You are much more knowledgeable than me about the details of
structure determination via resonance spectroscopy. I was attempting to
come up with a toy example that showed that there are reasons for the
absence of cross-peaks other than flexibility. I accept that the
misinterpretation I proposed would be difficult for a careful
experimenter to make.
I do get uncomfortable when I'm told that A implies B in a well
executed experiment but I have no way of knowing if the model I'm
looking at was constructed via a "well executed experiment". Am I right
that the PDB still has no validation slider for the quality of the fit
of an NMR model to its data?
I know, via existence proofs, that there are crystallographic models
in the PDB that fit their data poorly or are simply unjustified by the
experimental results. Does this never happen with NMR? How can I know
that the model I'm looking at in the PDB was created using all the
powerful techniques you describe, and that those techniques were
correctly performed?
Only with knowledge of those details can I say that the model I'm
looking at is one of your "well-determined NMR ensembles" and I can
trust that the variability in the ensemble reflects the structural
variability.
Dale Tronrud
On 5/26/2021 2:38 PM, Mark J. van Raaij wrote:
Dear Dale,
Aren’t NMR spectroscopists, in contrast to us crystallographers, not in the
lucky situation though that they should have noticed the absence of terminal
residues during the assignment phase though? I.e. they would usually have peaks
for the protons of those residues in the 1D, TOCSY, COSY spectra, even though
NOEs may be absent.
I agree with you that other reasons than flexibility could cause absence of
NOE’s, although I think that for well-determined NMR ensembles in almost all
cases it is indeed flexibility / multiple conformations. If not enough
restraints have been input, you might get artificial “flexible” regions, and
obtaining more NOEs, secondary structure restraints, measuring orientational
restraints should shore these up.
(Assuming that in the previous assignent phase all protons peaks could be
properly assigned of course).
Mark
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/
On 26 May 2021, at 23:06, Dale Tronrud <[email protected]> wrote:
Dear Boaz,
We are likely in agreement. "Deficient NOE's for some regions (e.g. loops) arise
from their flexibility, ..." This makes it sound like you agree that these
deficiencies in other regions may be caused by properties other than flexibility.
As an extreme example, the N-terminal region of a protein may have a broad
distribution in the ensemble model either because this region experiences many
conformations in solution, or because this peptide was cleaved from the protein
at some earlier time and its absence was not recognized by the experimentalist.
Dale Tronrud
On 5/26/2021 1:06 PM, Boaz Shaanan wrote:
Hi Dale and Cecil,
This is quite a circular argument, isn't it? Deficient NOE's for some regions
(e.g. loops) arise from their flexibility, hence they are not as well resolved
as other (e.g. internal ) regions for which the number of NOE is large. So they
are flexible by all accounts and, not surprisingly, align usually with high
B-factor regions in the corresponding crystal structures. In cases where such
flexible regions are held by crystal contacts the situations would likely be
different.
Cheers,
Boaz
/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [email protected]
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710 /
//
//
/
/
------------------------------------------------------------------------
*From:* CCP4 bulletin board <[email protected]> on behalf of Dale Tronrud
<[email protected]>
*Sent:* Wednesday, May 26, 2021 10:46 PM
*To:* [email protected] <[email protected]>
*Subject:* Re: [ccp4bb] Analysis of NMR ensembles
I agree with Dr Breyton. The variability in an NMR ensemble does not
reflect "mobility" but simply "uncertainty" in conformation. The spread
in coordinates in some regions simply reflects the lack of experimental
data which could define a single conformation. There are many reasons
why these data are be absent and high mobility is only one.
Dale Tronrud
On 5/26/2021 8:45 AM, Cécile Breyton wrote:
Hello,
In my understanding of NMR, the loops and terminii that adopt very different
conformations in the structure ensemble rather reflect the fact that for those
residues, the number of constraints is lower, thus the number of structures
that fulfil the constraints is larger.... A dynamics study of the protein will
be much more informative.
Cécile
Le 26/05/2021 à 17:29, S. Mohanty a écrit :
Hi Harry,
The superpose/overlay of all the structures in PyMol should inform you the
rigid part of the protein as well as the flexible part. The rigid part would
have very low backbone RMSD or overlay tightly and the flexible part (loops,
N-term and C-term etc.) would not superpose tightly. If you check literature,
the dynamics of the protein may have been studied through NMR relaxation.
Smita
On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB
<[email protected]> wrote:
Hi
Given that there are plenty of people on this BB who are structural biologists
rather than “just” crystallographers, I thought someone here might be able to
help.
If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures
that fit the NOEs, is there a tool available that will give me some idea about
the bits of the structure that do not vary much (“rigid”) and the bits that are
all over the place (“flexible”)?
Would superpose or gesamt be a good tool for this? Ideally I’d like something
that could add a figure to the B columns in a PDB file so I could see something
in QTMG (or PyMol if forced…) or do other useful things with the information.
Harry
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>>
This message was issued to members of www.jiscmail.ac.uk/CCP4BB
<http://www.jiscmail.ac.uk/CCP4BB>, a
mailing list hosted by www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms &
conditions are
available at https://www.jiscmail.ac.uk/policyandsecurity/
<https://www.jiscmail.ac.uk/policyandsecurity/>
<https://www.jiscmail.ac.uk/policyandsecurity/
<https://www.jiscmail.ac.uk/policyandsecurity/>>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
This message was issued to members of www.jiscmail.ac.uk/CCP4BB
<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk
<http://www.jiscmail.ac.uk>, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/ <https://www.jiscmail.ac.uk/policyandsecurity/>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
