Dear Dale,
It is more complex than just 'flexibility', but then it is always more
complicated. Here are the main possibilities for undetermined regions:
-1- fast, free movement - signals are easy to see, have 'random-coil'
chemical shifts, often overlap, and there are no NOEs
-2- intermediate-range exchange between several different
conformations, free/bound etc. Signals are broadened and harder to
observe, NOEs even more so.
-3- The molecule is too big and slow-moving - you might be able to
observe a domain linked by a flexible linker to a huge and invisible
protein (or virus, ...)
-4- Proximity to lanthanides or other kinds of unpaired electrons.
-5- Missing observations, due to overlapped signals combined with barely
adequate S/N ratio.
Arguably 1) and 2) are both movement, just in different time scales - 1)
can be identified from relaxation measurements and/or chemical shifts,
which should be pretty routine.
3) and 4) you would know about.
5) you could check by looking at, essentially, completeness.
Yours,
Rasmus
On 26/05/2021 22:06, Dale Tronrud 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: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710 /
//
//
/
/
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale
Tronrud <de...@daletronrud.com>
*Sent:* Wednesday, May 26, 2021 10:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*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
<0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> 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
otheruseful things with the information.
Harry
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