two such papers:
Long, SB, Casey, P., Beese, LS (2002) The reaction path of protein
farnesyltransferase at atomic resolution. Nature Oct 10;
419(6907):645-50.
http://www.ncb
> How could they not be snapshots of conformations adopted in solution?
Let me clarify--sorry about that. Consider several structures of the
same protein solved under different conditions, or several homologs
solved under similar conditions, or both. Further, let's say some
structural element, per
On Fri, Feb 10, 2012 at 12:29 PM, James Stroud wrote:
> How could they not be snapshots of conformations adopted in solution?
Packing billions of copies of an irregularly-shaped protein into a
compact lattice and freezing it to 100K isn't necessarily
representative of "solution", especially when
How could they not be snapshots of conformations adopted in solution?
James
On Feb 10, 2012, at 1:25 PM, Jacob Keller wrote:
> Dear Crystallographers,
>
> I am looking for references which discuss the validity of the
> assertion that multiple crystal structures of the same or similar
> protein
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins can be considered freeze-frame snapshots of actual
conformations assumed in solution. In a way, the assertion seems
almost definitely tru
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